Population structure at different minor allele frequency levels

BMC Proceedings

Proceedings

Omar De la Cruz¹  Paola Raska¹ 

[1] Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, 10900 Euclid Ave, 44106, Cleveland, OH, USA;

关键词: Minor Allele Frequency;    Common Variant;    Rare Variant;    Rare Allele;    Unrelated Individual;   

DOI  :  10.1186/1753-6561-8-S1-S55

来源: Springer

【 摘 要 】

Inferring population genetic structure from large-scale genotyping of single-nucleotide polymorphisms or variants is an important technique for studying the history and distribution of extant human populations, but it is also a very important tool for adjusting tests of association. However, the structures inferred depend on the minor allele frequency of the variants; this is very important when considering the phenotypic association of rare variants.Using the Genetic Analysis Workshop 18 data set for 142 unrelated individuals, which includes genotypes for many rare variants, we study the following hypothesis: the difference in detected structure is the result of a "scale" effect; that is, rare variants are likely to be shared only locally (smaller scale), while common variants can be spread over longer distances. The result is similar to that of using kernel principal component analysis, as the bandwidth of the kernel is changed. We show how different structures become evident as we consider rare or common variants.

【 授权许可】

CC BY   
© De la Cruz and Raska; licensee BioMed Central Ltd. 2014