Haplotype homozygosity and derived alleles in the human genome.
Haplotype-based techniques are being used to estimate the relative age of alleles--particularly in screening loci for signals of recent positive selection--but does this approach capture even coarse age differences? Using simulations and empirical data from the International HapMap Project, we show that a simple pairwise metric of haplotype homozygosity gives significantly higher mean values for human single-nucleotide-polymorphism alleles that appear to be derived than for those that appear to be ancestral, as determined by comparison with the chimpanzee genome. Our results support the use of haplotype-based techniques, such as extended haplotypic homozygosity, to assess the age of alleles.
Fry
Andrew E
AE
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom. afry@well.ox.ac.uk
Trafford
Clare J
CJ
Kimber
Martin A
MA
Chan
Man-Suen
MS
Rockett
Kirk A
KA
Kwiatkowski
Dominic P
DP