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Method for improving the sensitivity of detection in determining copy number variations

A technology of copy number and readout, applied in biochemical equipment and methods, microbiological determination/inspection, electrical digital data processing, etc.

Active Publication Date: 2016-08-03
VERINATA HEALTH INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0009] Limitations of existing methods in non-invasive prenatal diagnosis, including insufficient sensitivity stemming from limited levels of cfDNA, and sequencing bias stemming from the inherent nature of genomic information, constitute limitations to the ability to provide any or all specificity. , sensitivity, and applicability to the continuing need for non-invasive methods to reliably diagnose copy number alterations in a wide variety of clinical settings

Method used

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  • Method for improving the sensitivity of detection in determining copy number variations
  • Method for improving the sensitivity of detection in determining copy number variations
  • Method for improving the sensitivity of detection in determining copy number variations

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preparation example Construction

[0302] Sequencing library preparation

[0303] In one embodiment, the methods described herein can utilize next-generation sequencing (NGS), which allows multiple samples to be sequenced individually in a single sequencing run, either as genomic molecules (i.e., single-plex sequencing) or as genomic molecules containing indexes. pooled samples (eg, multiplexed sequencing). These methods can generate DNA sequences up to hundreds of millions of reads. In various embodiments, the sequence of genomic nucleic acid, and / or indexed genomic nucleic acid, can be determined using, for example, next generation sequencing (NGS) techniques described herein. In various embodiments, one or more processors as described herein can be utilized to analyze large amounts of sequence data obtained using NGS.

[0304] In various embodiments, the application of the sequencing techniques described above does not involve the preparation of sequencing libraries.

[0305] However, in certain embodim...

Embodiment 1

[0442] Preparation and sequencing of raw and enriched sequencing libraries

[0443] a. Preparation of sequencing library - simplified method (ABB)

[0444] All sequencing libraries, ie, raw and enriched libraries, were prepared from approximately 2 ng of purified cfDNA extracted from maternal plasma. Take advantage of NEBNext TM The reagent of DNASamplePrepDNAReagentSet1 (product number E6000L; NewEnglandBiolabs, Ipswich, MA) is used for library preparation, for as follows. Since cell-free plasma DNA is fragmented in nature, plasma DNA samples were not further fragmented by nebulization or sonication. according to EndRepairModule, at 20°C, by DNA polymerization in a 1.5 ml microcentrifuge tube with the aid of 5 μl of 10X phosphorylation buffer, 2 μl of deoxynucleotide solution mixture (10 mM for each dNTP), 1 μl of a 1:5 dilution Enzyme I, 1 μl of T4 DNA polymerase and 1 μl of T4 polynucleotide kinase, available at NEBNext TM In DNASamplePrepDNAReagentSet1, cfDNA w...

Embodiment 2

[0454] Accurate Aneuploidy Detection in Twin Pregnancies

[0455] introduction

[0456] Noninvasive prenatal testing (NIPT) of total cell-free DNA (cfDNA) using whole-genome massively parallel sequencing has been shown to be a very accurate and reliable method for detecting fetal chromosomal aneuploidy. 参见,BianchiDW,PlattLD,GoldbergJD,等人Genome-WidefetalaneuploidydetectionbymaternalplasmaDNAsequencing.ObstetGynecol2012;119:890-901;FanHC,BlumenfeldYJ,ChitkaraU,HudginsL,QuakeSR.NoninvasivediagnosisoffetalaneuploidybyshotgunsequencingDNAfrommaternalblood.ProcNatlAcadSciUSA2008;105:16266-71;SehnertAJ,RhecsB,ComstockD,等人 Optimal detectionoffetalchromosomalabnormalitiesbymassivelyparallelDNAsequencingofcell-freefetalDNAfrommaternalblood. ClinChem2011;57:1042-9. The point-of-care test described above detects trisomies 21, 18, 13 and sex chromosome aneuploidy from a single maternal blood sample. The point-of-care tests described above are currently indicated for pregnant women with...

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Abstract

The invention discloses a method for improving the sensitivity of detection in determining copy number variations. Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and / or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. Also disclosed are systems and computer program products for evaluation of CNV of sequences of interest.

Description

[0001] References to related applications [0002] U.S. Provisional Patent Application No. 61 / 893,830, entitled "METHODFORIMPROVINGTHESENSITIVITYOFDETECTIONINDETERMININGCOPYNUMBERVARIATIONS (METHOD FOR IMPROVING THE SENSITIVITY OF DETECTION IN DETERMINING COPY NUMBER VARIATIONS)," filed October 21, 2013 pursuant to 35 U.S.C. §119(e) Priority of , the entire contents of which are incorporated herein by reference. Background technique [0003] One of the key endeavors in human medical research is the discovery of genetic abnormalities that produce adverse health consequences. In many cases, specific genes and / or key diagnostic markers have been identified in multiple parts of the genome in abnormal copy numbers. For example, in prenatal diagnosis, extra or missing copies of whole chromosomes are frequently occurring genetic disorders. Deletion or doubling of copies of whole chromosomes or segments of chromosomes, and higher levels of amplification of specific regions of the ge...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20G06F19/22G16B20/10G16B25/10
CPCG16H50/20G16B25/00G16B20/10G16B25/10C12Q1/68G16B30/00G16B40/00
Inventor 达里娅·I·丘多瓦戴安娜·阿布杜伊瓦里查德·P·拉瓦
Owner VERINATA HEALTH INC
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