Sequence variants occur every few hundred bases in the human genome. We eva
luated the relationship between disease-causing mutations and neutral seque
nce variants at the 150 Kb ataxia-telangiectasia (A-T) locus. Mutations at
this locus cause a distinct autosomal recessive syndrome in homozygotes and
predispose heterozygotes to cancer and coronary heart disease. Nine common
neutral sequence variants were observed in the coding and splice junction
regions of 132 chromosomes from Caucasian individuals of European origin. E
ach of these variants appeared frequently in both A-T and non-A-T chromosom
es. However, there was remarkable linkage disequilibrium between the polymo
rphic loci, resulting in only 7 haplotypes in analyzed chromosomes. These 7
haplotypes fell into 3 major ancestral groups. No individual polymorphic v
ariant or haplotype correlated reliably with the presence of an A-T mutatio
n. Thus, comparing the frequency of neutral variants at the A-T locus in di
seased and non-diseased populations is unlikely to uncover the relationship
of mutations at this locus to common diseases. These data reflect general
limitations on using single nucleotide polymorphisms (SNPs) to identify loc
i for many common diseases. (C) 1999. Wiley-Liss, Inc.