Apolipoprotein E variation at the sequence haplotype level: Implications for the origin and maintenance of a major human polymorphism

Three common protein isoforms of apolipoprotein E (apoE), encoded by the (e psilon)2, (epsilon)3, and (epsilon)4 alleles of the APOE gene, differ in th eir association with cardiovascular and Alzheimer's disease risk. To gain a better understanding of the genetic variation underlying this important po lymorphism, we identified sequence haplotype variation in 5.5 kb of genomic DNA encompassing the whole of the APOE locus and adjoining flanking region s in 96 individuals from four populations: blacks from Jackson, MS (n = 48 chromosomes), Mayans from Campeche, Mexico (n 48), Finns from North Karelia , Finland (n = 48), and non-Hispanic whites from Rochester, MN (rt 48). In the region sequenced, 23 sites varied (21 single nucleotide polymorphisms, or SNPs, 1 diallelic indel, and 1 multiallelic indel). The 22 diallelic sit es defined 31 distinct haplotypes in the sample. The estimate of nucleotide diversity (site-specific heterozygosity) for the locus was 0.0005 +/- 0.00 03. Sequence analysis of the chimpanzee APOE gene showed that it was most c losely related to human (epsilon)4-type haplotypes, differing from the huma n consensus sequence at 67 synonymous (54 substitutions and 13 indels) and 9 nonsynonymous fixed positions. The evolutionary history of allelic diverg ence within humans was inferred from the pattern of haplotype relationships . This analysis suggests that haplotypes defining the (epsilon)3 and (epsil on)2 alleles are derived from the ancestral (epsilon)4s and that the (epsil on)3 group of haplotypes have increased in frequency, relative to (epsilon) 4s, in the past 200,000 years. Substantial heterogeneity exists within all three classes of sequence haplotypes, and there are important interpopulati on differences in the sequence variation underlying the protein isoforms th at may be relevant to interpreting conflicting reports of phenotypic associ ations with variation in the common protein isoforms.