title: Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
abstract: We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of selection can be localized more precisely, and whether such extra evidence can lead to increased biological insights. We used two tools: simulations under neutrality or selection, and experimental investigation of two regions identified by the HapMap2 project as putatively selected in human populations. Simulations suggested that neutral and selected regions should be readily distinguished and that it should be possible to localize the selected variant to within 40 kb at least half of the time. Re-sequencing of two ~300 kb regions (chr4:158Mb and chr10:22Mb) lacking known targets of selection in HapMap CHB individuals provided strong evidence for positive selection within each and suggested the micro-RNA gene hsa-miR-548c as the best candidate target in one region, and changes in regulation of the sperm protein gene SPAG6 in the other.
authors: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.
authors: Min
authors: M
authors: Hu
authors: Qasim
authors: Q
authors: Ayub
authors: José Afonso
authors: JA
authors: Guerra-Assunção
authors: Quan
authors: Q
authors: Long
authors: Zemin
authors: Z
authors: Ning
authors: Ni
authors: N
authors: Huang
authors: Irene Gallego
authors: IG
authors: Romero
authors: Lira
authors: L
authors: Mamanova
authors: Pelin
authors: P
authors: Akan
authors: Xin
authors: X
authors: Liu
authors: Alison J
authors: AJ
authors: Coffey
authors: Daniel J
authors: DJ
authors: Turner
authors: Harold
authors: H
authors: Swerdlow
authors: John
authors: J
authors: Burton
authors: Michael A
authors: MA
authors: Quail
authors: Donald F
authors: DF
authors: Conrad
authors: Anton J
authors: AJ
authors: Enright
authors: Chris
authors: C
authors: Tyler-Smith
authors: Yali
authors: Y
authors: Xue
mesh_terms: D015894:Genome, Human; D005838:Genotype; D060148:HapMap Project; D006239:Haplotypes; D006801:Humans; D008954:Models, Biological; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA