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Method and device for calculating purity and chromosome ploidy of cancer sample

A chromosome ploidy, cancer technology, applied in the field of cancer research, can solve the problems of inconvenience, poor accuracy, lack of accuracy, etc.

Active Publication Date: 2018-11-13
SHANGHAI INST OF MATERIA MEDICA CHINESE ACAD OF SCI
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Problems solved by technology

But its accuracy is poor, especially in the case of subclone in the genome
Patchwork uses two kinds of information at the same time, but in the intermediate step of calculating the genotype, manual identification is required, the result of manual judgment lacks accuracy, and this semi-automatic software brings a lot of inconvenience to the application
[0005] How to make full use of the existing next-generation sequencing data to accurately calculate the purity of cancer samples and the genome ploidy of cancer cells is still a challenging task

Method used

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  • Method and device for calculating purity and chromosome ploidy of cancer sample
  • Method and device for calculating purity and chromosome ploidy of cancer sample
  • Method and device for calculating purity and chromosome ploidy of cancer sample

Examples

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Embodiment

[0251] Example: According to the whole genome sequencing data of cancer tissue and normal tissue of sample TCGA-CM-4746, the purity and chromosomal ploidy of cancer samples were calculated using a hierarchical mixed Gaussian model.

[0252] 1. Collect sample data and download the whole genome sequencing data of TCGA-CM-4746-01A tumor samples and normal samples in TCGA. The bam file size of the cancer sample is 12.6G, and the bam file size of the normal sample is 10.1G. The bam file was processed into a fastq file with PICARD software. Align fastq to the reference genome hs37d5 using bwa mem to get bam files of new cancer samples and normal samples, the file sizes are 12.4G and 9.9G respectively.

[0253] 2. Download the vcf files of chromosomes 1 to 22 provided by the 1000genome project (ftp: / / ftp.1000genomes.ebi.ac.uk / vol1 / ftp / release / 20130502 / ), and use the SelectVariants method of GATK to extract the reference genome hs37d5 The BIALLELIC loci with an allele frequency grea...

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Abstract

The present invention provides a full-automatic, high-efficiency and high-accuracy method and device for calculating purity and chromosome ploidy of a cancer sample. Through a hierarchical Gaussian mixture model provided by the invention, the purity and the chromosome ploidy of the cancer sample are rapidly and accurately calculated; the time and the economic cost of purity estimation are saved; the accuracy of calculation results is increased at the same time; the method and the device have broad application prospects in the calculation of the purity and the chromosome ploidy of the cancer sample.

Description

technical field [0001] The invention belongs to the field of cancer research, and in particular relates to a method and a device for calculating the purity of cancer cells in cancer samples and intracellular chromosomal ploidy. Background technique [0002] Cancer research is an important research field in life medicine and has a major impact on human health and life. Cancer is a kind of disease caused by the malignant proliferation of cells. Because of its complex pathology, human beings have not been able to overcome this kind of disease. Next generation sequencing (next generation sequencing) provides the possibility to quickly detect the genetic information of patients. However, sequencing needs to extract samples from patient tissues, but usually cancer tissue does not simply contain cancer cells, it also has a very rich microenvironment. Cancer cell microenvironment refers to the environment of normal cells (non-cancerous cells) surrounding or accompanying cancer cel...

Claims

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Application Information

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IPC IPC(8): G06F19/22
CPCC12Q1/68G16B15/00G16B30/00
Inventor 黄宇罗志辉苏瑶范新平
Owner SHANGHAI INST OF MATERIA MEDICA CHINESE ACAD OF SCI
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