Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract

European Urology Open Science - Tập 44 - Trang 106-112 - 2022
Chen-Han Wilfred Wu1,2,3, Tze Y. Lim4, Chunyan Wang1, Steve Seltzsam1, Bixia Zheng1, Luca Schierbaum1, Sophia Schneider1, Nina Mann1, Dervla M. Connaughton1, Makiko Nakayama1, Amelie T. van der Ven1, Rufeng Dai1, Caroline M. Kolvenbach1, Franziska Kause1, Isabel Ottlewski1, Natasa Stajic5, Neveen A. Soliman6, Jameela A. Kari7, Sherif El Desoky7, Hanan M. Fathy8
1Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
2Department of Urology, Case Western Reserve University and University Hospitals, Cleveland, OH, USA
3Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals, Cleveland, OH, USA
4Division of Nephrology, Columbia University Irving Medical Center, New York, NY, USA
5Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
6Department of Pediatrics, Center of Pediatric Nephrology & Transplantation, Cairo University, Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
7Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia
8Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt

Tài liệu tham khảo

Chesnaye, 2014, Demographics of paediatric renal replacement therapy in Europe: a report of the ESPN/ERA-EDTA registry, Pediatr Nephrol, 29, 2403, 10.1007/s00467-014-2884-6 Vivante, 2014, Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans, Pediatr Nephrol, 29, 695, 10.1007/s00467-013-2684-4 Sanyanusin, 1995, Mutation of the Pax2 gene in a family with optic-nerve colobomas, renal anomalies and vesicoureteral reflux, Nat Genet, 9, 358, 10.1038/ng0495-358 Lindner, 1999, A novel syndrome of diabetes mellitus, renal dysfunction and genital malformation associated with a partial deletion of the pseudo-POU domain of hepatocyte nuclear factor-1 beta, Hum Mol Genet, 8, 2001, 10.1093/hmg/8.11.2001 Soliman, 2015, Pattern of clinical presentation of congenital anomalies of the kidney and urinary tract among infants and children, Nephrology, 20, 413, 10.1111/nep.12414 Ichikawa, 2002, Paradigm shift from classic anatomic theories to contemporary cell biological views of CAKUT, Kidney Int, 61, 889, 10.1046/j.1523-1755.2002.00188.x Costantini, 2012, Genetic controls and cellular behaviors in branching morphogenesis of the renal collecting system, Wiley Interdiscip Rev Dev Biol, 1, 693, 10.1002/wdev.52 Davies, 1996, Mesenchyme to epithelium transition during development of the mammalian kidney tubule, Acta Anat, 156, 187, 10.1159/000147846 Weber, 2011, Muscarinic acetylcholine receptor M3 mutation causes urinary bladder disease and a prune-belly-like syndrome, Am J Hum Genet, 89, 668, 10.1016/j.ajhg.2011.10.007 Hwang, 2014, Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract, Kidney Int, 85, 1429, 10.1038/ki.2013.508 Hoskins, 2007, Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome, Am J Hum Genet, 80, 800, 10.1086/513322 Ruf, 2004, SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes, Proc Natl Acad Sci U S A, 101, 8090, 10.1073/pnas.0308475101 Kohlhase, 1998, Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome, Nat Genet, 18, 81, 10.1038/ng0198-81 Vivante, 2016, Exploring the genetic basis of early-onset chronic kidney disease, Nat Rev Nephrol, 12, 133, 10.1038/nrneph.2015.205 Hardelin, 1992, X-chromosome-linked Kallmann syndrome — stop mutations validate the candidate gene, Proc Natl Acad Sci U S A, 89, 8190, 10.1073/pnas.89.17.8190 Saisawat, 2014, Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association, Kidney Int, 85, 1310, 10.1038/ki.2013.417 Humbert, 2014, integrin alpha 8 recessive mutations are responsible for bilateral renal agenesis in humans, Am J Hum Genet, 94, 288, 10.1016/j.ajhg.2013.12.017 van der Ven, 2018, whole-exome sequencing identifies causative mutations in families with congenital anomalies of the kidney and urinary tract, J Am Soc Nephrol, 29, 2348, 10.1681/ASN.2017121265 Vestergaard, 2021, Next generation sequencing technology in the clinic and its challenges, Cancers, 13, 1751, 10.3390/cancers13081751 Sathirapongsasuti, 2011, Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV, Bioinformatics, 27, 2648, 10.1093/bioinformatics/btr462 Sanna-Cherchi, 2012, copy-number disorders are a common cause of congenital kidney malformations, Am J Hum Genet, 91, 987, 10.1016/j.ajhg.2012.10.007 Schedl, 2007, Renal abnormalities and their developmental origin, Nat Rev Genet, 8, 791, 10.1038/nrg2205 Verbitsky, 2019, The copy number variation landscape of congenital anomalies of the kidney and urinary tract, Nat Genet, 51, 117, 10.1038/s41588-018-0281-y Wang, 2007, PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data, Genome Res, 17, 1665, 10.1101/gr.6861907 Firth, 2009, decipher: database of chromosomal imbalance and phenotype in humans using Ensembl resources, Am J Hum Genet, 84, 524, 10.1016/j.ajhg.2009.03.010 Swaminathan, 2012, DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders, Hum Mol Genet, 21, R37, 10.1093/hmg/dds362 Miller, 2010, Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies, Am J Hum Genet, 86, 749, 10.1016/j.ajhg.2010.04.006 Verbitsky, 2021, copy number variant analysis and genome-wide association study identify loci with large effect for vesicoureteral reflux, J Am Soc Nephrol, 32, 805, 10.1681/ASN.2020050681 Mefford, 2007, Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy, Am J Hum Genet, 81, 1057, 10.1086/522591 Nagamani, 2010, Clinical spectrum associated with recurrent genomic rearrangements in chromosome 17q12, Eur J Hum Genet, 18, 278, 10.1038/ejhg.2009.174 Peiffer, 2006, High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping, Genome Res, 16, 1136, 10.1101/gr.5402306