Common and rare ABCA1 variants affecting plasma HDL cholesterol

Mutations in ABCA1, a member of the ATP-binding cassette family, have been shown to underlie Tangier disease (TD) and familial hypoalphalipoproteinemi a (FHA), which are genetic disorders that are characterized by depressed co ncentrations of plasma high density lipoprotein (HDL) cholesterol. An impor tant question is whether common variants within the coding sequence of ABCA 1 can affect plasma HDL cholesterol in the general population. To address t his issue, we developed a screening strategy to find common ABCA1 variants. This strategy involved long-range amplification of genomic DNA by using co ding sequences only, followed by deep sequencing into the introns, This met hod helped us to characterize a new set of amplification primers, which per mitted amplification of virtually all of the coding sequence of ABCA1 and i ts intron-exon boundaries with a single DNA amplification program. With the se new sequencing primers, we found 3 novel ABCA1 mutations: a frameshift m utation (4570insA, A1484S-->X1492), a missense mutation (A986D) in a TD fam ily, and a missense mutation (R170C) in aboriginal subjects with FHA. We al so used these sequencing primers to characterize 4 novel common amino acid variants in ABCA1, in addition to 5 novel common silent variants. We tested for association of the ABCA1 I/M823 variant with plasma HDL cholesterol in Canadian Inuit and found that M823/M823 homozygotes had significantly high er plasma HDL cholesterol compared with subjects with the other genotypes. The results provide proof of principle of the effectiveness of this approac h to identify both rare and common ABCA1 genomic variants and also suggest that common amino acid variation in ABCA1 is a determinant of plasma HDL ch olesterol in the general population.