Simulated embryonic genetic profile

Abstract

Provided herein are methods, systems and apparatuses for generating a simulated embryonic genetic profile by obtaining a phased embryonic whole genome sequencing file, calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file, and processing calibrated embryonic whole genome sequencing file by introducing one or more mutations. Also, provided herein are methods, systems and apparatuses for generating a simulated embryonic genetic profile by obtaining a phased parental whole genome sequencing files, simulating generation of parental haploid data files using the phased parental whole genome sequencing files, introducing one or more mutations in the at least one of the parental haploid data file, calibrating at least one of the parental haploid data file using a reference sequencing data file, and combining the parental haploid data files.

Description

Attorney Docket No. 206979-712601 / PCTSIMULATED EMBRYONIC GENETIC PROFILECross Reference

[0001] This application claims priority to U.S. Provisional Application No. 63 / 742,575 filed January 7, 2025, with the entire disclosure incorporated herein by reference in its entirety.Field

[0002] The present disclosure relates generally to generating whole genome sequencing file.Background

[0003] There is a need for algorithms that work with low-coverage whole genome sequencing file, and that can be more closely represent actual data.Summary

[0004] The present disclosure provides for methods of generating whole genome sequencing file and uses thereof.Certain Embodiments

[0005] Provided herein are methods for generating a simulated embryonic genetic profile with one or more mutations, the methods comprise: obtaining a phased embryonic whole genome sequencing file; calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile. In some embodiments, the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises: obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, and changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy. In some embodiments, the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage. In some embodiments, the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information. In some embodiments, the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format. In some embodiments, the phased embryonic whole genome sequencing file isAttorney Docket No. 206979-712601 / PCTobtained from a benchmark genome. In some embodiments, the phased embryonic whole genome sequencing file is obtained using a phasing software. In some embodiments, the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file. In some embodiments, the phased embryonic whole genome sequencing file is in VCF or compressed VCF format. In some embodiments, the phased embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the methods further comprise obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file. In some embodiments, the methods comprise generating the calibrated embryonic whole genome sequencing file based on the adjusted embryonic whole genome sequencing file and the reference sequencing data file. In some embodiments, the calibrated embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the sequence alignment file is in SAM, BAM, or CRAM format. In some embodiments, the methods further comprise applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36,Atorney Docket No. 206979-712601 / PCT22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0006] Also described herein are methods for generating a simulated embryonic genetic profile with one or more mutations, the method comprising: obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file; simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file obtained from an embryo; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile. In some embodiments, the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file. In some embodiments, the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular based phasing method. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 *, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the humanAtorney Docket No. 206979-712601 / PCTgenome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0007] Also described herein are apparatuses for generating a simulated embryonic genetic profile, the apparatuses comprise a processor and a memory storing software instructions that, when executed by the processor, cause the apparatus to perform the methods described herein.

[0008] Also described herein are computer program products for generating a simulated embryonic genetic profile, the computer program products comprise at least one non-transitory computer-readable storage medium storing software instructions that, when executed by an apparatus, cause the apparatus to perform the methods described herein.

[0009] Also described herein are apparatuses for performing methods of generating a simulated embryonic genetic profile, the apparatuses comprise: a processor; and a memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files, wherein said plurality of data files comprise a phased embryonic whole genome sequencing file and a reference sequence file obtained from an embryo, and wherein said methods comprise: obtaining the phased embryonic whole genome sequencing file, calibrating the phased embryonic whole genome sequencing file using the reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile. In some embodiments, the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, wherein the processing comprises: obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, and changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy. In some embodiments, the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage. In some embodiments, the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file ofAttorney Docket No. 206979-712601 / PCTembryo genome information. In some embodiments, the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format. In some embodiments, the phased embryonic whole genome sequencing file is obtained from a benchmark genome. In some embodiments, the phased embryonic whole genome sequencing file is obtained using a phasing software. In some embodiments, the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file. In some embodiments, the phased embryonic whole genome sequencing file is in VCF or compressed VCF format. In some embodiments, the phased embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the methods further comprise obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file. In some embodiments, the methods comprise generating the calibrated embryonic whole genome sequencing file based on the adjusted embryonic whole genome sequencing file and the reference sequencing data file. In some embodiments, the calibrated embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the sequence alignment file is in SAM, BAM, or CRAM format. In some embodiments, the methods further comprise applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome),Atorney Docket No. 206979-712601 / PCTTrisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15ql 1-ql 3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation. Also described herein are apparatuses for performing methods of generating a simulated embryonic genetic profile, the apparatuses comprise: a processor; and a memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files, wherein said plurality of data files comprise a phased maternal whole genome sequencing file, a phased paternal whole genome sequencing file and a reference sequence file obtained from an embryo, and wherein said methods comprise: obtaining the phased maternal whole genome sequencing file and the phased paternal whole genome sequencing file; simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; calibrating at least one of the maternal haploid data file and the paternal haploid data file using the reference sequencing data file; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile. In some embodiments, the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file. In some embodiments, the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular based phasing method. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 *, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosomeAtorney Docket No. 206979-712601 / PCT18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0010] Also described herein are systems comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform a method of generating a simulated embryonic genetic profile, wherein said method comprises: obtaining a phased embryonic whole genome sequencing file, calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile. In some embodiments, the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, wherein the processing comprises: obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, and changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy. In some embodiments, the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage. In some embodiments, the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information. In some embodiments, the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format. In some embodiments, the phased embryonic whole genome sequencing file is obtained from a benchmark genome. In some embodiments, the phased embryonic whole genome sequencing file is obtained using a phasing software. In some embodiments, the calibratedAttorney Docket No. 206979-712601 / PCTembryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file. In some embodiments, the phased embryonic whole genome sequencing file is in VCF or compressed VCF format. In some embodiments, the phased embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the systems further comprise obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file. In some embodiments, the systems comprise generating the calibrated embryonic whole genome sequencing file based on the adjusted embryonic whole genome sequencing file and the reference sequencing data file. In some embodiments, the calibrated embryonic whole genome sequencing file is a sequence alignment file. In some embodiments, the sequence alignment file is in SAM, BAM, or CRAM format. In some embodiments, the systems further comprise applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXXAtorney Docket No. 206979-712601 / PCTsyndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0011] Also described herein are systems comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform the method of generating a simulated embryonic genetic profile, wherein said method comprises: obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file; simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile. In some embodiments, the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file. In some embodiments, the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular based phasing method. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome. In some embodiments, the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software. In some embodiments, the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 *, less than lx, or less than 5x. In some embodiments, the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the humanAtorney Docket No. 206979-712601 / PCTgenome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.Incorporation by reference

[0012] All publications, patents and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.Brief Description of the Drawings

[0013] FIG. 1 shows schematics of a method of generating a simulated embryonic genetic profile.Detailed Description of the Invention

[0014] It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only, and are not restrictive of the disclosure.

[0015] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

[0016] All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books and treatises, are hereby expressly incorporated by reference in their entirety for any purpose.Definitions

[0017] Unless otherwise indicated, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Unless otherwise indicated or obvious from context, the following terms have the following meanings:

[0018] The terms, “a,” “an,” and “the,” as used herein, include plural references unless the context clearly dictates otherwise.

[0019] The terms, “or” and “and / or,” as used herein, include any and all combinations of one or more of the associated listed items.

[0020] The terms, “including,” “includes,” “included,” and other forms, are not limiting.Atorney Docket No. 206979-712601 / PCT

[0021] The terms, “comprise” and its grammatical equivalents, as used herein, specify the presence of stated features, integers, steps, operations, elements and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components and / or groups thereof.

[0022] The term, “about,” as used herein in reference to a number or range of numbers, is understood to mean the stated number and numbers + / - 10% thereof, or 10% below the lower listed limit and 10% above the higher listed limit for the values listed for a range.Introduction

[0023] Pre-implantation genetic testing (PGT) samples can be scarce and hard-to-come by. For simulating mutations (e.g., aneuploidies, deletions, duplications, unbalanced translocations, haploid, polyploidy and mosaicism) from read data of the samples, phasing information, B allele frequencies and read depth information are some of the important considerations that are being used. Read depth profile and quality of analysis can be further improved by matching simulated mutations with PGT samples. However, it can be challenging to simulate mutations to develop and validate mutation-calling algorithms especially for read data having low-coverage.

[0024] Disclosed herein are systems, apparatuses and methods that can use low-coverage whole genome sequencing files as well as high-coverage whole genome sequencing files. More specifically, disclosed herein are systems, apparatuses and methods that match the profile of a given sequencing run at the read level. This can be useful for sequencing data with uneven coverage, for example from low-coverage pre-implantation genetic testing or exome sequencing, which can be biased towards exons. The systems, apparatuses and methods, as described herein, can also use a high-coverage whole genome sequencing file (e.g, bam file) and its phase (e.g., VCF file) of an individual, target profile, coverage profile, profile with desired mutations, or combination thereof as input, and provide an output file (e.g, bam file) that matches the target profile in coverage having the desired mutation(s), preserving phasing of the individual, or combinations thereof.

[0025] The systems, apparatuses and methods, as described herein, advantageously retain the familial information for phasing-based methods. Alternatively, the systems, apparatuses and methods described herein preserve phasing and variants information from whole genome sequencing files (e.g., bam files). With phasing, the systems, apparatuses and methods can further simulate more complex mutations. For example, in some embodiments, the systems, apparatuses and methods can add mutations defined as aneuploidy, copy number variation, or structural variation originating from one parent to the whole genome sequencing file. The systems, apparatuses and methods, as described herein, can also use phased whole genome sequencing filesAtorney Docket No. 206979-712601 / PCTe.g., bam files) of two individuals (e.g., parents), target profile, coverage profile, profiles with desired mutations or combinations thereof as input, and provide an output profile (e.g., bam file) of a simulated embryonic whole genome sequencing file that matches the target profile in coverage having desired mutation(s), having phasing that is compatible with the phasing of two individuals, or combinations thereof.

[0026] Disclosed herein are systems, apparatuses and methods for generating simulated embryonic genetic profiles. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, the methods can comprise: obtaining a phased embryonic whole genome sequencing file; calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

[0027] Disclosed herein are systems, apparatuses and methods for generating simulated embryonic genetic profiles with polyploidy. In some embodiments, the methods can comprise: obtaining a phased embryonic whole genome sequencing file; calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile, wherein one or more mutations can comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, and changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file.

[0028] Also disclosed herein are systems, apparatuses and methods for generating simulated embryonic genetic profiles. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, the methods can comprise obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file, simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file, introducing one or more mutations in at least one of the maternal haploid data file and the paternal haploid data file, calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file obtained from an embryo, andAtorney Docket No. 206979-712601 / PCTcombining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.Whole genome sequencing file

[0029] In some embodiments, a whole genome sequencing file, as disclosed herein, can comprise an embryonic whole genome sequencing file and a parental whole genome sequencing file (e.g., a maternal whole genome sequencing file, a paternal whole genome sequencing file). In some embodiments, a whole genome sequencing file, as disclosed herein, can be a high-coverage BAM file. In some embodiments, a whole genome sequencing file, as disclosed herein, can be a high-coverage SAM file. In some embodiments, a whole genome sequencing file, as disclosed herein, can be a high-coverage CRAM file. In some embodiments, a whole genome sequencing file, as disclosed herein, can be a low-coverage BAM file. In some embodiments, a whole genome sequencing file, as disclosed herein, can be a low-coverage SAM file. In some embodiments, a whole genome sequencing file, as disclosed herein, can be a low-coverage CRAM file.Phased genome sequencing file

[0030] In some embodiments, a phased genome sequencing file, as disclosed herein, can be a phased whole genome sequencing file. In some embodiments, a phased whole genome sequencing file can be generated by phasing a whole genome sequencing file. In some embodiments, a phased whole genome sequencing file can be in VCF or compressed VCF format. In some embodiments, phased whole genome sequencing files can be generated by phasing whole genome sequencing files using GLIMPSE, SHAPEIT, DuoHMM, or a combination thereof. In some embodiments, phased whole genome sequencing files can be generated by: imputing with GLIMPSE for low-coverage whole genome sequencing file(s), phasing the whole genome sequencing file(s) with SHAPEIT that’s pedigree-aware or with a reference population, and correcting phasing with trio-aware DuoHMM.

[0031] In some embodiments, a phased embryonic whole genome sequencing file can be generated by phasing an embryonic whole genome sequencing file. In some embodiments, a phased embryonic whole genome sequencing file can be obtained by phasing whole genome sequencing files (VCFs) obtained from an embryo with its parents and sibling(s). In some embodiments, phased embryonic whole genome sequencing files can be obtained using sequence alignment files of embryonic chromosome information. In some embodiments, sequence alignment files of embryonic chromosome information can be in SAM, BAM, or CRAM format. In some embodiments, phased embryonic whole genome sequencing files can be obtained using population-based phasing methods and / or molecular-based phasing methods. In some embodiments, phased embryonic whole genome sequencing files can be obtained from aAtorney Docket No. 206979-712601 / PCTbenchmark genome (e.g., Genome in a Bottle). In some embodiments, phased embryonic whole genome sequencing files can be obtained using one or more phasing software. In some embodiments, the one or more phasing software comprise GLIMPSE, SHAPEIT and DuoHMM. For example, in some embodiments, a phased embryonic whole genome sequencing file can be obtained by: imputing with GLIMPSE for low-coverage embryonic whole genome sequencing file(s); phasing the embryonic whole genome sequencing file with SHAPEIT that’s pedigree-aware or with a reference population; and correcting phasing with trio-aware DuoHMM.

[0032] In some embodiments, a phased maternal whole genome sequencing file can be generated by phasing a maternal whole genome sequencing file. In some embodiments, phased maternal whole genome sequencing files can be obtained using sequence alignment files of maternal chromosome information. In some embodiments, sequence alignment files of maternal chromosome information can be in SAM, BAM, or CRAM format. In some embodiments, phased maternal whole genome sequencing files can be obtained using population-based phasing methods and / or molecular-based phasing methods. In some embodiments, phased maternal whole genome sequencing files can be obtained from a benchmark genome. In some embodiments, phased maternal whole genome sequencing files can be obtained using one or more phasing software. In some embodiments, the one or more phasing software comprise GLIMPSE, SHAPEIT and DuoHMM. For example, in some embodiments, a phased maternal whole genome sequencing file can be obtained by: imputing with GLIMPSE for low-coverage maternal whole genome sequencing file(s); phasing the maternal whole genome sequencing file with SHAPEIT that’s pedigree-aware or with a reference population; and correcting phasing with trio-aware DuoHMM.

[0033] In some embodiments, a phased paternal whole genome sequencing file can be generated by phasing a paternal whole genome sequencing file. In some embodiments, phased paternal whole genome sequencing files can be obtained using sequence alignment files of paternal chromosome information. In some embodiments, sequence alignment files of paternal chromosome information can be in SAM, BAM, or CRAM format. In some embodiments, phased paternal whole genome sequencing files can be obtained using population-based phasing methods and / or molecular-based phasing methods. In some embodiments, phased paternal whole genome sequencing files can be obtained from a benchmark genome. In some embodiments, phased paternal whole genome sequencing files can be obtained using one or more phasing software. In some embodiments, the one or more phasing software comprise GLIMPSE, SHAPEIT and DuoHMM. For example, in some embodiments, a phased paternal whole genome sequencing file can be obtained by: imputing with GLIMPSE for low-coverage paternal whole genome sequencing file(s); phasing the paternal whole genome sequencing file with SHAPEIT that’s pedigree-aware or with a reference population; and correcting phasing with trio-aware DuoHMM.Atorney Docket No. 206979-712601 / PCTParental haploid data file

[0034] In some embodiments, parental haploid data files (e.g., a maternal haploid data file, a paternal haploid data file) can be generated using phased parental whole genome sequencing files (e.g., phased maternal whole genome sequencing file, phased paternal whole genome sequencing file). In some embodiments, parental haploid data files can be processed to introduce one or more mutations. In some embodiments, parental haploid data files can be calibrated using a reference sequencing data file obtained from an embryo.

[0035] In some embodiments, a maternal haploid data file can be generated using phased maternal whole genome sequencing file. In some embodiments, a maternal haploid data file can be processed to introduce one or more mutations. In some embodiments, a maternal haploid data file can be calibrated using a reference sequencing data file obtained from an embryo.

[0036] In some embodiments, a paternal haploid data file can be generated using phased paternal whole genome sequencing file. In some embodiments, a paternal haploid data file can be processed to introduce one or more mutations. In some embodiments, a paternal haploid data file can be calibrated using a reference sequencing data file obtained from an embryo.

[0037] In some embodiments, one or more mutations, disclosed herein, can be selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations can be located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15ql 1-q 13 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.Atorney Docket No. 206979-712601 / PCTCalibrated embryonic whole genome sequencing file

[0038] In some embodiments, a calibrated whole genome sequencing file, as disclosed herein, can be a calibrated embryonic whole genome sequencing file. In some embodiments, a calibrated embryonic whole genome sequencing file can be generated by calibrating a phased embryonic whole genome sequencing file using a reference sequencing data file. Alternatively, in some embodiments, a calibrated embryonic whole genome sequencing file can be generated by calibrating an adjusted embryonic whole genome sequencing file using a reference sequencing data file. In some embodiments, an adjusted embryonic whole genome sequence file can be obtained by adjusting difference(s) between a phased embryonic whole genome sequencing file in VCF format and a phased embryonic whole genome sequencing file in a sequence alignment format. In some embodiments, a reference sequencing data file can be obtained from an embryo. In some embodiments, a reference sequencing data file can be obtained from preimplantation genetic testing (PGT) sequencing profile of an embryo. In some embodiments, calibrated embryonic whole genome sequencing files can be VCF files. In some embodiments, calibrated embryonic whole genome sequencing files can be sequence alignment files. In some embodiments, sequence alignment files, as disclosed herein, are in SAM, BAM, or CRAM format.

[0039] In some embodiments, calibrated embryonic whole genome sequencing files comprise a read coverage correlation of >0.5 or >0.99 to a corresponding read coverage of the reference sequencing data file. In some embodiments, reference sequencing data files, as disclosed herein, have low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x. In some embodiments, one or more mutations, as described herein, are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in a reference sequencing data file having the low read coverage.Simulated embryonic genetic profile

[0040] In some embodiments, a simulated embryonic genetic profile, as described herein, can be obtained by processing a calibrated embryonic whole genome sequencing file. In some embodiments, processing a calibrated embryonic whole genome sequencing file comprises introducing one or more mutations. In some embodiments, a simulated embryonic genetic profile comprises one or more polygenic disease diseases, wherein the simulated embryonic genetic profile can be generated by applying at least one polygenic disease model to a calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations. For example, in some embodiments, a simulated embryonic genetic profile comprising polyploidy can be generated by introducing one or more mutations from a parent using a parental phased whole genome sequencing file, wherein the one or more mutations comprise diploid information.Atorney Docket No. 206979-712601 / PCT

[0041] Alternatively, in some embodiments, a simulated embryonic genetic profile can be generated by combining parental haploid data files (e.g., a maternal haploid data file and a paternal haploid data file). In some embodiments, a simulated embryonic genetic profile can be generated by combining parental haploid data files that were calibrated. In some embodiments, a parental haploid data file can be processed to introduce one or more mutations prior to calibrating the parental haploid data file.

[0042] In some embodiments, a simulated embryonic genetic profile can comprise one or more mutations. In some embodiments, the one or more mutations can be selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism. In some embodiments, the one or more mutations can be located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T). In some embodiments, the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.Methods

[0043] Disclosed herein are methods of generating simulated embryonic genetic profiles. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, the methods of generating simulated embryonic genetic profiles comprise: (a) obtaining a phased embryonic whole genome sequencing file; (b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and (c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.Atorney Docket No. 206979-712601 / PCT

[0044] Also, disclosed herein are methods of generating simulated embryonic genetic profiles. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, the methods of generating simulated embryonic genetic profiles comprise: (a) obtaining an embryonic whole genome sequencing file; (b) phasing the embryonic whole genome sequencing file, thereby generating a phased embryonic whole genome sequencing file; (c) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo; (d) processing the phased embryonic whole genome sequencing file by: (i) choosing region within the phased embryonic whole genome sequencing file, (ii) marking reads that are from maternal or paternal, and (ii) introducing one or more mutations, thereby generating the simulated embryonic genetic profile. The one or more mutations can be a duplication, deletion, uniparental disomy (UPD) (e.g., isodisomy, heterodisomy). FIG. 1 provides schematics of the method described herein.

[0045] Also, disclosed herein are methods of generating simulated embryonic genetic profiles with polyploidy, wherein the methods comprise: (a) obtaining a phased embryonic whole genome sequencing file; (b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and (c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises: (i) obtaining a first obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file; and (ii) changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file.

[0046] In some embodiments, a reference sequencing data file comprises preimplantation genetic testing (PGT) sequencing profile of embryo. In some embodiments, the PGT comprises one or more mutations located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome. In some embodiments, the one or more mutations comprise deletions, duplications, aneuploidy, uniparental disomy (UPD), balanced translocations, haploidy, polyploidy, mosaicism,Atorney Docket No. 206979-712601 / PCTor a combination thereof. In some embodiments, introduction of one or more deletions comprises deleting reads from the parental haplotype that are not being passed.

[0047] In some embodiments, methods, as described herein, comprise obtaining a phased embryonic / matemal / patemal whole genome sequencing file by: (a) imputing with GLIMPSE for low-coverage embryonic / maternal / paternal whole genome sequencing file, and (b) phasing with SHAPEIT that’s pedigree-aware or with a reference population. Alternatively, in some embodiments, a phased embryonic / maternal / paternal whole genome sequencing file can be generated by: imputing with GLIMPSE for low-coverage whole genome sequencing file(s), phasing the embryonic / matemal / patemal whole genome sequencing file(s) with SHAPEIT that’s pedigree-aware or with a reference population, and correcting phasing with trio-aware DuoHMM.

[0048] In some embodiments, the processing of the introduction of one or more duplications comprises combining reads of a normal downsampled reference sequencing data file and 2nd downsampled sequencing file with duplicated region. In some embodiments, the 2nddownsampled sequencing file is generated by: using 2nd downsampled reference sequencing data file with different reads than those used in the normal downsampled reference sequencing data file; marking informative reads that are coming from paternal or maternal side; and combining informative reads from maternal side or paternal side, 50% of the uninformative reads, and 2nd downsampled reference sequencing data file, wherein the duplicative reads are from maternal side or paternal side, respectively.

[0049] In some embodiments, methods, as described herein, comprise marking reads in the region that is to be mutated by: (a) using SNPs in the reads and phasing information in the phased embryonic whole genome sequencing file based on whether it come from paternal or maternal side, and (b) uninformative reads are arbitrarily assigned from maternal / paternal. In some embodiments, the methods, as described herein, comprise marking reads in the region that is to be mutated by: (a) identifying parental haplotype that is common between two sibling embryos, wherein the two sibling embryos comprise a sample embryo and a reference embryo, (b) identifying reads coming from maternal / paternal side, and (c) identifying uninformative reads.

[0050] Also disclosed herein are methods for generating a simulated embryonic genetic profile. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, the methods of generating simulated embryonic genetic profiles comprise: obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file; simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; calibrating at least one of the maternal haploidAtorney Docket No. 206979-712601 / PCTdata file and the paternal haploid data file using a reference sequencing data file obtained from an embryo; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile. In some embodiments, a phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file. In some embodiments, a phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file. In some embodiments, a sequence alignment file of a maternal whole genome sequencing file is in SAM, BAM, or CRAM format. In some embodiments, a sequence alignment file of a paternal whole genome sequencing file is in SAM, BAM, or CRAM format. In some embodiment, the maternal haploid data file (e.g., bam file) is generated by: (a) taking the phased maternal whole genome sequencing (e.g, VCF file); (b) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG; (c) generating phased maternal -recombined data file (e.g, VCF file); and (d) splitting the phased maternal-recombined data file (e.g., VCF file) into left-side and right side for creating two haploid data files (e.g., VCF file). In some embodiments, the paternal haploid data file (e.g., bam file) is generated by (a) taking the phased paternal whole genome sequencing (e.g., VCF file); (b) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG; (c) generating phased paternal -recombined data file (e.g., VCF file); and (d) splitting the phased paternal -recombined data file (e.g., VCF file) into left-side and right side for creating two haploid data files (e.g., VCF file). In some embodiments, a haploid data file (e.g., VCF file) is calibrated using a read simulation that takes the haploid data file input, thereby generating two sets of reads of calibrated haploid data files (e.g., fastq file). In some embodiments, a haploid data file (e.g., VCF file) is calibrated using a read simulation that takes the haploid data file input, thereby generating two sets of reads of calibrated haploid data files (e.g., fastq file) that comprise one or more mutations. In some embodiments, the one or more mutations comprise deletions, duplications, aneuploidy, uniparental disomy (UPD), balanced translocations, haploidy, polyploidy, mosaicism, or a combination thereof.Systems

[0051] Disclosed herein is a system comprising an apparatus and software instructions, that when executed by the apparatus, cause the apparatus to perform the methods described herein. Specifically, in some embodiments, a system disclosed herein comprises an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform the method of generating a simulated embryonic genetic profile, wherein said method comprises: (a) obtaining the phased embryonic whole genome sequencing file; (b) calibrating the phased embryonic wholeAtorney Docket No. 206979-712601 / PCTgenome sequencing file using the reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file; and (c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile. In some embodiments, the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and the processing comprises: obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file; and changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy. Alternatively, in some embodiments, in some embodiments, a system disclosed herein comprises an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform the method of generating a simulated embryonic genetic profile, wherein said method comprises: (a) obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file; (b) simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; (c) introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; (d) calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file obtained from an embryo; and (e) combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.Apparatus

[0052] Disclosed herein are apparatuses for generating a simulated embryonic genetic profile. In some embodiments, the simulated embryonic genetic profiles can comprise one or more mutations. In some embodiments, an apparatus comprises a processor and a memory storing software instructions that, when executed by the processor, cause the apparatus to perform the methods described herein. Specifically, in some embodiments, an apparatus disclosed herein comprises a processor; and a memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files, wherein said plurality of data files comprise a phased embryonic whole genome sequencing file and a reference sequence file obtained from an embryo, and wherein said method comprises: (a) obtaining the phased embryonic whole genome sequencing file; (b) calibrating the phased embryonic whole genome sequencing file using the reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file; and (c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, therebyovnc Docket No. 206979-712601 / PCTgenerating the simulated embryonic genetic profile. In some embodiments, the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and the processing comprises: (a) obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file; and (b) changing reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

[0053] Alternatively, in some embodiments, an apparatus disclosed herein comprises a processor; and a memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files, wherein said plurality of data files comprise a phased maternal whole genome sequencing file, a phased paternal whole genome sequencing file and a reference sequence file obtained from an embryo, and wherein said method comprises: (a) obtaining the phased maternal whole genome sequencing file and the phased paternal whole genome sequencing file; (b) simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file; (c) introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file; (d) calibrating at least one of the maternal haploid data file and the paternal haploid data file using the reference sequencing data file; and (e) combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.Illustrative Embodiments

[0054] Embodiment 1. A method for generating a simulated embryonic genetic profile with one or more mutations, the method comprising:obtaining a phased embryonic whole genome sequencing file;calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; andprocessing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

[0055] Embodiment 2. The method of Embodiment 1, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file; and1Atorney Docket No. 206979-712601 / PCTchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

[0056] Embodiment 3. The method of Embodiment 1 or 2, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.

[0057] Embodiment 4. The method of any one of Embodiments 1-3, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

[0058] Embodiment 5. The method of Embodiment 4, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

[0059] Embodiment 6. The method of any one of Embodiments 1-5, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.

[0060] Embodiment 7. The method of any one of Embodiments 1-5, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

[0061] Embodiment 8. The method of any one of Embodiments 1-6, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.

[0062] Embodiment 9. The method of any one of Embodiments 1-8, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

[0063] Embodiment 10. The method of any one of Embodiments 1-8, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

[0064] Embodiment 11. The method of any one of Embodiments 1-8, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

[0065] Embodiment 12. The method of Embodiment 11, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.

[0066] Embodiment 13. The method of any one of Embodiments 1-12, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

[0067] Embodiment 14. The method of Embodiment 13, wherein the sequence alignment file is in SAM, BAM, or CRAM format.Atorney Docket No. 206979-712601 / PCT

[0068] Embodiment 15. The method of any one of Embodiments 1-14, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.

[0069] Embodiment 16. A method for generating a simulated embryonic genetic profile with one or more mutations, the method comprising:obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file;simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file obtained from an embryo; andcombining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

[0070] Embodiment 17. The method of Embodiment 16, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

[0071] Embodiment 18. The method of Embodiment 17, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.

[0072] Embodiment 19. The method of any one of Embodiments 16-18, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

[0073] Embodiment 20. The method of any one of Embodiments 16-19, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

[0074] Embodiment 21. The method of any one of Embodiments 16-20, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.Atorney Docket No. 206979-712601 / PCT

[0075] Embodiment 22. The method of any one of Embodiment 1-21, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 *, less than lx, or less than 5x.

[0076] Embodiment 23. The method of any one of Embodiments 1-22, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

[0077] Embodiment 24. The method of any one of Embodiments 1-23, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.

[0078] Embodiment 25. The method of Embodiment 24, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

[0079] Embodiment 26. The method of any one of Embodiments 1-25, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0080] Embodiment 27. An apparatus for generating a simulated embryonic genetic profile, the apparatus comprising a processor and a memory storing software instructions that, when executed by the processor, cause the apparatus to perform the method of any one of Embodiments 1-26.

[0081] Embodiment 28. A computer program product for generating a simulated embryonic genetic profile, the computer program product comprising at least one non-transitory computer-readable storage medium storing software instructions that, when executed by an apparatus, cause the apparatus to perform the method of any one of Embodiments 1-26.

[0082] Embodiment 29. An apparatus for performing a method of generating a simulated embryonic genetic profile, the apparatus comprising:Atorney Docket No. 206979-712601 / PCTa processor; anda memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files,wherein said plurality of data files comprise a phased embryonic whole genome sequencing file and a reference sequence file obtained from an embryo, andwherein said method comprises:obtaining the phased embryonic whole genome sequencing file,calibrating the phased embryonic whole genome sequencing file using the reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

[0083] Embodiment 30. The apparatus of Embodiment 29, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, andchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

[0084] Embodiment 31. The apparatus of Embodiment 29 or 30, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.

[0085] Embodiment 32. The apparatus of any one of Embodiments 29-31, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

[0086] Embodiment 33. The apparatus of Embodiment 32, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

[0087] Embodiment 34. The apparatus of any one of Embodiments 29-33, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.

[0088] Embodiment 35. The apparatus of any one of Embodiments 29-33, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

[0089] Embodiment 36. The apparatus of any one of Embodiments 29-35, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.Atorney Docket No. 206979-712601 / PCT

[0090] Embodiment 37. The apparatus of any one of Embodiments 29-36, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

[0091] Embodiment 38. The apparatus of any one of Embodiments 29-36, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

[0092] Embodiment 39. The apparatus of any one of Embodiments 29-36, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

[0093] Embodiment 40. The apparatus of Embodiment 39, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.

[0094] Embodiment 41. The apparatus of any one of Embodiments 29-40, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

[0095] Embodiment 42. The apparatus of Embodiment 41, wherein the sequence alignment file is in SAM, BAM, or CRAM format.

[0096] Embodiment 43. The apparatus of any one of Embodiments 29-42, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.

[0097] Embodiment 44. An apparatus for performing a method of generating a simulated embryonic genetic profile, the apparatus comprising:a processor; anda memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files,wherein said plurality of data files comprise a phased maternal whole genome sequencing file, a phased paternal whole genome sequencing file and a reference sequence file obtained from an embryo, andwherein said method comprises:obtaining the phased maternal whole genome sequencing file and the phased paternal whole genome sequencing file;Atorney Docket No. 206979-712601 / PCTsimulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using the reference sequencing data file; andcombining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

[0098] Embodiment 45. The apparatus of Embodiment 44, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

[0099] Embodiment 46. The apparatus of Embodiment 45, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.

[0100] Embodiment 47. The apparatus of any one of Embodiments 44-46, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

[0101] Embodiment 48. The apparatus of any one of Embodiments 44-47, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

[0102] Embodiment 49. The apparatus of any one of Embodiments 44-48, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.

[0103] Embodiment 50. The apparatus of any one of Embodiments 29-49, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x.

[0104] Embodiment 51. The apparatus of any one of Embodiments 29-50, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

[0105] Embodiment 52. The apparatus d of any one of Embodiments 29-51, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13,Atorney Docket No. 206979-712601 / PCTnucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.

[0106] Embodiment 53. The apparatus of Embodiment 52, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

[0107] Embodiment 54. The apparatus of any one of Embodiments 29-53, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

[0108] Embodiment 55. A system comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform the method of generating a simulated embryonic genetic profile, wherein said method comprises:obtaining a phased embryonic whole genome sequencing file,calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, and processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

[0109] Embodiment 56. The system of Embodiment 32, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, andchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

[0110] Embodiment 57. The system of Embodiment 55 or 56, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.Atorney Docket No. 206979-712601 / PCT[OHl] Embodiment 58. The system of any one of Embodiments 55-57, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

[0112] Embodiment 59. The system of Embodiment 58, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

[0113] Embodiment 60. The system of any one of Embodiments 55-59, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.

[0114] Embodiment 61. The system of any one of Embodiments 55-59, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

[0115] Embodiment 62. The system of any one of Embodiments 55-61, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.

[0116] Embodiment 63. The system of any one of Embodiments 55-62, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

[0117] Embodiment 64. The system of any one of Embodiments 55-62, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

[0118] Embodiment 65. The system of any one of Embodiments 55-62, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

[0119] Embodiment 66. The system of Embodiment 65, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.

[0120] Embodiment 67. The system of any one of Embodiments 55-66, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

[0121] Embodiment 68. The system of Embodiment 67, wherein the sequence alignment file is in SAM, BAM, or CRAM format.

[0122] Embodiment 69. The system of any one of Embodiments 55-68, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.Atorney Docket No. 206979-712601 / PCT

[0123] Embodiment 70. A system comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform the method of generating a simulated embryonic genetic profile, wherein said method comprises:obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file;simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file; andcombining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

[0124] Embodiment 71. The system of Embodiment 70, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

[0125] Embodiment 72. The system of Embodiment 71, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.

[0126] Embodiment 73. The system of any one of Embodiments 70-72, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

[0127] Embodiment 74. The system of any one of Embodiments 70-73, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

[0128] Embodiment 75. The system of any one of Embodiments 70-74, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.

[0129] Embodiment 76. The system of any one of Embodiments 55-75, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x.Atorney Docket No. 206979-712601 / PCT

[0130] Embodiment 77. The system of any one of Embodiments 55-76, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

[0131] Embodiment 78. The system d of any one of Embodiments 55-77, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.

[0132] Embodiment 79. The system of Embodiment 78, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

[0133] Embodiment 80. The method of any one of Embodiments 55-79, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.Examples

[0134] The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.Example 1. Method of generating simulated embryonic genetic profiles using phased data

[0135] Phased sample whole genome sequencing file (e.g., bam files) with high-coverage is used for generating simulated embryonic genetic profiles. Specifically, the simulated embryonic genetic profiles are generated by:(a) obtaining embryonic whole genome sequencing file with high-coverage (e.g. bam or cram file) and its phase (e.g. a VCF file);Atorney Docket No. 206979-712601 / PCT(b) calibrating a high-coverage embryonic whole genome sequencing file with preimplantation genetic testing (PGT) sequencing profile of embryo, thereby generating a calibrated embryonic whole genome sequencing file; and(c) processing the calibrated embryonic whole genome sequencing file by:(1) marking reads in the region that is to be mutated using SNPs in the reads and phasing information in the calibrated embryonic whole genome sequencing file based on whether the read comes from paternal or maternal side, and(2) introducing one or more mutations, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184-28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000-21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome; thereby generating the simulated embryonic genetic profile, wherein:(i) if the one or more mutations are a paternal deletion, (A) delete reads in the deletion region that are marked as paternal and (B) delete 50% of the uninformative reads in the deletion region, and(ii) if the one or more mutations are duplication, the following reads are combined:(A) normal downsampled PGT -like sequencing file from step (a), and (B)2nddownsampled sequencing file for the duplicated region that is generated by:(al) 2nddownsampled PGT -like sequencing file is generated with different reads than those used in the normal downsampled PGT-like sequencing file;(a2) marking informative reads that are coming from paternal or maternal side; and(a3) if duplicative reads are from maternal side, then combine informative reads from maternal side (a2), 50% of the uninformative reads, and 2nddownsampled PGT-like sequencing file (al).Attorney Docket No. 206979-712601 / PCTExample 2. Method of generating simulated embryonic genetic profile using data acquired from samples

[0136] Parental whole genome sequencing files (e.g., bam files) are used for generating simulated embryonic genetic profile. Specifically, the simulated embryonic genetic profile is generated by:(a) obtaining a phased embryonic whole genome sequencing file by:(3) imputing with GLIMPSE for low-coverage embryonic whole genome sequencing file(s),(4) phasing the embryonic whole genome sequencing file with SHAPEIT that’s pedigree-aware or with a reference population, and(5) correcting phasing with trio-aware DuoHMM;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file;(c) processing the calibrated embryonic whole genome sequencing file by:(1) marking reads that support SNP or not for variants in region to be mutated, wherein:(i) for sequencing reads that contain the SNP, classify if sequencing read is inherited from maternal or paternal side, and (ii) if the read is uninformative, arbitrarily assigning the read from matemal / patemal, and(2) introducing one or more mutations, thereby generating the simulated embryonic genetic profile.Example 3. Method of generating simulated embryonic genetic profile with monosomy using data acquired from a sample

[0137] A simulated embryonic genetic profile with monosomy of a deleted chromosome from the maternal side is generated. Specifically, the simulated embryonic genetic profile is generated by:(a) obtaining a phased embryonic whole genome sequencing file by:(1) imputing with GLIMPSE for low-coverage whole genome sequencing file(s), (2) phasing with SHAPEIT that’s pedigree-aware or with a reference population, and (3) correcting phasing with trio-aware DuoHMM;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file;(c) processing the calibrated embryonic whole genome sequencing file by introducing the monosomy, wherein the processing comprises:Atorney Docket No. 206979-712601 / PCT(1) marking reads in the calibrated embryonic whole genome sequencing file (bam) that correspond to deleted chromosome, wherein:(iii)for sequencing reads that are located inside the deleted chromosome, classifying if sequencing read is inherited from maternal or paternal side, and(iv)if the read is uninformative, arbitrarily assigning the read from matemal / patemal, and(6) deleting all the reads coming from the maternal side and arbitrarily selected half of the uninformative reads to create the monosomy.Example 4. Method of generating simulated embryonic genetic profile with deletion using data acquired from a sample

[0138] A simulated embryonic genetic profile with a deletion from the maternal side is generated. Specifically, the simulated embryonic genetic profile is generated by:(a) obtaining a phased embryonic whole genome sequencing data file by:(7) imputing with GLIMPSE for low-coverage whole genome sequencing file(s), (8) phasing with SHAPEIT that’s pedigree-aware or with a reference population, and (9) correcting phasing with trio-aware DuoHMM;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file;(c) processing the calibrated embryonic whole genome sequencing file by introducing the maternal deletion,(1) marking reads that are inside the deletion region(s), wherein:(i) for sequencing reads that are inside the deletion region(s), classifying if sequencing read is inherited from maternal or paternal side, and(ii) if the read is uninformative, arbitrarily assigning the read from matemal / patemal, and(10) deleting all the maternal reads coming in the deletion region(s).Example 5. Method of generating simulated embryonic genetic profile with duplication using data acquired from a sample

[0139] For generating simulated embryonic genetic profile with duplication, reads from another sibling embryo, which is more realistic than duplicating existing reads in the region or a simulation, is used. In this example, Embryo-A and Embryo-B refer to sibling embryos. Embryo-A is theAtorney Docket No. 206979-712601 / PCTembryo that is to be simulated to comprise the duplication from the maternal side. The methods comprise:(a) obtaining a phased Embryo-A whole genome sequencing file and a phased Embryo-B whole genome sequencing file;(b) calibrating the phased Embryo-A whole genome sequencing file using a reference sequencing data file, thereby generating a calibrated Embryo-A whole genome sequencing file;(c) calibrating the phased Embryo-B whole genome sequencing file using a reference sequencing data file, thereby generating a calibrated Embryo-B whole genome sequencing file;(d) marking reads by:(1) identifying reads coming from maternal side in Embryo-B whole genome sequencing file in the duplicated region, and(2) identifying uninformative reads from Embryo-B whole genome sequencing file in the duplicated region;(e) processing the calibrated Embryo-A whole genome sequencing file and calibrated Embry o- B whole genome sequencing file by combining reads coming from maternal and half uninformative reads of calibrated Embryo-B whole genome sequencing file in the duplicated region of calibrated Embryo-A whole genome sequencing file (e.g., bam file).Example 6. Method of generating simulated embryonic genetic profile with uniparental disomy (UPD) using data acquired from a sample

[0140] Chromosomes 15, 11, 7, 14, 16 and X are most often involved in UPD formation, chromosome 15 being by far the most often observed one.

[0141] For generating a simulated embryonic genetic profile from a mother with isodisomy and a father with deletion, the methods comprise:(a) obtaining a phased embryonic whole genome sequencing file;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and(c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, wherein the processing comprises:(11) identifying reads from mother, reads from father, and uninformative reads, andAttorney Docket No. 206979-712601 / PCT(12) changing the reads from father, thereby, matching the reads with variants from the mother.

[0142] For generating a simulated embryonic genetic profile from a mother with heterodisomy and a father with deletion, the methods comprise:(a) obtaining a phased embryonic whole genome sequencing file, a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; and(c) processing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, wherein the processing comprises:(1) marking reads from mother, reads from father and uninformative reads by analy a phased paternal whole genome sequencing file, wherein:(i) for uninformative reads, arbitrarily assign half as coming from father, half as coming from mother;(ii) for all reads now marked as coming from mother,Father Motherchrl 123 l|0 0|lchrl 234 l|0 l|0embryo inheriting left side of each parent,chrl 123 l|0chrl 234 1|1father’s reads encompassing left sidechrl 123 1chrl 234 1, and(13) changing father’s reads mother’s right side-haplotypechrl 123 1,chrl 123 0 <- only 50% of the reads will be changed to 0.Example 7. Method of generating simulated embryonic genetic profile with unbalanced translocations using data acquired from a sample

[0143] In this example, the embryo(s) have unbalanced translocations between chr4q and chr20q. Methods for generating simulated embryonic genetic profile comprise:Atorney Docket No. 206979-712601 / PCT(a) obtaining a phased Embryo-A whole genome sequencing file and a phased Embryo-B whole genome sequencing file;(b) calibrating the phased Embryo-A whole genome sequencing file and the phased Embryo- B whole genome sequencing file using a reference sequencing data file; and(c) processing the calibrated Embryo-A whole genome sequencing file and the calibrated Embryo-B whole genome sequencing file:(1) optionally, marking reads in the Embryo-A whole genome sequencing file and Embryo-B whole genome sequencing file inherited from father’s side for 4q and chr20q + / i uninformative reads, and(2) moving reads from father’s 4q from Embryo-A whole genome sequencing file to Embryo-B whole genome sequencing file and reads from father’s 20q from Embryo-B whole genome sequencing file to Embryo-A whole genome sequencing file, thereby generating two embryonic genetic profiles with unbalanced translocation.Example 8. Method of generating simulated embryonic genetic profile with haploidy using data acquired from a sample

[0144] In this example, mother provides the full haploid set of chromosomes to the embryo, father does not. Methods for generating simulated embryonic genetic profile comprise:(a) obtaining a phased embryonic whole genome sequencing file;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo; and(c) processing the calibrated embryonic whole genome sequencing file by:(1) identifying reads from mother, reads from father, and uninformative reads in the calibrated embryonic whole genome sequencing file for all chromosomes, and (2) deleting all reads from father and arbitrarily selected half of the uninformative reads for all chromosomes, thereby generating simulated embryonic genetic profile with haploidy.Example 9. Method of generating simulated embryonic genetic profile with polyploidy using data acquired from a sample

[0145] In this example, simulated embryonic genetic profile with polyploidy is generated, wherein polyploidy comes from father,wherein father’s phased genome ischr2 123 l|0Atorney Docket No. 206979-712601 / PCTchr2 456 0|lchr2 800 0|lwherein, if Embryo’s inherited left side from fatherchr2 123 l|0chr2 456 0|lchr2 800 0|lthen for polyploidy, need to also add reads from father’s ‘right side’chr2 123 0chr2 456 1chr2 800 1

[0146] Methods generating simulated embryonic genetic profile with polyploidy comprise:(a) obtaining a phased embryonic whole genome sequencing file, maternal whole genome sequencing file and a phased paternal whole genome sequencing;(b) calibrating the embryonic whole genome sequencing file using a reference sequencing data file, Embry o-A’s bam file, thereby generating a calibrated embryonic whole genome sequencing file;(c) processing the calibrated embryonic whole genome sequencing file for creating a polyploidy originating from the father, wherein the processing comprises:(1) introducing one or more mutations by:(i) taking 14 of reads from Embryo-B whole genome sequencing file to represent haploid genome (optionally, also take into account coverage of Embryo-A whole genome sequencing file relative to coverage of Embryo-B whole genome sequencing file), and(ii) changing the reads to match expected genotype of the father’s ‘right side’, thereby generating simulated embryonic genetic profile with polyploidy. (2) Combining the reads from Embryo-B in step c with the reads from Embryo-A whole genome sequencing file.Example 10. Method of generating simulated embryonic genetic profile with mosaicism using data acquired from a sample

[0147] In this example, a simulated embryonic genetic profile with mosaicism is generated. Specifically, the methods disclosed herein makes use of high-quality sequencing files of family with normal and aneuploid embryo, wherein the methods comprise:Attorney Docket No. 206979-712601 / PCT(a) obtaining a phased embryonic whole genome sequencing file;(b) calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file; and(c) processing the calibrated embryonic whole genome sequencing file for generating simulated embryonic genetic profile with mosaicism, wherein the processing comprises:(14) identifying reads from mother, reads from father, and uninformative reads in the embryo whole genome sequencing file for all chromosomes by using phasing data, and(15) deleting a proportion of reads coming from the maternal side and the same proportion of the uninformative reads.Example 11. Method of generating simulated embryonic genetic profile using simulated data

[0148] Methods disclosed herein comprise use of phased father variant call format (VCF), phased mother VCF, and a reference genome. Specifically, the methods comprise:(a) simulating generation of father’s haploid bam files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating father haploid l .vcf and father_haploid_2.vcf files by:using read simulation that takes a VCF as input, thereby generating two sets of reads having 5x-coverage in fastq format, father haploid l.fastq and father_haploid_2.fastq, andAtorney Docket No. 206979-712601 / PCTaligning each of the father haploid l .fastq and father_haploid_2. fastq with a reference sequencing data file of PGT profiles at / i the desired coverage to create father’s haploid bam files;(c) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(d) calibrating mother haploid l .vcf and mother_haploid_2.vcf files by:using read simulation that takes a VCF as input, thereby generating mother haploid l. fastq and mother_haploid_2. fastq having 5x coverage, and aligning each of the mother haploid l. fastq and mother_haploid_2. fastq with a reference sequencing data file of PGT profile at / i the desired coverage to create mother haploid l .bam and mother_haploid_2.bam, and doing the same with the father to create father haploid l .bam and father_haploid_2.bam; and(e) combining a father’s haploid bam file with a mother’s haploid bam file, thereby generating simulated embryonic genetic profile(s) with the desired coverage of lOx.Example 12. Method of generating simulated embryonic genetic profile with aneuploidy using simulated dataAtorney Docket No. 206979-712601 / PCT

[0149] Methods disclosed herein comprise use of phased father variant call format (VCF), phased mother VCF, and a reference genome, wherein chr22 is deleted from the maternal side. Specifically, the methods comprise:(a) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0,(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating father haploid l .vcf and father_haploid_2.vcf files by using read simulation that takes a VCF as input, thereby two sets of reads having 5x-coverage in fastq format, father haploid l. fastq and father_haploid_2. fastq;(c) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid aneuploidy l .vcf and mother haploid aneuploidy _2.vcf files,Atorney Docket No. 206979-712601 / PCTwherein mother haploid aneuploidy l.vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother haploid aneuploidy _2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(d) introducing one or more mutations by:i. deleting chr22 sequence from the reference genome, and ii. deleting chr22 SNPs in mother haploid aneuploidy l.vcf,(e) calibrating mother haploid aneuploidy l .vcf file by creating a 5x-coverage using read simulation that takes as input modified reference genome from (i) and VCF (ii), thereby generating mother haploid aneuploidy l .fastq,(f) combining mother haploid aneuploidy l .fastq with the father haploid l .fastq or father_haploid_2. fastq, thereby generating simulated embryonic genetic profile(s) with aneuploidy.Example 13. Method of generating simulated embryonic genetic profile with deletions using simulated data

[0150] Methods disclosed herein comprise use of phased father variant call format (VCF), phased mother VCF, and a reference genome, wherein deletions are from the maternal side. Specifically, the methods comprise:(a) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0Attorney Docket No. 206979-712601 / PCTchrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating father haploid l.vcf and father_haploid_2.vcf files having 5x-coverage using read simulation that takes a VCF as input, thereby generating two sets of reads in fastq format, father haploid l .fastq and father_haploid_2. fastq;(c) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0,(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(d) introducing one or more mutations by:i. deleting sequence from the reference genome,ii. shifting variant POS in in mother haploid deletion.vcf,(e) calibrating mother haploid l.vcf and mother_haploid_2.vcf files by creating a 5x- coverage using read simulation that takes as input modified reference genome from (i) and VCF (ii), thereby generating mother haploid deletion. fastq,Atorney Docket No. 206979-712601 / PCT(f) combining mother haploid deletion. fastq with the father haploid l. fastq or father_haploid_2. fastq, thereby generating simulated embryonic genetic profile(s) with a deletion.Example 14. Method of generating simulated embryonic genetic profile with duplications using simulated data

[0151] Methods disclosed herein comprise use of phased father variant call format (VCF), phased mother VCF, and a reference genome, wherein duplications are from the maternal side. Specifically, the methods comprise:(a) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating father haploid l.vcf and father_haploid_2.vcf files having 5x-coverage using read simulation that takes a VCF as input, thereby generating two sets of reads in fastq format, father haploid l .fastq and father_haploid_2. fastq;(c) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingAttorney Docket No. 206979-712601 / PCTchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(d) introducing one or more mutations by:i. duplicating sequence for the reference genome at appropriate place, ii. creating a mother haploid duplication.vcf by adding back any phased variants in the duplicated region with new location relative to the modified reference genome, and shifting variant POS for variants downstream of the duplication appropriately in mother haploid l .vcf and / or mother_haploid_2.vcf files, and(e) calibrating mother haploid l .vcf and mother_haploid_2.vcf files, thereby creating mother haploid duplication. fastq by creating a 5x-coverage using read simulation that takes as input modified reference genome from (i) and VCF (ii), thereby generating mother hapl oi d dupli cati on . fastq,(f) combining mother haploid duplicati on. fastq with the father haploid l .fastq or father_haploid_2. fastq, thereby generating simulated embryonic genetic profile(s) with a duplication.Example 15. Method of generating simulated embryonic genetic profile with uniparental disomy (UPD) using simulated data

[0152] Chromosomes 15, 11, 7, 14 and 16 are most often involved in UPD formation, chromosome 15 being by far the most often observed one, which might possibly reflect in parts an ascertainment bias. Chromosomes 1, 2 and 6 have a moderate frequency of UPD, while the remainder chromosomes are sparsely contributing to UPD.Atorney Docket No. 206979-712601 / PCT

[0153] For generating a simulated embryonic genetic profile from a mother with chrl5 isodisomy and a father with deletion:(a) simulating generation of a father’s haploid data file by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) introducing one or more mutations by deleting chrl 5 from the reference genome, and removing chrl 5 SNPs from father haploid l .vcf and / or father_haploid_2.vcf,;(c) calibrating father haploid l .vcf and father_haploid_2.vcf files by using read simulation that takes modified reference genome, and father haploid l .vcf and / or father_haploid_2.vcf as input, thereby, generating father haploid l .fastq and / or father_haploid_2.fastq at 5x-coverage where chrl 5 is deleted,(d) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, andAtorney Docket No. 206979-712601 / PCT(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(e) calibrating mother haploid l .vcf using read simulation that takes as input the reference genome and, mother haploid l .vcf and, generating mother haploid isodisomy.fastq where chrl 5 has 1 Ox-coverage and all other chromosomes have 5x-coverage;(f) combining mother isodisomy.fastq with father haploid l .fastq or father_haploid_2.fastq, thereby generating simulated embryonic genetic profile(s) with maternal isodisomy.

[0154] For generating simulated embryonic genetic profile(s) from a mother with heterodisomy and a father with deletion:(a) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;Atorney Docket No. 206979-712601 / PCT(b) introducing one or more mutations by deleting chrl5 from the reference genome, and removing chrl5 SNPs from father haploid l .vcf and / or father_haploid_2.vcf;(c) calibrating father haploid l .vcf and / or father_haploid_2.vcf files by using read simulation that takes modified reference genome, and father haploid l .vcf and / or father_haploid_2.vcf as input, thereby, generating father haploid l .fastq and / or father_haploid_2. fastq;(d) simulating generation of a mother’s haploid data file by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(e) calibrating mother haploid l .vcf and mother_haploid_2.vcf files having 1 Ox-coverage using:i. 5x-coverage through read simulation that takes as input the reference genome and, mother haploid l .vcf, thereby generating mother haploid l .fastq,ii. 5x-coverage through read simulation that takes as input the reference genome with chrl 5 and, mother_haploid_2.vcf with chrl 5 SNPs, thereby generating mother_haploid_2. fastq, andiii. combining mother haploid l .fastq and mother_haploid_2. fastq, thereby generating mother heterodisomy. fastq, andAtorney Docket No. 206979-712601 / PCT(f) combining mother heterodisomy.fastq with father haploid l.fastq and / or father_haploid_2.fastq, thereby generating simulated embryonic genetic profile(s) with maternal heterodisomy.Example 16. Method of generating simulated embryonic genetic profiles with unbalanced translocation using simulated data

[0155] In this example, father has balanced translocation between chr4q and chr20q. Specifically, the father has derivative chromosome 4, normal chromosome 4, derivative chromosome 20 and normal chromosome 20. For generating simulated embryonic genetic profiles, the methods comprise:(a) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating mother haploid l .vcf and mother_haploid_2.vcf files by using read simulation that takes mother haploid l .vcf and mother_haploid_2.vcf files as input, thereby generating mother haploid l.fastq and mother_haploid_2.fastq having 5x-coverage;(c) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,Atorney Docket No. 206979-712601 / PCT(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG while preventing crossover events at translocation region,(3) performing random assortment of chromosomes for generating a plurality of father haploid.vcf files;(d) introducing one or more mutations by:(1) selecting informative SNP to confirm presence of derivative chromosome, and (2) generating input phased father whole genome sequencing file and modified reference genome files that comprise:i. a modified reference genome file with normal chromosome 4 and 20, wherein the reference genome and haploid vcf files, each comprising chr20q and chr4q sequence files, were used for simulation read as input,ii. a modified reference genome file with balanced translocation, wherein a reference genome with swapped sequences between chr20q and chr4q, and a haploid vcf file with swapped haplotype blocks between chr20q and chr4q that matches the reference genome were used for simulation read as input, iii. a modified reference genome file with unbalanced translocation, wherein the reference genome file comprises a derivative chromosome 20, wherein a reference genome with a sequence from chr4q is added to chr20q, wherein a haplotype block from chr4q is added to end of chr20q, and wherein positions of sequences are readjusted in chr20q,iv. a modified reference genome file with unbalanced translocation, wherein the reference genome file comprises a derivative chromosome 4, wherein a reference genome with a sequence from chr20q is added to chr4q, wherein a haplotype block from chr20q is added to end of chr4q, wherein positions of sequences are readjusted in chr4q, and (e) calibrating the plurality of father’s haploid VCF files by creating 5x-coverage using read simulation that takes modified reference genome and plurality of father haploid.vcf files as input, thereby generating a plurality of father haploid. fastq files; and(f) combining each of the plurality of father haploid.fastq files with a mother haploid l .fastq and / or mother_haploid_2. fastq, thereby creating simulated embryonic genetic profile(s).Example 17. Method of generating simulated embryonic genetic profiles with haploidy using simulated dataAtorney Docket No. 206979-712601 / PCT

[0156] In this example, mother’s phased whole genome sequencing file is used for generating the simulated embryonic genetic profiles comprising mother haploid l .fastq and / or mother_haploid_2. fastq. The methods comprise:(a) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0,(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) using read simulation that takes the reference genome vcf (no chr Y) and mother haploid l .vcf as input, thereby generating mother haploid l .fastq having half the expected coverage (e.g. 5x-coverage); and(c) the mother haploid l .fastq file represents a simulated embryonic genetic profile with haploidy.Example 18. Method of generating simulated embryonic genetic profiles with polyploidy using simulated data

[0157] In this example, the polyploidy in the simulated embryonic genetic profile is due to an extra haploid set of chromosomes from the father. The methods comprise:(a) simulating generation of mother’s haploid VCF files by:(1) taking mother’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,Atorney Docket No. 206979-712601 / PCT(3) generating phased mother-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased mother-recombined VCF into left-side and right side VCFs for creating mother haploid l .vcf and mother_haploid_2.vcf files,wherein mother haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein mother_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1chrl 321 0;(b) calibrating mother haploid l .vcf and mother_haploid_2.vcf files by using read simulation that takes the reference genome vcf (no chr Y), mother haploid l .vcf and / or mother_haploid_2.vcf files as input, thereby generating mother haploid l .fastq and / or mother_haploid_2.fastq having 5x-coverage;(c) simulating generation of father’s haploid VCF files by:(1) taking father’s phased VCF files,(2) creating crossover events for all chromosomes (e.g., simulating meiosis) using ORIGAMI, Ped-sim or simlOOOG,(3) generating phased father-recombined VCF havingchrl 123 0|lchrl 224 1|1chrl 321 l|0, and(4) splitting the phased father-recombined VCF into left-side and right side VCFs for creating father haploid l .vcf and father_haploid_2.vcf files,wherein father haploid l .vcf comprises left side of chrlchrl 123 0chrl 224 1chrl 321 1, andwherein father_haploid_2.vcf comprises right side of chrlchrl 123 1chrl 224 1Atorney Docket No. 206979-712601 / PCTchrl 321 0;(d) calibrating father haploid l .vcf and father_haploid_2.vcf files by using read simulation that takes the reference genome vcf (sex adjusted), father haploid l .vcf and father_haploid_2.vcf files as input, thereby generating father haploid l. fastq and father_haploid_2. fastq, both having 5x-coverage; and(e) combining mother haploid l .fastq or mother_haploid_2. fastq with father haploid l.fastq and father_haploid_2. fastq, thereby generating simulated embryonic genetic profile(s) with polyploidy.

Claims

Attorney Docket No. 206979-712601 / PCTClaimsWhat is claimed is:

1. A method for generating a simulated embryonic genetic profile with one or more mutations, the method comprising:obtaining a phased embryonic whole genome sequencing file;calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file obtained from an embryo, thereby generating a calibrated embryonic whole genome sequencing file; andprocessing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

2. The method of claim 1, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file; andchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

3. The method of claim 1 or 2, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.

4. The method of any one of claims 1-3, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

5. The method of claim 4, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

6. The method of any one of claims 1-5, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.Atorney Docket No. 206979-712601 / PCT7. The method of any one of claims 1-5, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

8. The method of any one of claims 1-6, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.

9. The method of any one of claims 1-8, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

10. The method of any one of claims 1-8, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

11. The method of any one of claims 1-8, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

12. The method of claim 11, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.

13. The method of any one of claims 1-12, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

14. The method of claim 13, wherein the sequence alignment file is in SAM, BAM, or CRAM format.

15. The method of any one of claims 1-14, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.Atorney Docket No. 206979-712601 / PCT16. A method for generating a simulated embryonic genetic profile with one or more mutations, the method comprising:obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file;simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file obtained from an embryo; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

17. The method of claim 16, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

18. The method of claim 17, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.

19. The method of any one of claims 16-18, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

20. The method of any one of claims 16-19, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

21. The method of any one of claims 16-20, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.Atorney Docket No. 206979-712601 / PCT22. The method of any one of claim 1-21, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than O.lx, less than lx, or less than 5x.

23. The method of any one of claims 1-22, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

24. The method of any one of claims 1-23, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184- 28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000- 21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.

25. The method of claim 24, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

26. The method of any one of claims 1-25, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

27. An apparatus for generating a simulated embryonic genetic profile, the apparatus comprising a processor and a memory storing software instructions that, when executed by the processor, cause the apparatus to perform the method of any one of claims 1-26.

28. A computer program product for generating a simulated embryonic genetic profile, the computer program product comprising at least one non-transitory computer-readableAtorney Docket No. 206979-712601 / PCTstorage medium storing software instructions that, when executed by an apparatus, cause the apparatus to perform the method of any one of claims 1-26.

29. An apparatus for performing a method of generating a simulated embryonic genetic profile, the apparatus comprising:a processor; anda memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files,wherein said plurality of data files comprise a phased embryonic whole genome sequencing file and a reference sequence file obtained from an embryo, and wherein said method comprises:obtaining the phased embryonic whole genome sequencing file, calibrating the phased embryonic whole genome sequencing file using the reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, andprocessing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

30. The apparatus of claim 29, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, and wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, andchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

31. The apparatus of claim 29 or 30, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.Atorney Docket No. 206979-712601 / PCT32. The apparatus of any one of claims 29-31, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

33. The apparatus of claim 32, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

34. The apparatus of any one of claims 29-33, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.

35. The apparatus of any one of claims 29-33, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

36. The apparatus of any one of claims 29-35, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.

37. The apparatus of any one of claims 29-36, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

38. The apparatus of any one of claims 29-36, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

39. The apparatus of any one of claims 29-36, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

40. The apparatus of claim 39, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.Atorney Docket No. 206979-712601 / PCT41. The apparatus of any one of claims 29-40, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

42. The apparatus of claim 41, wherein the sequence alignment file is in SAM, BAM, or CRAM format.

43. The apparatus of any one of claims 29-42, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.

44. An apparatus for performing a method of generating a simulated embryonic genetic profile, the apparatus comprising:a processor; anda memory for receiving a plurality of data files and for storing software instruction that, when executed by the processor, cause the apparatus to perform the method using the plurality of data files,wherein said plurality of data files comprise a phased maternal whole genome sequencing file, a phased paternal whole genome sequencing file and a reference sequence file obtained from an embryo, andwherein said method comprises:obtaining the phased maternal whole genome sequencing file and the phased paternal whole genome sequencing file;simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using the reference sequencing data file; and combining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

45. The apparatus of claim 44, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing fileAtorney Docket No. 206979-712601 / PCTand / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

46. The apparatus of claim 45, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.

47. The apparatus of any one of claims 44-46, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

48. The apparatus of any one of claims 44-47, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

49. The apparatus of any one of claims 44-48, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.

50. The apparatus of any one of claims 29-49, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 x, less than lx, or less than 5x.

51. The apparatus of any one of claims 29-50, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

52. The apparatus of any one of claims 29-51, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184- 28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000- 21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.Atorney Docket No. 206979-712601 / PCT53. The apparatus of claim 52, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

54. The apparatus of any one of claims 29-53, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15ql l-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22del (DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

55. A system comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform a method of generating a simulated embryonic genetic profile, wherein said method comprises:obtaining a phased embryonic whole genome sequencing file,calibrating the phased embryonic whole genome sequencing file using a reference sequencing data file, thereby generating a calibrated embryonic whole genome sequencing file, andprocessing the calibrated embryonic whole genome sequencing file by introducing one or more mutations, thereby generating the simulated embryonic genetic profile.

56. The system of claim 55, wherein the one or more mutations comprise diploid information that is introduced from a parent using a parental phased whole genome sequencing file, wherein the processing comprises:obtaining a first phased parental whole genome sequencing file and a second phased parental whole genome sequencing file, andchanging reads to match expected genotypes of the first phased parental whole genome sequencing file in the calibrated embryonic whole genome sequencing file, thereby generating simulated embryonic genetic profile with polyploidy.

57. The system of claim 55 or 56, wherein the one or more mutations are located in a chromosome of the calibrated embryonic whole genome sequencing file relative to a corresponding region in the reference sequencing data file having low read coverage.Attorney Docket No. 206979-712601 / PCT58. The system of any one of claims 55-57, wherein the phased embryonic whole genome sequencing file is obtained based on a sequence alignment file of embryo genome information.

59. The system of claim 58, wherein the sequence alignment file of embryo genome information is in SAM, BAM, or CRAM format.

60. The system of any one of claims 55-59, wherein the phased embryonic whole genome sequencing file is obtained from a benchmark genome.

61. The system of any one of claims 55-59, wherein the phased embryonic whole genome sequencing file is obtained using a phasing software.

62. The system of any one of claims 55-61, wherein the calibrated embryonic whole genome sequencing file comprises a read coverage correlation of >0.05 or >0.99 to a corresponding read coverage of the reference sequencing data file.

63. The system of any one of claims 55-62, wherein the phased embryonic whole genome sequencing file is in VCF or compressed VCF format.

64. The system of any one of claims 55-62, wherein the phased embryonic whole genome sequencing file is a sequence alignment file.

65. The system of any one of claims 55-62, wherein the method further comprises obtaining the phased embryonic whole genome sequencing file in VCF format and in a sequence alignment format, and adjusting differences between the phased embryonic whole genome sequencing file in VCF format and the phased embryonic whole genome sequencing file in the sequence alignment format to obtain an adjusted embryonic whole genome sequencing file.

66. The system of claim 65, wherein the method comprises generating the calibrated embryonic whole genome sequencing file using the adjusted embryonic whole genome sequencing file and the reference sequencing data file.Atorney Docket No. 206979-712601 / PCT67. The system of any one of claims 55-66, wherein the calibrated embryonic whole genome sequencing file is a sequence alignment file.

68. The system of claim 67, wherein the sequence alignment file is in SAM, BAM, or CRAM format.

69. The system of any one of claims 55-68, further comprising applying at least one polygenic disease model to the calibrated embryonic whole genome sequencing file to include one or more polygenic disease mutations indicative of the simulated embryonic genetic profile having the one or more polygenic diseases.

70. A system comprising an apparatus and software instruction that, when executed by the apparatus, cause the apparatus to perform a method of generating a simulated embryonic genetic profile, wherein said method comprises:obtaining a phased maternal whole genome sequencing file and a phased paternal whole genome sequencing file;simulating generation of a maternal haploid data file using the phased maternal whole genome sequencing file and a paternal haploid data file using the phased paternal whole genome sequencing file;introducing one or more mutations in the at least one of the maternal haploid data file and the paternal haploid data file;calibrating at least one of the maternal haploid data file and the paternal haploid data file using a reference sequencing data file; andcombining the maternal haploid data file and the paternal haploid data file, thereby generating the simulated embryonic genetic profile.

71. The system of claim 70, wherein the phased maternal whole genome sequencing file is obtained using a sequence alignment file of a maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file is obtained using a sequence alignment file of a paternal whole genome sequencing file.

72. The system of claim 71, wherein the sequence alignment file of maternal whole genome sequencing file and / or the sequence alignment file of paternal whole genome sequencing file is in SAM, BAM, or CRAM format.Atorney Docket No. 206979-712601 / PCT73. The system of any one of claims 70-72, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a population-based phasing method and / or a molecular-based phasing method.

74. The system of any one of claims 70-73, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained from a benchmark genome.

75. The system of any one of claims 70-74, wherein the phased maternal whole genome sequencing file and / or the phased paternal whole genome sequencing file are obtained using a phasing software.

76. The system of any one of claims 55-75, wherein the reference sequencing data file has low read coverage with a sequencing depth of less than 0.1 x, less than lx, or less than 5x.

77. The system of any one of claims 55-76, wherein the one or more mutations are selected from the group consisting of an aneuploidy, a deletion, a duplication, an unbalanced translocation, a haploid, a polyploidy, and / or a mosaicism.

78. The system of any one of claims 55-77, wherein the one or more mutations are located in a region of nucleotides 1-48129895 in chromosome 21, nucleotides 1-78077248 of chromosome 18, nucleotides 1-115169878 of chromosome 13, nucleotides 23810184- 28525505 of chromosome 15, nucleotides 22816713-28530182 of chromosome 15, nucleotides 18892575-21460220 of chromosome 22, nucleotides 151736-11411700 of chromosome 5, nucleotides 823964-6828363 of chromosome 1, nucleotides 19040000- 21470000 of chromosome 22, nucleotides 1-155270560 of chromosome X, nucleotides 1-59373566 of chromosome Y, between chromosomes 13 and 14, or between chromosomes 14 and 21 in a human genome.

79. The system of claim 78, wherein the human genome is Genome Reference Consortium Human Build 37 (GRCh37), Genome Reference Consortium Human Build 38 (GRCh38) or Telomere 2 telomere (T2T).

80. The system of any one of claims 55-79, wherein the one or more mutations are associated with Trisomy 21 (Down syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 13, 15qll-ql3 / DEL (Prader-Willi syndrome), 15qll-ql3 DEL (Angelman syndrome), 22delAtorney Docket No. 206979-712601 / PCT(DiGeorge syndrome), 5p deletion syndrome (Cru-di-chat syndrome), Monosomy lp36, 22qll.2del (Di George syndrome), 22qll.2dup, Monosomy X (Turner syndrome), XXX syndrome (Jacob’s syndrome), XYY syndrome, XXY syndrome (Klinefelter syndrome), or Robertsonian translocation.

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