Massive Sequencing Embryo Mutation Detection Method
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Solution Overview
Problem
Current Preimplantation Genetic Diagnosis (PGD) techniques face limitations in simultaneously detecting aneuploidies (PGD-A) and monogenic diseases (PGD-M) in embryos using a single biopsy, with high costs, high Allele-Dropout rates, and inability to detect structural anomalies or mosaicism, making it difficult to select healthy embryos effectively.
Innovation Solution
A method combining PGD-A and PGD-M using massive sequencing with a single biopsy, involving the preparation of PGD-A and PGD-M libraries, enrichment of SNPs, and standard sequencing protocols, allowing for independent analysis of aneuploidies and monogenic diseases, which is faster and more economical than existing methods like Karyomapping.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional PGD techniques (PCR, fragment analysis, Karyomapping) are used to detect monogenic diseases and aneuploidies, then genetic diagnosis can be obtained, but the cost increases substantially and the time required exceeds the 24-hour response window needed for embryo transfer
Solution Approach 1:
The patent combines PGD-A (aneuploidy detection) and PGD-M (monogenic disease detection) into a single massively parallel sequencing assay. By merging the detection of chromosomal aneuploidies and single-gene mutations into one unified workflow using the same library preparation and sequencing steps, the method achieves both diagnostic goals within the required 24-hour timeframe while avoiding the sequential processing time of traditional separate assays
Solution Approach 2:
The patent changes the detection parameters by using massively parallel sequencing with reduced representation (targeting specific genomic regions) instead of traditional PCR-based methods or whole-genome sequencing. This parameter change enables faster data acquisition and analysis while maintaining diagnostic precision for both aneuploidies and monogenic diseases
2Adaptability or versatility
If multiple separate PGD techniques are used to simultaneously detect aneuploidies and monogenic diseases, then comprehensive genetic screening is achieved, but the cost and complexity of the procedure increases substantially
Solution Approach 1:
The patent creates a universal PGD platform that can simultaneously detect aneuploidies, monogenic diseases, and structural chromosomal abnormalities using a single massively parallel sequencing assay. The method uses universal library preparation steps and a unified data analysis pipeline that handles multiple diagnostic objectives, eliminating the need for separate specialized assays for each type of genetic abnormality
Solution Approach 2:
The patent merges multiple diagnostic functions (aneuploidy detection, monogenic disease detection, structural abnormality detection) into one integrated workflow. The same sequencing data is used to detect all three types of abnormalities through different analysis approaches, reducing procedural complexity while maintaining comprehensive screening capability
3Quantity of substance
If traditional PGD methods with prior amplification are used, then genetic material from single cells can be analyzed, but the Allele-Dropout rate remains high at about 5%
Solution Approach 1:
The patent changes the amplification parameters by using a modified whole-genome amplification approach with multiple displacement amplification (MDA) using Phi29 polymerase, followed by targeted enrichment. This parameter change reduces bias in allele amplification and lowers the Allele-Dropout rate compared to traditional PCR-based methods, improving the reliability of detecting both maternal and paternal alleles
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach enables rapid and cost-effective simultaneous analysis of aneuploidies and monogenic diseases, reducing the time and cost of embryo selection, and is adaptable to various sample numbers, allowing for efficient identification of healthy embryos.
Implementation Method 1
a method known as MDA (Multiple Displacement Amplification) that amplifies the genetic material thanks to the Phi29 polymerase at a constant temperature
Implementation Method 2
A method for the study of embryo mutations in in vitro reproduction processes with the particular feature that it combines the detection techniques of Aneuploidy (PGD-A) and the study of monogenic diseases in embryos (PGD-M) by SNP (single nucleotide polymorphism) analysis by massive sequencing
Data Source
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AI summary
The invention relates to a method for the study of embryo mutations in in vitro reproduction processes with the particular feature that it combines the detection techniques of Aneuploidy (PGD-A) and the study of monogenic diseases in embryos (PGD-M), and wherein the method comprises: a SNP selection process, wherein the values of some n candidate SNPs (t1... tk) of each subject x, in a chromosomal region of interest and specifically extracted for a study population, are taken as input; a SNP selection process, wherein all the SNP combinations are evauated to obtain a minimum set t of tagSNPs from the matrix M obtained in the first SNP selection process; and a process involving in-silico validation of the tagSNP panel obtained in the second process.