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一种从单核苷酸多态性基因分型数据检查培养细胞系基因组完整性的方法。

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

作者信息

Danecek Petr, McCarthy Shane A, Durbin Richard

机构信息

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom.

出版信息

PLoS One. 2016 May 13;11(5):e0155014. doi: 10.1371/journal.pone.0155014. eCollection 2016.

DOI:10.1371/journal.pone.0155014
PMID:27176002
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4866717/
Abstract

Genomic screening for chromosomal abnormalities is an important part of quality control when establishing and maintaining stem cell lines. We present a new method for sensitive detection of copy number alterations, aneuploidy, and contamination in cell lines using genome-wide SNP genotyping data. In contrast to other methods designed for identifying copy number variations in a single sample or in a sample composed of a mixture of normal and tumor cells, this new method is tailored for determining differences between cell lines and the starting material from which they were derived, which allows us to distinguish between normal and novel copy number variation. We implemented the method in the freely available BCFtools package and present results based on induced pluripotent stem cell lines obtained in the HipSci project.

摘要

在建立和维持干细胞系时，对染色体异常进行基因组筛查是质量控制的重要组成部分。我们提出了一种新方法，利用全基因组SNP基因分型数据灵敏检测细胞系中的拷贝数改变、非整倍体和污染情况。与其他用于识别单个样本或由正常细胞与肿瘤细胞混合组成的样本中拷贝数变异的方法不同，这种新方法专门用于确定细胞系与其来源起始材料之间的差异，这使我们能够区分正常拷贝数变异和新的拷贝数变异。我们在免费可用的BCFtools软件包中实现了该方法，并展示了基于在HipSci项目中获得的诱导多能干细胞系的结果。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/3ab989aa2c37/pone.0155014.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/4831abc914b1/pone.0155014.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/a9529a137c57/pone.0155014.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/72098d9a3ddb/pone.0155014.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/67e80169eded/pone.0155014.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/3ab989aa2c37/pone.0155014.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/4831abc914b1/pone.0155014.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/a9529a137c57/pone.0155014.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/72098d9a3ddb/pone.0155014.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/67e80169eded/pone.0155014.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/380c/4866717/3ab989aa2c37/pone.0155014.g005.jpg

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