RT Journal Article
SR Electronic
T1 The rate of false polymorphisms introduced when imputing genotypes from global imputation panels
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 080770
DO 10.1101/080770
A1 Ida Surakka
A1 Antti-Pekka Sarin
A1 Sanni E Ruotsalainen
A1 Richard Durbin
A1 Veikko Salomaa
A1 Mark J Daly
A1 Aarno Palotie
A1 Samuli Ripatti
A1 SISu project group
YR 2016
UL http://biorxiv.org/content/early/2016/10/13/080770.abstract
AB Previous studies1,2 have shown that large multi-population imputation reference panels increases the number of well-imputed variants. However, to our knowledge, no previous studies have evaluated the rate of introduced variation in monomorphic sites of the study population when using imputation panels with admixed populations. In this study we evaluate the rate of false positive variants introduced by the imputation of Finnish genotype data using global reference panels (Haplotype Reference Consortium1; HRC, and the 1000Genomes project Phase I3; 1000G) and compare the results to a Finnish population-specific reference panel combining whole genome and exome sequenced samples. In sites that were monomorphic in our test set, we observed high false positive rates for the global reference panels (4.0% for 1000G and 2.6% for HRC) compared to the Finnish panel (0.26%). This rate was even higher (7.4%) when using a combination panel of 1000G and Finnish whole genome sequences with cross-panel imputation.