{"doi":"10.1101/2023.04.24.538128","title":"Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk","abstract":"The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ~50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":390057,"datarank":0.40620753016533157,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.0,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9471,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":399702,"name":"Jonathan R. 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Marcovina","orcid":"0000-0002-9118-8488","position":10,"is_corresponding":false},{"id":662069,"name":"Massimiliano Rossi","orcid":"0000-0002-3012-1394","position":11,"is_corresponding":false},{"id":1161892,"name":"Eric Roller","orcid":null,"position":12,"is_corresponding":false},{"id":599655,"name":"James Han","orcid":"0009-0002-0333-7568","position":13,"is_corresponding":false},{"id":63729,"name":"Vitor Onuchic","orcid":"0000-0002-3284-8837","position":14,"is_corresponding":false},{"id":274762,"name":"Christy L. Avery","orcid":"0000-0002-1044-8162","position":15,"is_corresponding":false},{"id":233725,"name":"Christie M. Ballantyne","orcid":"0000-0002-6432-1730","position":16,"is_corresponding":false},{"id":74999,"name":"Carlos J. Rodríguez","orcid":"0000-0003-0860-9008","position":17,"is_corresponding":false},{"id":440310,"name":"Robert C. Kaplan","orcid":"0000-0003-3271-801X","position":18,"is_corresponding":false},{"id":1751,"name":"Donna M. Muzny","orcid":"0000-0002-3055-0359","position":19,"is_corresponding":false},{"id":57703,"name":"Ginger Metcalf","orcid":"0000-0002-8316-0071","position":20,"is_corresponding":false},{"id":1753,"name":"Richard A. Gibbs","orcid":"0000-0002-1356-5698","position":21,"is_corresponding":false},{"id":51217,"name":"Bing Yu","orcid":"0000-0003-4818-1077","position":22,"is_corresponding":false},{"id":245381,"name":"Eric Boerwinkle","orcid":"0000-0001-8813-0544","position":23,"is_corresponding":false},{"id":62166,"name":"Michael A. Eberle","orcid":"0000-0001-8965-1253","position":24,"is_corresponding":false},{"id":49032,"name":"Fritz J. 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