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Genet Epidemiol. 2019 Aug 20. doi: 10.1002/gepi.22250. [Epub ahead of print]

Effect of population stratification on SNP-by-environment interaction.

An J1, Won S1,2,3,4, Lutz SM5, Hecker J4,6, Lange C4,6.

Author information

1
Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea.
2
Interdisciplinary Program for Bioinformatics, College of Natural Science, Seoul National University, Seoul, South Korea.
3
Institute of Health and Environment, Seoul National University, Seoul, South Korea.
4
Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.
5
Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts.
6
Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.

Abstract

Proportions of false-positive rates in genome-wide association analysis are affected by population stratification, and if it is not correctly adjusted, the statistical analysis can produce the large false-negative finding. Therefore various approaches have been proposed to adjust such problems in genome-wide association studies. However, in spite of its importance, a few studies have been conducted in genome-wide single nucleotide polymorphism (SNP)-by-environment interaction studies. In this report, we illustrate in which scenarios can lead to the false-positive rates in association mapping and approach to maintaining the overall type-1 error rate.

KEYWORDS:

SNP-by-environment interaction; genetic association; population stratification

PMID:
31429121
DOI:
10.1002/gepi.22250

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