A comprehensive map of single-base polymorphisms in the hypervariable LPA kringle IV type 2 copy number variation region

Lipoprotein (a) Lp(a) concentrations are among the strongest genetic risk factors for cardiovascular disease and present pronounced interethnic and interindividual differences. Approximately 90#x0025; of Lp(a) variance is controlled by the LPA gene, which contains a 5.6-kb-large copy number variation kringle IV type 2 (KIV-2) repeat that generates >40 protein isoforms. Variants within the KIV-2 region are not called in common sequencing projects, leaving up to 70#x0025; of the LPA coding region currently unaddressed. To completely assess the variability in LPA, we developed a sequencing strategy for this region and report here the first map of genetic variation in the KIV-2 region, a comprehensively evaluated ultradeep sequencing protocol, and an easy-to-use variant analysis pipeline. We sequenced 123 Central-European individuals and reanalyzed public data of 2,504 individuals from 26 populations. We found 14 different loss-of-function and splice-site mutations, as well as >100, partially even common, missense variants. Some coding variants were frequent in one population but absent in others. This provides novel candidates to explain the large ethnic and individual differences in Lp(a) concentrations. Importantly, our approach and pipeline are also applicable to other similar copy number variable regions, allowing access to regions that are not captured by common genome sequencing. Lipoprotein (a) Lp(a) concentrations are among the strongest genetic risk factors for cardiovascular disease and present pronounced interethnic and interindividual differences. Approximately 90#x0025; of Lp(a) variance is controlled by the LPA gene, which contains a 5.6-kb-large copy number variation kringle IV type 2 (KIV-2) repeat that generates >40 protein isoforms. Variants within the KIV-2 region are not called in common sequencing projects, leaving up to 70#x0025; of the LPA coding region currently unaddressed. To completely assess the variability in LPA, we developed a sequencing strategy for this region and report here the first map of genetic variation in the KIV-2 region, a comprehensively evaluated ultradeep sequencing protocol, and an easy-to-use variant analysis pipeline. We sequenced 123 Central-European individuals and reanalyzed public data of 2,504 individuals from 26 populations. We found 14 different loss-of-function and splice-site mutations, as well as >100, partially even common, missense variants. Some coding variants were frequent in one population but absent in others. This provides novel candidates to explain the large ethnic and individual differences in Lp(a) concentrations. Importantly, our approach and pipeline are also applicable to other similar copy number variable regions, allowing access to regions that are not captured by common genome sequencing. Lipoprotein(a) Lp(a) is one of the strongest genetic risk factors for CVD. Approximately 25#x0025; of the Caucasian population present concentrations that increase their risk for CVD by >2- to 3-fold (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google Scholar, 2Kamstrup P.R. Tybjaerg-Hansen A. Steffensen R. Nordestgaard B.G. Genetically elevated lipoprotein(a) and increased risk of myocardial infarction.JAMA. 2009; 301: 2331-2339Crossref PubMed Scopus (859) Google Scholar). Lp(a) presents extraordinary large inter- and intrapopulation variation (3Schmidt K. Noureen A. Kronenberg F. Utermann G. Structure, function, and genetics of lipoprotein (a).J. Lipid Res. 2016; 57: PubMed Scopus Google Scholar, G. G. K. factors explain a of the lipoprotein(a) concentrations in PubMed Scopus Google Scholar). Lp(a) concentrations are and an interindividual (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google and even within concentrations by to 3-fold G. G. K. factors explain a of the lipoprotein(a) concentrations in PubMed Scopus Google Scholar, A. and the risk of cardiovascular disease in the from the PubMed Scopus Google Scholar, G. A. Utermann G. of the the lipoprotein(a) in ethnic PubMed Scopus Google Scholar, G. of PubMed Scopus Google Scholar). in Lp(a) concentrations are and the is (3Schmidt K. Noureen A. Kronenberg F. Utermann G. Structure, function, and genetics of lipoprotein (a).J. Lipid Res. 2016; 57: PubMed Scopus Google Scholar). G. G. K. factors explain a of the lipoprotein(a) concentrations in PubMed Scopus Google Scholar, A. and the risk of cardiovascular disease in the from the PubMed Scopus Google Scholar, G. A. Utermann G. of the the lipoprotein(a) in ethnic PubMed Scopus Google Scholar, G. of PubMed Scopus Google Scholar). LPA of the Lp(a) variance (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google Scholar). of IV by (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google and a KIV-2 is by a copy number variation that contains 2 and by a and present in to >40 (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google Scholar, Utermann G. (a) a lipoprotein (a) PubMed Scopus Google Scholar, of (a) as by PubMed Scopus Google Scholar). of 14 and of the first KIV-2 of is to PubMed Scopus Google KIV-2 of is to PubMed Scopus Google Scholar, F. Utermann G. common in the of in a protein and PubMed Scopus Google that to different among A. F. Utermann G. K. variation within the KIV-2 copy number of the LPA in and PubMed Scopus Google Scholar). KIV-2 number to 70#x0025; (1Kronenberg F. Utermann G. Lipoprotein(a): resurrected by genetics.J. Intern. Med. 2013; 273: 6-30Crossref PubMed Scopus (336) Google of Lp(a) variance in an G. G. 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