Lp(a) was measured in YFS from serum stored at –70 °C by the
immunoturbidimetric method (Lp(a)-HA reagent, Wako Chemicals GmbH). Lp(a) was
measured in FINRISK97 from serum stored at –70 °C using a
commercially available latex immunoassay on an
Architect c8000 system (Quantia
Lp(a), Abbott Diagnostics). The imputed genotype batches PredictCVD, COROGENE
and FR97 were combined to generate as complete a genotyped sample as possible
for the genetic analyses (FINRISK97). We then performed a GWAS for natural
logarithm transformed Lp(a) in FINRISK97 using sex, age and ten genetic
principal components as covariates in linear models. Variants associated with
Lp(a) at genome-wide significance were iteratively added to the association
model for identification of independent variants. SNPs with info >0.7 and
minor allele frequency >0.5% were considered. All 18 independent
variants identified in FINRISK97 were replicated in the independent YFS cohort
(
Supplementary Data 1).
We used weighted effect estimates from FINRISK97 to generate a gene score for
Lp(a) and tested the proportion of variance explained in the FINRISK97 discovery
and YFS replication cohorts. We also tested the association between the Lp(a)
gene score and metabolites using linear regression adjusted for the same
covariates as for the GWAS.
Kettunen J., Demirkan A., Würtz P., Draisma H.H., Haller T., Rawal R., Vaarhorst A., Kangas A.J., Lyytikäinen L.P., Pirinen M., Pool R., Sarin A.P., Soininen P., Tukiainen T., Wang Q., Tiainen M., Tynkkynen T., Amin N., Zeller T., Beekman M., Deelen J., van Dijk K.W., Esko T., Hottenga J.J., van Leeuwen E.M., Lehtimäki T., Mihailov E., Rose R.J., de Craen A.J., Gieger C., Kähönen M., Perola M., Blankenberg S., Savolainen M.J., Verhoeven A., Viikari J., Willemsen G., Boomsma D.I., van Duijn C.M., Eriksson J., Jula A., Järvelin M.R., Kaprio J., Metspalu A., Raitakari O., Salomaa V., Slagboom P.E., Waldenberger M., Ripatti S, & Ala-Korpela M. (2016). Genome-wide study for circulating metabolites identifies 62 loci and reveals novel systemic effects of LPA. Nature Communications, 7, 11122.