1 line
20 KiB
Plaintext
1 line
20 KiB
Plaintext
{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T11:32:37Z","timestamp":1678102357668},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Eur J Hum Genet"],"published-print":{"date-parts":[[2023,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Anorectal malformations (ARM) represent a spectrum of rare malformations originating from a perturbated development of the embryonic hindgut. 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. Prevalence estimation of anorectal malformations using German diagnosis related groups system. Pediatr Surg Int. 2007;23:1161\u20135.","journal-title":"Pediatr Surg Int"},{"key":"1216_CR2","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1055\/s-0041-1740338","volume":"31","author":"C Marcelis","year":"2021","unstructured":"Marcelis C, Dworschak G, de Blaauw I, van Rooij IALM. Genetic counseling and diagnostics in anorectal malformation. Eur J Pediatr Surg. 2021;31:482\u201391.","journal-title":"Eur J Pediatr Surg"},{"key":"1216_CR3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.ejmg.2010.09.001","volume":"54","author":"C Schramm","year":"2011","unstructured":"Schramm C, Draaken M, Bartels E, Boemers TM, Aretz S, Brockschmidt FF, et al. De novo microduplication at 22q11.21 in a patient with VACTERL association. Eur J Med Genet. 2011;54:9\u201313.","journal-title":"Eur J Med Genet"},{"key":"1216_CR4","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1002\/ajmg.a.33820","volume":"155A","author":"C Schramm","year":"2011","unstructured":"Schramm C, Draaken M, Bartels E, Boemers TM, Schmiedeke E, Grasshoff-Derr S, et al. De novo duplication of 18p11.21-18q12.1 in a female with anorectal malformation. Am J Med Genet A. 2011;155A:445\u20139.","journal-title":"Am J Med Genet A"},{"key":"1216_CR5","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1017\/thg.2013.29","volume":"16","author":"F Baudisch","year":"2013","unstructured":"Baudisch F, Draaken M, Bartels E, Schmiedeke E, Bagci S, Bartmann P, et al. CNV analysis in monozygotic twin pairs discordant for urorectal malformations. Twin Res Hum Genet. 2013;16:802\u20137.","journal-title":"Twin Res Hum Genet"},{"key":"1216_CR6","doi-asserted-by":"publisher","first-page":"3035","DOI":"10.1002\/ajmg.a.36153","volume":"161A","author":"GC Dworschak","year":"2013","unstructured":"Dworschak GC, Draaken M, Marcelis C, de Blaauw I, Pfundt R, van Rooij IALM, et al. De novo 13q deletions in two patients with mild anorectal malformations as part of VATER\/VACTERL and VATER\/VACTERL-like association and analysis of EFNB2 in patients with anorectal malformations. Am J Med Genet A. 2013;161A:3035\u201341.","journal-title":"Am J Med Genet A"},{"key":"1216_CR7","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1038\/ejhg.2013.58","volume":"21","author":"A Hilger","year":"2013","unstructured":"Hilger A, Schramm C, Pennimpede T, Wittler L, Dworschak GC, Bartels E, et al. De novo microduplications at 1q41, 2q37.3, and 8q24.3 in patients with VATER\/VACTERL association. Eur J Hum Genet. 2013;21:1377\u201382.","journal-title":"Eur J Hum Genet"},{"key":"1216_CR8","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1002\/bdra.23321","volume":"103","author":"GC Dworschak","year":"2015","unstructured":"Dworschak GC, Draaken M, Hilger AC, Schramm C, Bartels E, Schmiedeke E, et al. Genome-wide mapping of copy number variations in patients with both anorectal malformations and central nervous system abnormalities. Birth Defects Res A Clin Mol Teratol. 2015;103:235\u201342.","journal-title":"Birth Defects Res A Clin Mol Teratol"},{"key":"1216_CR9","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1111\/cge.12848","volume":"91","author":"GC Dworschak","year":"2017","unstructured":"Dworschak GC, Cr\u00e9tolle C, Hilger A, Engels H, Korsch E, Reutter H, et al. Comprehensive review of the duplication 3q syndrome and report of a patient with Currarino syndrome and de novo duplication 3q26.32-q27.2. Clin Genet. 2017;91:661\u201371.","journal-title":"Clin Genet"},{"key":"1216_CR10","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1002\/bdr2.1042","volume":"109","author":"R Zhang","year":"2017","unstructured":"Zhang R, Marsch F, Kause F, Degenhardt F, Schmiedeke E, M\u00e4rzheuser S, et al. Array-based molecular karyotyping in 115 VATER\/VACTERL and VATER\/VACTERL-like patients identifies disease-causing copy number variations. Birth Defects Res. 2017;109:1063\u20139.","journal-title":"Birth Defects Res"},{"key":"1216_CR11","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1002\/bdra.10012","volume":"67","author":"SA Rasmussen","year":"2003","unstructured":"Rasmussen SA, Olney RS, Holmes LB, Lin AE, Keppler-Noreuil KM, Moore CA. et al. Guidelines for case classification for the National Birth Defects Prevention Study. Birth Defects Res A Clin Mol Teratol. 2003;67:193\u2013201.","journal-title":"Birth Defects Res A Clin Mol Teratol"},{"key":"1216_CR12","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1093\/hmg\/dds451","volume":"22","author":"EH Wong","year":"2013","unstructured":"Wong EH, Cui L, Ng CL, Tang CS, Liu XL, So MT, et al. Genome-wide copy number variation study in anorectal malformations. Hum Mol Genet. 2013;22:621\u201331.","journal-title":"Hum Mol Genet"},{"key":"1216_CR13","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1067\/mhj.2002.123579","volume":"144","author":"A Schmermund","year":"2002","unstructured":"Schmermund A, M\u00f6hlenkamp S, Stang A, Gr\u00f6nemeyer D, Seibel R, Hirche H, et al. Assessment of clinically silent atherosclerotic disease and established and novel risk factors for predicting myocardial infarction and cardiac death in healthy middle-aged subjects: rationale and design of the Heinz Nixdorf RECALL Study. Risk Factors, Evaluation of Coronary Calcium and Lifestyle. Am Heart J. 2002;144:212\u20138.","journal-title":"Am Heart J"},{"key":"1216_CR14","doi-asserted-by":"publisher","first-page":"W21","DOI":"10.1093\/nar\/gkab402","volume":"49","author":"V Geoffroy","year":"2021","unstructured":"Geoffroy V, Guignard T, Kress A, Gaillard JB, Solli-Nowlan T, Schalk A, et al. AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis. Nucleic Acids Res. 2021;49:W21\u2013W28. W1","journal-title":"Nucleic Acids Res"},{"key":"1216_CR15","doi-asserted-by":"publisher","DOI":"10.1186\/1750-1172-4-9","volume":"7","author":"T Mattina","year":"2009","unstructured":"Mattina T, Perrotta CS, Grossfeld P. Jacobsen syndrome. Orphanet J Rare Dis. 2009;7:9.","journal-title":"Orphanet J Rare Dis"},{"key":"1216_CR16","doi-asserted-by":"publisher","first-page":"2692","DOI":"10.1002\/ajmg.a.34253","volume":"155A","author":"C Marcelis","year":"2011","unstructured":"Marcelis C, de Blaauw I, Brunner H. Chromosomal anomalies in the etiology of anorectal malformations: a review. Am J Med Genet A. 2011;155A:2692\u2013704.","journal-title":"Am J Med Genet A"},{"key":"1216_CR17","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1016\/j.ajhg.2009.03.010","volume":"84","author":"HV Firth","year":"2009","unstructured":"Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, et al. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009;84:524\u201333.","journal-title":"Am J Hum Genet"},{"key":"1216_CR18","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gky1056","volume":"47","author":"CJ Bult","year":"2019","unstructured":"Bult CJ, Blake JA, Smith CL, Kadin JA, Richardson JE, et al. Mouse Genome Database (MGD) 2019. Nucleic Acids Res. 2019;47:D801\u2013D806. the Mouse Genome Database Group. 2019D1","journal-title":"Nucleic Acids Res"},{"key":"1216_CR19","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1002\/humu.9396","volume":"27","author":"W Borozdin","year":"2006","unstructured":"Borozdin W, Steinmann K, Albrecht B, Bottani A, Devriendt K, Leipoldt M, et al. Detection of heterozygous SALL1 deletions by quantitative real time PCR proves the contribution of a SALL1 dosage effect in the pathogenesis of Townes-Brocks syndrome. Hum Mutat. 2006;27:211\u20132.","journal-title":"Hum Mutat"},{"key":"1216_CR20","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1086\/343821","volume":"71","author":"R Al-Baradie","year":"2002","unstructured":"Al-Baradie R, Yamada K, St Hilaire C, Chan WM, Andrews C, McIntosh N, et al. Duane radial ray syndrome (Okihiro syndrome) maps to 20q13 and results from mutations in SALL4, a new member of the SAL family. Am J Hum Genet. 2002;71:1195\u20139.","journal-title":"Am J Hum Genet"},{"key":"1216_CR21","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1007\/s00335-012-9413-3","volume":"23","author":"L Geffers","year":"2012","unstructured":"Geffers L, Herrmann B, Eichele G. Web-based digital gene expression atlases for the mouse. Mamm Genome. 2012;23:525\u201338.","journal-title":"Mamm Genome"},{"key":"1216_CR22","doi-asserted-by":"publisher","first-page":"2919","DOI":"10.1002\/ajmg.a.33718","volume":"152A","author":"CB Arrington","year":"2010","unstructured":"Arrington CB, Patel A, Bacino CA, Bowles NE. Haploinsufficiency of the LIM domain containing preferred translocation partner in lipoma (LPP) gene in patients with tetralogy of Fallot and VACTERL association. Am J Med Genet A. 2010;152A:2919\u201323.","journal-title":"Am J Med Genet A"},{"key":"1216_CR23","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1002\/ajmg.a.35391","volume":"158A","author":"A Hern\u00e1ndez-Garc\u00eda","year":"2012","unstructured":"Hern\u00e1ndez-Garc\u00eda A, Brosens E, Zaveri HP, de Jong EM, Yu Z, Namwanje M, et al. Contribution of LPP copy number and sequence changes to esophageal atresia, tra-cheoesophageal fistula, and VACTERL association. Am J Med Genet A. 2012;158A:1785\u20137.","journal-title":"Am J Med Genet A"},{"key":"1216_CR24","doi-asserted-by":"publisher","first-page":"3784","DOI":"10.1002\/ajmg.a.62447","volume":"185","author":"CM Kolvenbach","year":"2021","unstructured":"Kolvenbach CM, van der Ven AT, Kause F, Shril S, Scala M, Connaughton DM, et al. Exome survey of indi-viduals affected by VATER\/VACTERL with renal phenotypes identifies phenocopies and novel candidate genes. Am J Med Genet A. 2021;185:3784\u201392.","journal-title":"Am J Med Genet A"},{"key":"1216_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/1750-1172-6-56","volume":"16","author":"BD Solomon","year":"2011","unstructured":"Solomon BD. VACTERL\/VATER association. Orphanet J Rare Dis. 2011;16:56.","journal-title":"Orphanet J Rare Dis"},{"key":"1216_CR26","first-page":"100093","volume":"3","author":"J Gehlen","year":"2022","unstructured":"Gehlen J, Giel AS, K\u00f6llges R, Haas SL, Zhang R, Trcka J, et al. First genome-wide association study of esophageal atresia with or without tracheoesophageal fistula (EA\/TEF) identifies three genetic risk loci at CTNNA3, FOXF1\/FOXC2\/FOXL1 and HNF1B. HHG Adv. 2022;3:100093.","journal-title":"HHG Adv"},{"key":"1216_CR27","doi-asserted-by":"publisher","first-page":"2845","DOI":"10.1242\/dev.063594","volume":"138","author":"SD Harding","year":"2011","unstructured":"Harding SD, Armit C, Armstrong J, Brennan J, Cheng Y, Haggarty B, et al. The GUDMAP database \u2013 an online resource for genitourinary research. Development. 2011;138:2845\u201353.","journal-title":"Development"},{"key":"1216_CR28","doi-asserted-by":"publisher","first-page":"2255","DOI":"10.1126\/science.1104935","volume":"306","author":"PA Gray","year":"2004","unstructured":"Gray PA, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, et al. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science. 2004;306:2255\u20137.","journal-title":"Science"},{"key":"1216_CR29","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1101\/SQB.1978.042.01.105","volume":"42","author":"RP Lifton","year":"1978","unstructured":"Lifton RP, Goldberg ML, Karp RW, Hogness DS. The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications. Cold Spring Harb Symposia Quant Biol. 1978;42:1047\u201351.","journal-title":"Cold Spring Harb Symposia Quant Biol"}],"container-title":["European Journal of Human Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41431-022-01216-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41431-022-01216-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41431-022-01216-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,7]],"date-time":"2023-01-07T00:06:04Z","timestamp":1673049964000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41431-022-01216-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,1]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1]]}},"alternative-id":["1216"],"URL":"http:\/\/dx.doi.org\/10.1038\/s41431-022-01216-5","relation":{},"ISSN":["1018-4813","1476-5438"],"issn-type":[{"value":"1018-4813","type":"print"},{"value":"1476-5438","type":"electronic"}],"subject":["Genetics (clinical)","Genetics"],"published":{"date-parts":[[2022,11,1]]},"assertion":[{"value":"18 March 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2022","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2022","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 November 2022","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"All experiments involving human materials adhered to the recommendations of the World Medical Association, as stated in the revised Declaration of Helsinki from Seoul 2008. 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"}}]}} |