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Nature Research, Nature Communications, (6), p. 6065

DOI: 10.1038/ncomms7065

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Genome of the Netherlands population - specific imputations identify an ​ABCA6 variant associated with cholesterol levels

Journal article published in 2015 by L. Cupples, van Leeuwen Em, Elisabeth M. van Leeuwen, Mannis van Oven, Karssen Lc, Leonard H. van den Berg, Jessica van Setten, Barbera D. C. van Schaik, Joris Deelen ORCID, Gert-Jan B. van Ommen, Lennart C. Karssen, Aaron Isaacs, Carolina Medina-gomez ORCID, Hamdi Mbarek, Alexandros Kanterakis and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10(-4)), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR.