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Analysis Name and Accession

Note: This analysis was released as part of the study entitled STAMPEED: Northern Finland Birth Cohort 1966 (NFBC1966)

Name: Genomewide association analysis of low density lipoproteins (LDL) in a birth cohort from a founder population
Accession: pha002902.1

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Analysis Description
This analysis of association between genotype and nine quantitative traits related to metabolic syndrome was conducted in a population sample from the 1966 Northern Finland Birth Cohort (NFBC66). NFBC66 individuals are from the two northernmost provinces of Finland, were all born in 1966 and were age 31 at the time of assessment, were not ascertained for any particular disorder/disease, consented to the use of their DNA for genetic analysis studies, and were successfully genotyped on the Illumina 370 CNV platform. Genotyping was done at the Broad Institute using the Illumina 370CNV Genotyping Beadchip.

Please note: Following publication of our paper Nat Genet. 2009 Jan;41(1):35-46, the project was able to have more samples genotyped and we have used this final set of genotype data in the submission to dbGaP; therefore the number of genotyped subjects in dbGaP is higher than that in our previously published analysis.

Analysis Methods
Participants were excluded from analysis if they had withdrawn consent, if their reported sex was discrepant with sex determined from the X chromosome, if they were related to another individual at the level of sib or half-sib, if their sample appeared contaminated, or if call rate was < 95%. SNPs were excluded from analysis if call rate was < 95%, HWE P < 0.0001 or MAF < 1%. Phenotypes were regressed on a factor that accounted for sex, use of oral contraceptives and pregnancy status, and residuals from this regression used as the final outcome. In our primary analysis we used these residuals as the outcome in a main effects model that tested the association between SNP markers and trait. SNP genotypes were coded as 0, 1 or 2 copies of the minor allele. An additive effect of genotype was assumed, where the effect on the trait of the heterozygote was estimated to be midway between the levels of the two homozygotes. Association testing proceeded via regression analysis, and was performed in PLINK. Please see Sabatti et al. 2009 41:35-46 for additional details.
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