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
View PDF3 Cites 3 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

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,...

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
  • 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

Experimental program
Comparison scheme
Effect test

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...

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

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

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
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
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

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

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap