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An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines.

ABSTRACT: Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.

SUBMITTER: Dutil J

PROVIDER: S-EPMC6445675 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines.

Dutil Julie J Chen Zhihua Z Monteiro Alvaro N AN Teer Jamie K JK Eschrich Steven A SA

Cancer research 20190320 7

Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancest ...[more]

PMID: 30894373

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Dataset Information

An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines.

Publications

An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines.

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