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 Arya Iranmehr
A1 Mehrdad Bakhtiari
A1 Siavash Mirarab
A1 Vineet Bafna
YR 2017
UL http://biorxiv.org/content/early/2017/06/02/139055.abstract
AB Methods that scan population genomics data to identify signatures of selective sweep have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE that uses population genetics signals and a boosting approach to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and 22 known sweeps in human populations using the 1000 genome project data with some evidence for the favored mutation. iSAFE ranked the candidate mutation among the top 13 (out of ~21,000 variants) in 14 of the 22 loci, did not show a strong signal in 3. We identified previously unreported mutations as being favored in the remaining 5 regions. For these pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection.