Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

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
View PDF2 Cites 23 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

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

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • 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

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[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...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

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...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
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
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com