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Apes Project



Determination of Ancestral Alleles for Human Single Nucleotide Polymorphisms Using High Density Oligonucleotide Arrays

Joseph G. Hacia1, Jian-Bing Fan2, Oliver Ryder3, Li Jin4,5, Keith Edgemon1, Ghassan Ghandour2, R. Aeryn Mayer1, Bryan Sun1, Linda Hsie2, Christiane M. Robbins1, Lawrence C Brody1, David Wang6, Eric S. Lander6, Robert Lipshutz2, Stephen P.A. Fodor2, & Francis S. Collins1

1National Human Genome Research Institute, Building 49/3A14, National Institutes of Health, Bethesda, Maryland 20892, USA

2Affymetrix, 3380 Central Expressway, Santa Clara, California 95051, USA

3Center for Reproduction of Endangered Species, Zoological Society of San Diego, P.O. Box 551, San Diego, California 92112-0551, USA

4Institute of Genetics, Fudan University, Shanghai, People's Republic of China

5Human Genetics Institute, University of Texas-Houston, Houston, Texas 77225, USA

6Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142

Correspondence should be addressed to F.S.C.

Nature Genetics, in press, 1999.

Abstract

We applied high density oligonucleotide array (DNA chip)-based hybridization analysis to determine the history of single nucleotide polymorphisms (SNPs) in current human populations. Orthologys from 397 human SNP sites were analyzed from 23 common chimpanzee (Pan troglodytes, Ptr), 19 pygmy chimpanzee (Pan paniscus, Ppa), and 11 gorilla (Gorilla gorilla, Ggo) genomic DNA samples. A total of 214 proposed ancient ancestral alleles were determined. In a diverse human population set, we found SNP alleles with higher frequencies more likely to be ancestral than less frequently occurring alleles, but there were exceptions. Three shared human/pygmy chimpanzee polymorphisms, all involving CpG dinucleotides, along with two shared human/gorilla polymorphisms, one involving a CpG dinucleotide, were found. We could not readily determine whether these represent polymorphisms which existed in the common primate ancestor, or the independent origin of the same polymorphism. DNA-chip based assays allow rapid comparative sequence analysis of intra- and interspecies genetic variation.



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