Next Article in Journal
KCa3.1 Transgene Induction in Murine Intestinal Epithelium Causes Duodenal Chyme Accumulation and Impairs Duodenal Contractility
Next Article in Special Issue
A Prediction Model for Preoperative Risk Assessment in Endometrial Cancer Utilizing Clinical and Molecular Variables
Previous Article in Journal
Every Coin Has Two Sides: Reactive Oxygen Species during Rice–Magnaporthe oryzae Interaction
Previous Article in Special Issue
Molecular Characterization of Non-responders to Chemotherapy in Serous Ovarian Cancer
Open AccessCommunication

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

1
Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
2
Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
3
Compass Oncology, Portland, OR 97227, USA
4
Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(5), 1192; https://doi.org/10.3390/ijms20051192
Received: 31 January 2019 / Revised: 26 February 2019 / Accepted: 4 March 2019 / Published: 8 March 2019
(This article belongs to the Special Issue Data Analysis and Integration in Cancer Research)
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. View Full-Text
Keywords: population substructure; genetic admixture; endometrial cancer; ovarian cancer; The Cancer Genome Atlas population substructure; genetic admixture; endometrial cancer; ovarian cancer; The Cancer Genome Atlas
Show Figures

Figure 1

MDPI and ACS Style

Miller, M.D.; Devor, E.J.; Salinas, E.A.; Newtson, A.M.; Goodheart, M.J.; Leslie, K.K.; Gonzalez-Bosquet, J. Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA. Int. J. Mol. Sci. 2019, 20, 1192.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop