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

Bibliographic Collection: 
MOCA Reference, APE
Publication Type: Journal Article
Authors: Fullerton, S M; Clark, A G; Weiss, K M; Nickerson, D A; Taylor, S L; Stengârd, J H; Salomaa, V; Vartiainen, E; Perola, M; Boerwinkle, E; Sing, C F
Year of Publication: 2000
Journal: Am J Hum Genet
Volume: 67
Issue: 4
Pagination: 881-900
Date Published: 2000 Oct
Publication Language: eng
ISSN: 0002-9297
Keywords: Alleles, Alzheimer Disease, Apolipoproteins E, Base Sequence, Cardiovascular Diseases, Ethnic groups, Evolution, Molecular, Finland, Gene Frequency, Genetic Variation, Germ Cells, Haplotypes, Heterozygote, Humans, Linkage Disequilibrium, Mexico, Missouri, New York, Nucleotides, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Protein Isoforms, Regulatory Sequences, Nucleic Acid, Time Factors

Three common protein isoforms of apolipoprotein E (apoE), encoded by the epsilon2, epsilon3, and epsilon4 alleles of the APOE gene, differ in their association with cardiovascular and Alzheimer's disease risk. To gain a better understanding of the genetic variation underlying this important polymorphism, we identified sequence haplotype variation in 5.5 kb of genomic DNA encompassing the whole of the APOE locus and adjoining flanking regions 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 (n=48). In the region sequenced, 23 sites varied (21 single nucleotide polymorphisms, or SNPs, 1 diallelic indel, and 1 multiallelic indel). The 22 diallelic sites defined 31 distinct haplotypes in the sample. The estimate of nucleotide diversity (site-specific heterozygosity) for the locus was 0.0005+/-0.0003. Sequence analysis of the chimpanzee APOE gene showed that it was most closely related to human epsilon4-type haplotypes, differing from the human consensus sequence at 67 synonymous (54 substitutions and 13 indels) and 9 nonsynonymous fixed positions. The evolutionary history of allelic divergence within humans was inferred from the pattern of haplotype relationships. This analysis suggests that haplotypes defining the epsilon3 and epsilon2 alleles are derived from the ancestral epsilon4s and that the epsilon3 group of haplotypes have increased in frequency, relative to epsilon4s, in the past 200,000 years. Substantial heterogeneity exists within all three classes of sequence haplotypes, and there are important interpopulation differences in the sequence variation underlying the protein isoforms that may be relevant to interpreting conflicting reports of phenotypic associations with variation in the common protein isoforms.

DOI: 10.1086/303070
Alternate Journal: Am. J. Hum. Genet.
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