This project focuses on the systematic factors that affect linkage disequilibrium (Id) in different populations, different regions of the genome, and in regions of putative selection. The populations (about 40, with an average of more than 50 samples in each) represent a global sampling of our species. The 12 regions of the genome to be studied come from ten different chromosomes and each has a 200 kb span which may fully contain one or more haplotype blocks; and four of the 200 kb regions will be centered around genes with strong evidence of selection (around MC1R, LCT, CCR5, and HBB). All genomic regions to be studied will be typed for polymorphisms at 5-10 kb intervals in every population. We shall thus be able to (1) identify whether Id is distributed in blocks in the studied regions in all, most, or any populations, (2) determine the molecular extent of the blocks we find, (3) determine how generalizable across populations the block boundaries are, (4) examine any other pattern of Id decay if we do not find it to be punctate, and (5) examine the Id in and around loci with selection to identify """"""""footprints"""""""" of selection.
| Heffelfinger, Christopher; Pakstis, Andrew J; Speed, William C et al. (2014) Haplotype structure and positive selection at TLR1. Eur J Hum Genet 22:551-7 |
| Murdoch, John D; Speed, William C; Pakstis, Andrew J et al. (2013) Worldwide population variation and haplotype analysis at the serotonin transporter gene SLC6A4 and implications for association studies. Biol Psychiatry 74:879-89 |
| Donnelly, Michael P; Paschou, Peristera; Grigorenko, Elena et al. (2012) A global view of the OCA2-HERC2 region and pigmentation. Hum Genet 131:683-96 |
| Reich, David; Patterson, Nick; Campbell, Desmond et al. (2012) Reconstructing Native American population history. Nature 488:370-4 |
| Pakstis, Andrew J; Fang, Rixun; Furtado, Manohar R et al. (2012) Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs. Eur J Hum Genet 20:1148-54 |
| Nakagome, Shigeki; Mano, Shuhei; Kozlowski, Lukasz et al. (2012) Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Mol Biol Evol 29:1569-85 |
| Godshalk, S E; Paranjape, T; Nallur, S et al. (2011) A Variant in a MicroRNA complementary site in the 3' UTR of the KIT oncogene increases risk of acral melanoma. Oncogene 30:1542-50 |
| Pelletier, Cory; Speed, William C; Paranjape, Trupti et al. (2011) Rare BRCA1 haplotypes including 3'UTR SNPs associated with breast cancer risk. Cell Cycle 10:90-9 |
| Liu, Nianjun; Zhao, Hongyu; Patki, Amit et al. (2011) Controlling Population Structure in Human Genetic Association Studies with Samples of Unrelated Individuals. Stat Interface 4:317-326 |
| Kidd, Judith R; Friedlaender, Françoise; Pakstis, Andrew J et al. (2011) Single nucleotide polymorphisms and haplotypes in Native American populations. Am J Phys Anthropol 146:495-502 |
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