Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA

In the era of large genetic and genomic datasets, it has become crucially important to validate results of individual studies using data from publicly available sources, such as The Cancer Genome Atlas (TCGA). However, how generalizable are results from either an independent or a large public datase...

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Bibliographic Details
Published inInternational journal of molecular sciences Vol. 20; no. 5; p. 1192
Main Authors Miller, Marina D, Devor, Eric J, Salinas, Erin A, Newtson, Andreea M, Goodheart, Michael J, Leslie, Kimberly K, Gonzalez-Bosquet, Jesus
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 08.03.2019
MDPI
Subjects
African Americans
Breast cancer
Cancer
Clinical outcomes
Communication
Datasets
Endometrial cancer
Endometrium
Ethnicity
Gene expression
genetic admixture
Genomes
Genomics
Hispanic Americans
Histology
Minority & ethnic groups
Ovarian cancer
Patients
population substructure
Populations
Social factors
Studies
Substructures
The Cancer Genome Atlas
Tumors
Womens health
United States > US
Iowa
endometrial cancer
ovarian cancer
population substructure
genetic admixture
The Cancer Genome Atlas
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Summary:In the era of large genetic and genomic datasets, it has become crucially important to validate results of individual studies using data from publicly available sources, such as The Cancer Genome Atlas (TCGA). However, how generalizable are results from either an independent or a large public dataset to the remainder of the population? The study presented here aims to answer that question. Utilizing next generation sequencing data from endometrial and ovarian cancer patients from both the University of Iowa and TCGA, genomic admixture of each population was analyzed using STRUCTURE and ADMIXTURE software. In our independent data set, one subpopulation was identified, whereas in TCGA 4⁻6 subpopulations were identified. Data presented here demonstrate how different the genetic substructures of the TCGA and University of Iowa populations are. Validation of genomic studies between two different population samples must be aware of, account for and be corrected for background genetic substructure.
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ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms20051192