{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T22:58:55Z","timestamp":1762642735385,"version":"build-2065373602"},"reference-count":24,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T00:00:00Z","timestamp":1660089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Polish Mother\u2019s Memorial Hospital\u2014Research Institute","award":["2016\/X\/9-SZB"],"award-info":[{"award-number":["2016\/X\/9-SZB"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Familial hypercholesterolemia (FH) is an inherited, autosomal dominant metabolic disorder mostly associated with disease-causing variant in LDLR, APOB or PCSK9. Although the dominant changes are small-scale missense, frameshift and splicing variants, approximately 10% of molecularly defined FH cases are due to copy number variations (CNVs). The first-line strategy is to identify possible pathogenic SNVs (single nucleotide variants) using multiple PCR, Sanger sequencing, or with more comprehensive approaches, such as NGS (next-generation sequencing), WES (whole-exome sequencing) or WGS (whole-genome sequencing). The gold standard for CNV detection in genetic diagnostics are MLPA (multiplex ligation-dependent amplification) or aCGH (array-based comparative genome hybridization). However, faster and simpler analyses are needed. Therefore, it has been proposed that NGS data can be searched to analyze CNV variants. The aim of the study was to identify novel CNV changes in FH patients without detected pathogenic SNVs using targeted sequencing and evaluation of CNV calling tool (DECoN) working on gene panel NGS data; the study also assesses its suitability as a screening step in genetic diagnostics. A group of 136 adult and child patients were recruited for the present study. The inclusion criteria comprised at least \u201cpossible FH\u201d according to the Simon Broome diagnostic criteria in children and the DLCN (Dutch Lipid Clinical Network) criteria in adults. NGS analysis revealed potentially pathogenic SNVs in 57 patients. Thirty selected patients without a positive finding from NGS were subjected to MLPA analysis; ten of these revealed possibly pathogenic CNVs. Nine patients were found to harbor exons 4\u20138 duplication, two harbored exons 6\u20138 deletion and one demonstrated exon 9\u201310 deletion in LDLR. To test the DECoN program, the whole study group was referred for bioinformatic analysis. The DECoN program detected duplication of exons 4\u20138 in the LDLR gene in two patients, whose genetic analysis was stopped after the NGS step. The integration of the two methods proved to be particularly valuable in a five-year-old girl presenting with extreme hypercholesterolemia, with both a pathogenic missense variant (c.1747C&gt;T) and exons 9\u201310 deletion in LDLR. This is the first report of a heterozygous deletion of exons 9 and 10 co-occurring with SNV. Our results suggest that the NGS-based approach has the potential to identify large-scale variation in the LDLR gene and could be further applied to extend CNV screening in other FH-related genes. Nevertheless, the outcomes from the bioinformatic approach still need to be confirmed by MLPA; hence, the latter remains the reference method for assessing CNV in FH patients.<\/jats:p>","DOI":"10.3390\/genes13081424","type":"journal-article","created":{"date-parts":[[2022,8,11]],"date-time":"2022-08-11T01:58:30Z","timestamp":1660183110000},"page":"1424","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Identification of New Copy Number Variation and the Evaluation of a CNV Detection Tool for NGS Panel Data in Polish Familial Hypercholesterolemia Patients"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2120-9842","authenticated-orcid":false,"given":"Lena","family":"Rutkowska","sequence":"first","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iwona","family":"Pinkier","sequence":"additional","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kinga","family":"Sa\u0142aci\u0144ska","sequence":"additional","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2882-5448","authenticated-orcid":false,"given":"\u0141ukasz","family":"K\u0119pczy\u0144ski","sequence":"additional","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominik","family":"Salachna","sequence":"additional","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanna","family":"Lewek","sequence":"additional","affiliation":[{"name":"Department of Preventive Cardiology and Lipidology, Medical University of Lodz, 90-419 Lodz, Poland"},{"name":"Department of Cardiology and Congenital Diseases of Adults, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6690-6874","authenticated-orcid":false,"given":"Maciej","family":"Banach","sequence":"additional","affiliation":[{"name":"Department of Preventive Cardiology and Lipidology, Medical University of Lodz, 90-419 Lodz, Poland"},{"name":"Department of Cardiology and Congenital Diseases of Adults, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"},{"name":"Cardiovascular Research Centre, University of Zielona Gora, 65-417 Zielona Gora, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8943-7051","authenticated-orcid":false,"given":"Pawe\u0142","family":"Matusik","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Pediatric Obesity and Metabolic Bone Diseases, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ewa","family":"Starostecka","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolic Diseases, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8748-3337","authenticated-orcid":false,"given":"Andrzej","family":"Lewi\u0144ski","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolic Diseases, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"},{"name":"Department of Endocrinology and Metabolic Diseases, Medical University of Lodz, 90-419 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-5526","authenticated-orcid":false,"given":"Rafa\u0142","family":"P\u0142oski","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piotr","family":"Stawi\u0144ski","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agnieszka","family":"Gach","sequence":"additional","affiliation":[{"name":"Department of Genetics, Polish Mother\u2019s Memorial Hospital\u2014Research Institute, 93-338 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1016\/j.jacc.2020.03.057","article-title":"Worldwide Prevalence of Familial Hypercholesterolemia: Meta-Analyses of 11 Million Subjects","volume":"75","author":"Beheshti","year":"2020","journal-title":"J. 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