Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data

• 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.

Subject headings

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

Keyword

microRNA

article

chromosome 10

chromosome 4

controlled study

gene

gene control

gene frequency

gene locus

gene rearrangement

gene sequence

genetic selection

genetic transcription

genetic variability

genome analysis

genotype

haplotype map

human

human genome

nonhuman

polymerase chain reaction

priority journal

sequence analysis

simulation

single nucleotide polymorphism

sperm protein gene spag6

biological model

DNA sequence

genetic polymorphism

haplotype

Genome

Human

Haplotypes

HapMap Project

Humans

Models

Biological

Polymorphism

Genetic

Selection

Genetic

Sequence Analysis

DNA

Publication and Content Type

ref (subject category)

art (subject category)