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Identifying Cryptic Relationships
Lei Sun1,2, Apostolos Dimitromanolakis3,4, Wei-Min Chen5,6
1Department of Statistical Sciences, Faculty of Arts and Sciences, University of Toronto, 100 St. George Street, Toronto, ON, Canada, M5S 3G3. sun@utstat.toronto.edu.
Abstract:
Cryptic relationships such as first-degree relatives often appear in studies that collect population samples, including genome-wide association studies (GWAS) and next-generation sequencing (NGS) analyses. Cryptic relatedness not only increases type 1 error rate of association tests but also affects other analytical aspects of GWAS and NGS such as population stratification via principal component analysis. Here, we discuss three effective methods, as implemented in PREST, PLINK, and KING, to detect and correct for the problem of cryptic relatedness using high-throughput SNP data collected from GWAS and NGS experiments. We provide the analytical and practical details involved using three application examples.
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