Comprehensive Analysis of Genomic Variation in the
LPA
Locus and Its Relationship to Plasma Lipoprotein(a) in South Asians, Chinese, and European Caucasians
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abstract
Background—
Functional copy number variation in the apolipoprotein(a) gene (
LPA
) underlies a variable number of protein kringle domains repeated in tandem in the lipoprotein(a) [Lp(a)] particle. Genomic analysis of
LPA
, including both single-nucleotide polymorphisms (SNPs) and kringle IV type 2 (KIV-2) copy number, has yet to be performed.
Methods and Results—
First, we genotyped 49 SNPs within 100 kb of
LPA
in a multiethnic sample comprising South Asians (n=330), Chinese (n=304), and European Caucasians (n=272). Second, using quantitative polymerase chain reaction, we estimated the KIV-2 copy number in each sample. European Caucasians had the lowest KIV-2 copy number but displayed the strongest correlation between KIV-2 copy number and plasma Lp(a) concentration (
rs
=−0.31,
P
=4.2�10
−7
). SNP rs10455872, only prevalent in European Caucasians, was strongly associated with both plasma Lp(a) concentration (
P
=4.2�10
−29
) and KIV-2 copy number (
P
=7.2�10
−5
).
LPA
SNP rs6415084, within the same haplotype block as the KIV-2 variation, was significantly associated with both Lp(a) concentration and KIV-2 copy number in the same direction in all 3 ethnicities [Lp(a),
P
=5.3�10
−7
; KIV-2,
P
=2.6�10
−4
]. SNPs and KIV-2 copy number together explain a larger proportion of variation in plasma Lp(a) concentrations in European Caucasians (36%) than in Chinese (27%) or South Asians (21%).
Conclusions—LPA
SNPs are in linkage disequilibrium with KIV-2 copy number, but KIV-2 copy number explains an increment in plasma Lp(a) variation over SNPs alone. Thus, both SNPs and KIV-2 copy number should be included in future genetic epidemiology studies of Lp(a).
