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Approximately 60% occur as a part of a defined genetic syndrome or within the spectrum of additional congenital anomalies. Rare copy number variations (CNVs) have been associated with both syndromic and non-syndromic forms. The present study represents the largest study to date to explore the contribution of CNVs to the expression of ARMs. SNP-array-based molecular karyotyping was applied in 450 individuals with ARM and 4392 healthy controls. CNVs were identified from raw intensity data using PennCNV. Overlapping CNVs between cases and controls were discarded. Remaining CNVs were filtered using a stringent filter algorithm of nine filter steps. Prioritized CNVs were confirmed using qPCR. Filtering prioritized and qPCR confirmed four microscopic chromosomal anomalies and nine submicroscopic CNVs comprising seven microdeletions (del2p13.2, del4p16.2, del7q31.33, del9p24.1, del16q12.1, del18q32, del22q11.21) and two microduplications (dup2p13.2, dup17q12) in 14 individuals (12 singletons and one affected sib-pair). Within these CNVs, based on their embryonic expression data and function, we suggest <jats:italic>FOXK2<\/jats:italic>, <jats:italic>LPP<\/jats:italic>, and <jats:italic>SALL3<\/jats:italic> as putative candidate genes. Overall, our CNV analysis identified putative microscopic and submicroscopic chromosomal rearrangements in 3% of cases. Functional characterization and re-sequencing of suggested candidate genes is warranted.<\/jats:p>","DOI":"10.1038\/s41431-022-01216-5","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T06:02:37Z","timestamp":1667282557000},"page":"105-111","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations"],"prefix":"10.1038","volume":"31","author":[{"given":"Julia","family":"Fabian","sequence":"first","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0015-6964","authenticated-orcid":false,"given":"Gabriel C.","family":"Dworschak","sequence":"additional","affiliation":[]},{"given":"Lea","family":"Waffenschmidt","sequence":"additional","affiliation":[]},{"given":"Luca","family":"Schierbaum","sequence":"additional","affiliation":[]},{"given":"Charlotte","family":"Bendixen","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1057-465X","authenticated-orcid":false,"given":"Stefanie","family":"Heilmann-Heimbach","sequence":"additional","affiliation":[]},{"given":"Sugirthan","family":"Sivalingam","sequence":"additional","affiliation":[]},{"given":"Andreas","family":"Buness","sequence":"additional","affiliation":[]},{"given":"Nicole","family":"Schwarzer","sequence":"additional","affiliation":[]},{"given":"Thomas M.","family":"Boemers","sequence":"additional","affiliation":[]},{"given":"Eberhard","family":"Schmiedeke","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg","family":"Neser","sequence":"additional","affiliation":[]},{"given":"Johannes","family":"Leonhardt","sequence":"additional","affiliation":[]},{"given":"Ferdinand","family":"Kosch","sequence":"additional","affiliation":[]},{"given":"Sandra","family":"Weih","sequence":"additional","affiliation":[]},{"given":"Helen Maya","family":"Gielen","sequence":"additional","affiliation":[]},{"given":"Stuart","family":"Hosie","sequence":"additional","affiliation":[]},{"given":"Carmen","family":"Kabs","sequence":"additional","affiliation":[]},{"given":"Markus","family":"Palta","sequence":"additional","affiliation":[]},{"given":"Stefanie","family":"M\u00e4rzheuser","sequence":"additional","affiliation":[]},{"given":"Lena Marie","family":"Bode","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Lacher","sequence":"additional","affiliation":[]},{"given":"Frank-Mattias","family":"Sch\u00e4fer","sequence":"additional","affiliation":[]},{"given":"Maximilian","family":"Stehr","sequence":"additional","affiliation":[]},{"given":"Christian","family":"Knorr","sequence":"additional","affiliation":[]},{"given":"Benno","family":"Ure","sequence":"additional","affiliation":[]},{"given":"Katharina","family":"Kleine","sequence":"additional","affiliation":[]},{"given":"Udo","family":"Rolle","sequence":"additional","affiliation":[]},{"given":"Marcin","family":"Zaniew","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9254-1458","authenticated-orcid":false,"given":"Grote","family":"Phillip","sequence":"additional","affiliation":[]},{"given":"Nadine","family":"Zwink","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-5415-8784","authenticated-orcid":false,"given":"Ekkehart","family":"Jenetzky","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-3591-5265","authenticated-orcid":false,"given":"Heiko","family":"Reutter","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0354-7584","authenticated-orcid":false,"given":"Alina C.","family":"Hilger","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"1216_CR1","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1007\/s00383-007-2023-6","volume":"23","author":"E Jenetzky","year":"2007","unstructured":"Jenetzky E. 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The proposed project has been approved by the Ethics Commission of the University of Bonn (Lfd. Nr. 031\/19). In addition, the applicants abided to all regulations specified in German Data Protection Law. Informed consent was obtained from all subjects involved in the study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}}]}}