Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene

Genetics in Medicine

Volumn 19, Issue 4, 2017, Pages 412-420

  Bekheirnia, Mir Reza ^a,b   Bekheirnia, Nasim ^a,b   Bainbridge, Matthew N ^a   Gu, Shen ^a   Akdemir, Zeynep Hande Coban ^a   Gambin, Tomek ^a   Janzen, Nicolette K ^a,b   Jhangiani, Shalini N ^a   Muzny, Donna M ^a   Michael, Mini ^a,b   Brewer, Eileen D ^a,b   Elenberg, Ewa ^a,b   Kale, Arundhati S ^a,b   Riley, Alyssa A ^a,b   Swartz, Sarah J ^a,b   Scott, Daryl A ^a,b   Yang, Yaping ^a   Srivaths, Poyyapakkam R ^a,b   Wenderfer, Scott E ^a,b   Bodurtha, Joann ^c   Applegate, Carolyn D ^c   Velinov, Milen ^d   Myers, Angela ^e   Borovik, Lior ^e   Craigen, William J ^a,b   Hanchard, Neil A ^a,b   Rosenfeld, Jill A ^a   Lewis, Richard Alan ^a,b   Gonzales, Edmond T ^a,b   Gibbs, Richard A ^a   Belmont, John W ^a,b   Roth, David R ^a,b   Eng, Christine ^a   Braun, Michael C ^a,b   Lupski, James R ^a,b   Lamb, Dolores J ^a   more..

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b TEXAS CHILDREN S HOSPITAL   (United States)

^c JOHNS HOPKINS CHILDREN S CENTER   (United States)

^d NEW YORK STATE INSTITUTE FOR BASIC RESEARCH IN DEVELOPMENTAL DISABILITIES   (United States)

^e Sanford Children's Hospital   (United States)

Author keywords

CAKUT; FOXP1; HNF1B; PAX2; WES

Indexed keywords

TRANSCRIPTION FACTOR FOXP1; TRANSCRIPTION FACTOR FOXP2; UNCLASSIFIED DRUG; EYA1 PROTEIN, HUMAN; FORKHEAD TRANSCRIPTION FACTOR; FOXP1 PROTEIN, HUMAN; HEPATOCYTE NUCLEAR FACTOR 1BETA; HNF1B PROTEIN, HUMAN; NUCLEAR PROTEIN; PAX2 PROTEIN, HUMAN; PROTEIN TYROSINE PHOSPHATASE; REPRESSOR PROTEIN; SIGNAL PEPTIDE; TRANSCRIPTION FACTOR PAX2;

ADULT; ARTICLE; COPY NUMBER VARIATION; FEMALE; GENE SEQUENCE; GENETIC IDENTIFICATION; HUMAN; KIDNEY MALFORMATION; MAJOR CLINICAL STUDY; MALE; MOLECULAR DIAGNOSIS; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; URINARY TRACT MALFORMATION; WHOLE EXOME SEQUENCING; ADOLESCENT; CHILD; GENETIC PREDISPOSITION; GENETICS; INFANT; PEDIGREE; PRESCHOOL CHILD; PROCEDURES; UROGENITAL TRACT MALFORMATION; VESICOURETERAL REFLUX; YOUNG ADULT;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; DNA COPY NUMBER VARIATIONS; FEMALE; FORKHEAD TRANSCRIPTION FACTORS; GENETIC PREDISPOSITION TO DISEASE; HEPATOCYTE NUCLEAR FACTOR 1-BETA; HUMANS; INFANT; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MALE; NUCLEAR PROTEINS; PAX2 TRANSCRIPTION FACTOR; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN TYROSINE PHOSPHATASES; REPRESSOR PROTEINS; UROGENITAL ABNORMALITIES; VESICO-URETERAL REFLUX; WHOLE EXOME SEQUENCING; YOUNG ADULT;

EID: 85017157261     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2016.131     Document Type: Article

References (39)

1. Sanna-Cherchi S, Ravani P, Corbani V, et al. Renal outcome in patients with congenital anomalies of the kidney and urinary tract. Kidney Int 2009;76: 528-533.
2. Mansoor O, Chandar J, Rodriguez MM, et al. Long-term risk of chronic kidney disease in unilateral multicystic dysplastic kidney. Pediatr Nephrol 2011;26: 597-603.
3. Groothoff JW. Long-term outcomes of children with end-stage renal disease. Pediatr Nephrol 2005;20:849-853.
4. Vivante A, Kohl S, Hwang DY, Dworschak GC, Hildebrandt F. Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans. Pediatr Nephrol 2014;29:695-704.
5. Yang Y, Muzny DM, Reid JG, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369:1502-1511. http:// www.ncbi.nlm.nih.gov/pubmed/24088041.
6. Yang Y, Muzny DM, Xia F, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 2014;312:1870-1879.
7. Karaca E, Harel T, Pehlivan D, et al. Genes that affect brain structure and function identified by rare variant analyses of mendelian neurologic disease. Neuron 2015;88:499-513.
8. Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: A normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res 2015;43:e39.
9. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-1303.
10. Challis D, Yu J, Evani US, et al. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 2012;13:8.
11. Krumm N, Sudmant PH, Ko A, et al.; NHLBI Exome Sequencing Project. Copy number variation detection and genotyping from exome sequence data. Genome Res 2012;22:1525-1532.
12. Vijayarangakannan P, Fitzgerald T. Detection of copy number variation from exomes in the DDD and UK10K projects. Uk10KOrg. 2012;10:7319. http:// www.uk10k.org/assets/ashg-vijayarangakannan-etal-2012.pdf.
13. Sanna-Cherchi S, Kiryluk K, Burgess KE, et al. Copy-number disorders are a common cause of congenital kidney malformations. Am J Hum Genet 2012;91:987-997.
14. Verbitsky M, Sanna-Cherchi S, Fasel DA, et al. Genomic imbalances in pediatric patients with chronic kidney disease. J Clin Invest 2015;125:2171-2178.
15. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17:405-423.
16. Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 2011;13:680-685.
17. Nicolaou N, Renkema KY, Bongers EM, Giles RH, Knoers NV. Genetic, environmental, and epigenetic factors involved in CAKUT. Nat Rev Nephrol 2015;11:720-731.
18. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:e164.
19. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010;26:2069-2070.
20. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011;32:894-899.
21. Kong A, Frigge ML, Masson G, et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 2012;488:471-475.
22. Chang SW, Mislankar M, Misra C, et al. Genetic abnormalities in FOXP1 are associated with congenital heart defects. Hum Mutat 2013;34:1226-1230.
23. Hamdan FF, Daoud H, Rochefort D, et al. De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment. Am J Hum Genet 2010;87:671-678.
24. Sollis E, Graham SA, Vino A, et al. Identification and functional characterization of de novo FOXP1 variants provides novel insights into the etiology of neurodevelopmental disorder. Hum Mol Genet 2016;25:546-557.
25. McTaggart KE, Budarf ML, Driscoll DA, Emanuel BS, Ferreira P, McDermid HE. Cat eye syndrome chromosome breakpoint clustering: identification of two intervals also associated with 22q11 deletion syndrome breakpoints. Cytogenet Cell Genet 1998;81:222-228.
26. Barua M, Stellacci E, Stella L, et al. Mutations in PAX2 associate with adult-onset FSGS. J Am Soc Nephrol 2014;25:1942-1953.
27. Stockley TL, Mendoza-Londono R, Propst EJ, Sodhi S, Dupuis L, Papsin BC. A recurrent EYA1 mutation causing alternative RNA splicing in branchio-otorenal syndrome: implications for molecular diagnostics and disease mechanism. Am J Med Genet A 2009;149A:322-327.
28. Hwang DY, Dworschak GC, Kohl S, et al. Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract. Kidney Int 2014;85:1429-1433.
29. Sanna-Cherchi S, Sampogna RV, Papeta N, et al. Mutations in DSTYK and dominant urinary tract malformations. N Engl J Med 2013;369:621-629.
30. Saisawat P, Kohl S, Hilger AC, et al. Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association. Kidney Int 2014;85:1310-1317.
31. Gonzaga-Jauregui C, Lupski JR, Gibbs RA. Human genome sequencing in health and disease. Annu Rev Med 2012;63:35-61.
32. Vivante A, Kleppa MJ, Schulz J, et al. Mutations in TBX18 cause dominant urinary tract malformations via transcriptional dysregulation of ureter development. Am J Hum Genet 2015;97:291-301.
33. Gonzaga-Jauregui C, Harel T, Gambin T, et al.; Baylor-Hopkins Center for Mendelian Genomics. Exome sequence analysis suggests that genetic burden contributes to phenotypic variability and complex neuropathy. Cell Rep 2015;12:1169-1183.
34. Yuan B, Pehlivan D, Karaca E, et al. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. J Clin Invest 2015;125:636-651.
35. Shu W, Lu MM, Zhang Y, Tucker PW, Zhou D, Morrisey EE. Foxp2 and Foxp1 cooperatively regulate lung and esophagus development. Development 2007;134:1991-2000.
36. Wangler MF, Gonzaga-Jauregui C, Gambin T, et al.; Baylor-Hopkins Center for Mendelian Genomics. Heterozygous de novo and inherited mutations in the smooth muscle actin (ACTG2) gene underlie megacystis-microcolon-intestinal hypoperistalsis syndrome. PLoS Genet 2014;10:e1004258.
37. Retterer K, Scuffins J, Schmidt D, et al. Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genet Med 2015;17:623-629.
38. Rosias PR, Sijstermans JM, Theunissen PM, et al. Phenotypic variability of the cat eye syndrome. Case report and review of the literature. Genet Couns 2001;12:273-282.
39. Knijnenburg J, van Bever Y, Hulsman LO, et al. A 600 kb triplication in the cat eye syndrome critical region causes anorectal, renal and preauricular anomalies in a three-generation family. Eur J Hum Genet 2012;20:986-989.