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

Marina D Miller; Eric J Devor; Erin A Salinas; Andreea M Newtson; Michael J Goodheart; Kimberly K Leslie; Jesus Gonzalez-Bosquet

doi:10.3390/ijms20051192

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

Journal article

Open access

Peer reviewed

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

Marina D Miller, Eric J Devor, Erin A Salinas, Andreea M Newtson, Michael J Goodheart, Kimberly K Leslie and Jesus Gonzalez-Bosquet

International journal of molecular sciences, Vol.20(5), p.1192

03/08/2019

DOI: 10.3390/ijms20051192

PMCID: PMC6429328

PMID: 30857229

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Abstract

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.

Ovarian Neoplasms - genetics

Endometrial Neoplasms - genetics

Humans

Middle Aged

Databases, Genetic

Female

Software

Genome, Human

Genomics - methods

High-Throughput Nucleotide Sequencing - methods

Details

Title: Subtitle: Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA
Creators: Marina D Miller - Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. marina-miller@uiowa.edu
Eric J Devor - Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. eric-devor@uiowa.edu
Erin A Salinas - Compass Oncology, Portland, OR 97227, USA. Erin.Salinas@compassoncology.com
Andreea M Newtson - Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. andreea-newtson@uiowa.edu
Michael J Goodheart - Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. michael-goodheart@uiowa.edu
Kimberly K Leslie - Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. kimberly-leslie@uiowa.edu
Jesus Gonzalez-Bosquet - Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA. jesus-gonzalezbosquet@uiowa.edu
Resource Type: Journal article
Publication Details: International journal of molecular sciences, Vol.20(5), p.1192
DOI: 10.3390/ijms20051192
PMID: 30857229
PMCID: PMC6429328
NLM abbreviation: Int J Mol Sci
ISSN: 1661-6596
eISSN: 1422-0067
Publisher: Switzerland
Grant note: R01CA184101 / National Institutes of Health Basic research fund / Department of Obstetrics & Gynecology at the University of Iowa R01CA99908 / National Institutes of Health P30 CA086862 / NCI NIH HHS
Language: English
Date published: 03/08/2019
Academic Unit: Obstetrics and Gynecology
Record Identifier: 9983931487402771

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