Determining variants in a genome of a heterogeneous sample

A genome and reference genome technology, applied in the field of determining the variation in the genome of heterogeneous samples, can solve all mutation difficulties and other problems

Inactive Publication Date: 2014-11-19
COMPLETE GENOMICS INC
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Problems solved by technology

This heterogeneity in the sample can lead to difficulties in identifying all mutations in the genome of the sample

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  • Determining variants in a genome of a heterogeneous sample
  • Determining variants in a genome of a heterogeneous sample
  • Determining variants in a genome of a heterogeneous sample

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[0045] Cancer samples are complex. For example, different cells of a tumor sample may have different genomes. These samples often exhibit this heterogeneity in the genome due to contamination of normal DNA and / or multiple branches in tumor evolution. When these different cells are analyzed within the same sequencing experiment, the measured copy number of the allele at a particular locus may vary. For example, the percentage of DNA with a particular allele (allele fraction) may have any value between 0% and 100%. Therefore, a major challenge in studying cancer genomes is to be able to detect variants present in small fractions of cells in a cancer sample.

[0046] To address this challenge, a process for determining the genome of a sample in a particular region can explicitly allow the allele fraction to vary between ranges of values ​​(eg, any value between 0% and 100%). This determined genome of a sample may effectively be a composite of the genomes of the different cells w...

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Abstract

After DNA fragments are sequenced and mapped to a reference, various hypotheses for the sequences in a variant region can be scored to find which sequence hypotheses are more likely. A hypothesis can include a specific variable fraction for the plurality of alleles that comprise the sequence hypothesis in the region. A likelihood of each hypothesis can be determined using a probability that accounts for the fraction of the alleles specified in the respective sequence hypothesis. Thus, other hypotheses besides standard homozygous and equal heterozygous (i.e., one chromosome with A and one with B in a cell) can be explored by explicitly including the variable fractions of the alleles as a parameter in the optimization. Also, a variant score can be determined for a variant relative to a reference. The variant score can be used to determine a variant calibrated score indicating a likelihood that the variant call is correct.

Description

[0001] Cross References to Related Applications [0002] This application claims U.S. Provisional Application No. 61 / 535,926, filed September 16, 2011, entitled "Techniques For Calling Small Variants In Polynucleotide Sequences," and filed March 2, 2012, entitled "Techniques For Small Variant Assembler" Provisional Application No. 61 / 606,306 of priority, and non-provisional applications thereof, which are hereby incorporated by reference in their entirety for all purposes. [0003] This application is jointly owned with U.S. Patent Application No. 12 / 770,089, entitled "Method And System For Calling Variations In A Sample Polynucleotide Sequence With Respect To A Reference Polynucleotide Sequence," filed April 29, 2012 by Carnevali et al. (Attorney Docket No. 92171-002110US), the entire disclosure of which is incorporated by reference. technical field [0004] The present disclosure relates generally to the determination of genomes using sequencing technology, and more specifi...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F17/18G01N33/48C12Q1/68G16B40/10G16B30/10G16B30/20G16B40/00
CPCG06F17/18G06F19/22G06F19/24G16B30/00G16B40/00G16B40/10G16B30/10G16B30/20
Inventor J.巴卡什A.哈尔彭C.田K.潘特P.卡尼瓦利
Owner COMPLETE GENOMICS INC
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