RT Journal Article
SR Electronic
T1 Fine-mapping the Favored Mutation in a Positive Selective Sweep
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 139055
DO 10.1101/139055
A1 Ali Akbari
A1 Joseph J. Vitti
A1 Arya Iranmehr
A1 Mehrdad Bakhtiari
A1 Pardis C. Sabeti
A1 Siavash Mirarab
A1 Vineet Bafna
YR 2017
UL http://biorxiv.org/content/early/2017/10/01/139055.abstract
AB Methods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and in human populations from the 1000 Genomes Project, at 22 loci with previously characterized selective sweeps. For 14 of the 22 loci, iSAFE ranked the previously characterized candidate mutation among the 13 highest scoring (out of ∼ 21, 000 variants). Three loci did not show a strong signal. For the remaining loci, iSAFE identified previously unreported mutations as being favored. In these regions, all of which involve pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection. The iSAFE software can be downloaded from https://github.com/alek0991/iSAFE.