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Resolving genome fractions using polymorphism counts

A genomics, fractional technology, used in genomics, sequence analysis, proteomics, etc.

Active Publication Date: 2014-05-14
VERINATA HEALTH INC
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] A disadvantage of existing methods for detecting fetal fraction is that they rely on measures of the abundance of sex chromosomes (which can only be used to reliably measure the relative abundance of DNA in male embryos) or are known to be between pregnancy and embryonic tissue. mRNA sequences of differentially expressed genes (which are subject to variability in expression due to gestational age or other factors)

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  • Resolving genome fractions using polymorphism counts
  • Resolving genome fractions using polymorphism counts
  • Resolving genome fractions using polymorphism counts

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Embodiment Construction

[0054] Introduction and Overview

[0055] Certain disclosed embodiments relate to analyzing DNA obtained from the blood of a pregnant female, and using the analysis to determine the fraction of that DNA from the fetus. The fetal fraction of DNA can then be used to attribute a certain level of confidence to another measure or characterization of the fetus based on a separate analysis of DNA obtained from the mother's blood. For example, a fetal DNA sample obtained from maternal blood can be analyzed separately to detect aneuploidy in a fetus conceived by a pregnant woman. The determination of aneuploidy by this separate analysis can be given by a statistically robust confidence level based on the fractional amount of fetal DNA present in the DNA obtained from the maternal blood. A lower fraction of fetal DNA in the total complement of DNA indicates low confidence in any characterization based on fetal DNA.

[0056] Typically, but not necessarily, the analyzed DNA in materna...

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Abstract

Methods of reliably estimating genomic fraction (e.g., fetal fraction) from polymorphisms such as small base variations or insertions-deletions are disclosed. Sequenced data from a multigenomic source is used to determine allele counts for one or more of the polymorphisms. For one or more of the polymorphisms, zygosity is assigned, and genomic fraction is determined from the zygosity and allele counts. Certain embodiments employ SNPs as the relevant polymorphism. The disclosed methods can be applied as part of an intentional, pre-designed re-sequencing study targeted against known polymorphisms or can be used in a retrospective analysis of variations found by coincidence in overlapping sequences generated from maternal plasma (or any other setting where a mixture of DNA from several people are present).

Description

[0001] Cross References to Related Applications [0002] This application claims priority to US Provisional Application Serial No. 61 / 474362, filed April 12, 2011, the contents of which are hereby incorporated by reference in their entirety for all purposes. Background technique [0003] The discovery of free-floating fetal DNA (sometimes referred to as "cell free DNA" or "cfDNA") in maternal blood allows the possibility of detection of chromosomal abnormalities, aneuploidy and aberrations from blood samples. The fractional abundance of fetal DNA in maternal plasma is not constant and varies with several factors, including sample processing and gestational age. [0004] When using DNA sequencing to identify chromosomal aberrations or genetic defects, it is important to know the relative abundance of fetal DNA in the total population of DNA. For example, when the fetal fraction is known, statistical power (probability of identifying anomalies, or sensitivity) can be calculate...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G16B20/20G16B20/10G16B30/10G16B40/00G16B45/00
CPCG16B20/00C12Q1/6809C12Q1/6827C12Q1/6883G16B40/00G16B30/00C12Q2600/156G16B20/10G16B20/20G16B30/10C12Q2535/122C12Q2537/16C12Q2537/165G16B45/00C12Q1/6876
Inventor 里查德·P·拉瓦布莱恩·K·利思约翰·P·伯克
Owner VERINATA HEALTH INC
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