Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations

Judith R. Kidd*, Andrew J. Pakstis, Hongyu Zhao, Ru Band Lu, Friday E. Okonofua, Adekunle Odunsi, Elena Grigorenko, Batsheva Bonne-Tamir, Jonathan Friedlaender, Leslie O. Schulz, Josef Parnas, Kenneth K. Kidd

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

127 Scopus citations


Because defects in the phenylalanine hydroxylase gene (PAH) cause phenylketonuria (PKU), PAH was studied for normal polymorphisms and linkage disequilibrium soon after the gene was cloned. Studies in the 1980s concentrated on European populations in which PKU was common and showed that haplotype-frequency variation exists between some regions of the world. In European populations, linkage disequilibrium generally was found not to exist between RFLPs at opposite ends of the gene but was found to exist among the RFLPs clustered at each end. We have now undertaken the first global survey of normal variation and disequilibrium across the PAH gene. Four well-mapped single-nucleotide polymorphisms (SNPs) spanning ~75 kb, two near each end of the gene, were selected to allow linkage disequilibrium across most of the gene to be examined. These SNPs were studied as PCR-RFLP markers in samples of, on average, 50 individuals for each of 29 populations, including, for the first time, multiple populations from Africa and from the Americas. All four sites are polymorphic in all 29 populations. Although all but 5 of the 16 possible haplotypes reach frequencies >5 % somewhere in the world, no haplotype was seen in all populations. Overall linkage disequilibrium is highly significant in all populations, but disequilibrium between the opposite ends is significant only in Native American populations and in one African population. This study demonstrates that the physical extent of linkage disequilibrium can differ substantially among populations from different regions of the world, because of booth ancient genetic drift in the ancestor common to a large regional group of modern populations and recent genetic drift affecting individual populations.

Original languageEnglish
Pages (from-to)1882-1899
Number of pages18
JournalAmerican Journal of Human Genetics
Issue number6
StatePublished - 2000


FundersFunder number
National Science FoundationSBR-9632509
National Institutes of Health
National Institute of General Medical SciencesP01GM057672
National Institute of Diabetes and Digestive and Kidney Diseases
Directorate for Social, Behavioral and Economic Sciences9632509
Alfred P. Sloan Foundation
National Science Council88-2314-B-016-081


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