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

International Journal of Molecular Sciences

ErinA. Salinas¹  MarinaD. Miller²  EricJ. Devor²  KimberlyK. Leslie²  AndreeaM. Newtson³  Jesus Gonzalez-Bosquet⁴  MichaelJ. Goodheart⁴ 

[1] Compass Oncology, Portland, OR 97227, USA;Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;Division of Gynecologic Oncology, Department of Obstetrics and Gynecologic, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;

关键词: population substructure;    genetic admixture;    endometrial cancer;    ovarian cancer;    The Cancer Genome Atlas;   

DOI  :  10.3390/ijms20051192

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown