Changing interpretation of chromosomal microarray over time in a community cohort with intellectual disability

American Journal of Medical Genetics, Part A

Volumn 164, Issue 2, 2014, Pages 377-385

  Palmer, Emma ^a,b   Speirs, Helen ^b   Taylor, Peter J ^c   Mullan, Glenda ^c   Turner, Gill ^d,e   Einfeld, Stewart ^e   Tonge, Bruce ^f   Mowat, David ^a,b  

^a SYDNEY CHILDREN'S HOSPITAL   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c South Eastern Area Laboratory Services   (Australia)

^d Hunter Genetics   (Australia)

^e UNIVERSITY OF SYDNEY   (Australia)

^f MONASH UNIVERSITY   (Australia)

Author keywords

Aberrations; Chromosome; Diagnostic test; Intellectual disability; Oligonucleotide array

Indexed keywords

ANALYTICAL EQUIPMENT; ARTICLE; CHROMOSOMAL MICROARRAY; COHORT ANALYSIS; COPY NUMBER VARIATION; FEMALE; FRAGILE X SYNDROME; GENETIC COUNSELING; GENETIC SUSCEPTIBILITY; HUMAN; INTELLECTUAL IMPAIRMENT; KARYOTYPING; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; PRIORITY JOURNAL; SCORING SYSTEM;

ABERRATIONS; CHROMOSOME; DIAGNOSTIC TEST; INTELLECTUAL DISABILITY; OLIGONUCLEOTIDE ARRAY;

CHROMOSOME ABERRATIONS; COHORT STUDIES; DNA COPY NUMBER VARIATIONS; FEMALE; HUMANS; INTELLECTUAL DISABILITY; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84892869125     PISSN: 15524825     EISSN: 15524833     Source Type: Journal    
DOI: 10.1002/ajmg.a.36279     Document Type: Article

References (40)

1. Bernardini L, Alesi V, Loddo S, Novelli A, Bottillo I, Battaglia A, Digilio MC, Zampino G, Ertel A, Fortina P, Surrey S, Dallapiccola B. 2010. High-resolution SNP arrays in mental retardation diagnostics: How much do we gain? Eur J Hum Genet 18:178-185.
2. Birch HG, Richardson SA, Baird D, Horobin G, Ilsley R. 1970. Mental subnormality in the community: A clinical and epidemiological study. Baltimore, MD: Williams & Wilkins.
3. Corpas M, Bragin E, Clayton S, Bevan P, Firth HV. 2012. Interpretation of genomic copy number variants using DECIPHER. Curr Protoc Hum Genet Chapter 8:14.
4. De Schepper S, Maertens O, Callens T, Naeyaert JM, Lambert J, Messiaen L. 2008. Somatic mutation analysis in NF1 café au lait spots reveals two NF1 hits in the melanocytes. J Invest Dermatol 128:1050-1053.
5. De Vries BB, Winter R, Schinzel A, van Ravenswaaij-Arts C. 2003. Telomeres: A diagnosis at the end of the chromosomes. J Med Genet 40:385-398.
6. Duong L, Klitten LL, Møller RS, Ingason A, Jakobsen KD, Skjødt C, Didriksen M, Hjalgrim H, Werge T, Tommerup N. 2012. Mutations in NRXN1 in a family multiply affected with brain disorders: NRXN1 mutations and brain disorders. Am J Med Genet Part B 159B:354-358.
7. Ellaway CJ, Ho G, Bettella E, Knapman A, Collins F, Hackett A, McKenzie F, Darmanian A, Peters GB, Fagan K, Christodoulou J. 2012. 14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype. Eur J Hum Genet 21:522-527.
8. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
9. Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. 2009. DECIPHER: Database of chromosomal imbalance and phenotype in humans using ensemble resources. Am J Hum Genet 84:524-533.
10. Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gécz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE. 2010. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet 42:203-209.
11. Girirajan S, Rosenfeld JA, Coe B, Pankh S, Froedman N, Goldstein A, Filipink RA, McConnll JS, Angle B, Meschino WS, Nezarati MM, Asamoah A, Jackson KE, Gowans GC, Martin JA, Carmany EP, Stockton DW, Schnur RE, Penney LS, Martin DM, Raskin S, Leppig K, Thiese H, Smith R, Aberg E, Niyazov DM, Escobar LF, El-Khechen D, Johnson KD, Lebel RR, Siefkas K, Ball S, Shur N, McGuire M, Brasington CK, Spence JR, Martin LS, Clericuzio C, Ballif BC, Shaffer LG, Eichler EE. 2012. Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 367:1321-1331.
12. Hehir-Kwa JY, Wieskamp N, Webber C, Pfundt R, Brunner HG, Gilissen C, de Vries BB, Ponting CP, Veltman JA. 2010. Accurate distinction of pathogenic from benign CNVs in mental retardation. PLoS Comput Biol 22:6.
13. Hochstenbach R, Poot M, Nijman IJ, Renkens I, Duran KJ, Van't Slot R, van Binsbergen E, van der Zwaag B, Vogel MJ, Terhal PA, Ploos van Amstel HK, Kloosterman WP, Cuppen E. 2012. Discovery of variants unmasked by hemizygous deletions. Eur J Hum Genet 20:748-753.
14. Itsara A, Wu H, Smith JD, Nickerson DA, Romieu I, London SJ, Eichler EE. 2010. De novo rates and selection of large copy number variation. Genome Res 20:1469-1481.
15. Knierim E, Schwarz JM, Schuelke M, Seelow D. 2013. CNVinsepctor: A web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts. J Med Genet 50:529-533.
16. Knight SJ, Regan R, Nicod A. 1999. Deletion of large-scale variation in the human genome. Nat Genet 36:949-951.
17. Koolen DA, Nillesen WM, Versteeg MHA, Merkx GFM, Knoers NVAM, Kets MM, Vermeer S, van Ravenswaaij CMA, de Kovel CG, Brunner HG, Smeets D, de Vries BBA, Sistermans EA. 2004. Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA). J Med Genet 41:892-899.
18. Koolen DA, Pfundt R, de Leeuw N, Hehir-Kwa JY, Nillesen WM, Neefs I, Scheltinga I, Sistermans E, Smeets D, Brunner HG, van Kessel AG, Veltman JA, de Vries BB. 2009. Genomic microarrays in mental retardation: A practical workflow for diagnostic applications. Hum Mutat 30:283-292.
19. Ku CS, Polychronakos C, Tan EK, Naidoo N, Pawitan Y, Roukos DH, Mort M, Cooper DN. 2013. A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Mol Psychiatry 18:141-153.
20. Lifton RP, Dluhy RG, Powers M, Rich GM, Cook S, Ulick S, Lalouel JM. 1992. A chimaeric 11 beta-hydroxylase/aldosterone synthase gene causes glucocorticoid-remediable aldosteronism and human hypertension. Nature 355:262-265.
21. Lundvall M, Rajaei S, Erlandson A, Kyllerman M. 2012. Aetiology of severe mental retardation and further genetic analysis by high-resolution microarray in a population-based series of 6- to 17-year-old children. Acta Paediatr 101:85-91.
22. Lupski JR, Stankiewicz P. 2005. Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1:e49.
23. Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. 2011. What can exome sequencing do for you? J Med Genet 48:580-589.
24. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. 2010. Consensus statement: Chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86:749-764.
25. Mullan GL, Taylor PJ, Elakis G, Lang S, van Rheeden J, Spiers H, Einfeld S, Tonge B, Turner G, Buckley MF, Mowat DR. 2008. The use of genome-wide SNP arrays for the diagnosis of genetic abnormalities in a selected cohort of young people with intellectual disability. Poster presentation, Human Genetic Society of Australasia.
26. Neill NJ, Ballif BC, Lamb AN, Parikh S, Ravnan JB, Schultz RA, Torchia BS, Rosenfeld JA, Shaffer LG. 2011. Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH. Genome Res 21:535-544.
27. Palmer EE, Peters GB, Mowat D. 2012. Chromosome microarray in Australia: A guide for paediatricians. J Paediatr Child Health 48:E59-E67.
28. Partington M, Mowat D, Einfeld S, Tonge B, Turner G. 2000. Genes on the X chromosome are important in undiagnosed mental retardation. Am J Med Genet 92:57-61.
29. Pfundt R, Veltman JA. 2012. Structural genomic variation in intellectual disability. Methods Mol Biol 838:77-95.
30. Rehder CW, David KL, Hirsch B, Toriello HV, Wilson CM, Kearney HM. 2013. American College of Medical Genetics and Genomics: Standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med 15:150-152.
31. Reiff M, Bernhardt BA, Mulchandani S, Soucier D, Cornell D, Pyeritz RE, Spinner NB. 2012. " What does it mean?": Uncertainties in understanding results of chromosomal microarray testing. Genet Med 14:250-258.
32. Reiff M, Ross K, Mulchandani S, Propert KJ, Pyeritz RE, Spinner NB, Bernhardt BA. 2013. Physicians' perspectives on the uncertainties and implications of chromosomal microarray testing of children and families. Clin Genet 83:23-30.
33. Schaefer GB, Mendelsohn NJ. Professional Practice and Guidelines Committee. 2013. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. Genet Med 15:399-407.
34. Talkowski ME, Mullegama SV, Rosenfeld JA, van Bon BW, Shen Y, Repnikova EA, Gastier-Foster J, Thrush DL, Kathiresan S, Ruderfer DM, Chiang C, Hanscom C, Ernst C, Lindgren AM, Morton CC, An Y, Astbury C, Brueton LA, Lichtenbelt KD, Ades LC, Fichera M, Romano C, Innis JW, Williams CA, Bartholomew D, Van Allen MI, Parikh A, Zhang L, Wu BL, Pyatt RE, Schwartz S, Shaffer LG, de Vries BB, Gusella JF, Elsea SH. 2011. Assessment of 2q23.1 micro-deletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder. Am J Hum Genet 89:551-563.
35. The International HapMap Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467:52-58.
36. Toro R, Konyukh M, Delorme R, Leblond C, Chaste P, Fauchereau F, Coleman M, Leboyer M, Gillberg C, Bourgeron T. 2010. Key role for gene dosage and synaptic homeostasis in autism spectrum disorders. Trends Genet 26:363-372.
37. Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. 2011. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics 4:25.
38. Wain KE, Riggs E, Hanson K, Savage M, Riethmaier D, Muirhead A, Mitchell E, Packard BS, Faucett WA. 2012. The laboratory-clinician team: A professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing. J Genet Couns 21:631-637.
39. Wincent J, Anderlid BM, Lagerberg M, Nordenskjöld M, Schoumans J. 2011. High-resolution molecular karyotyping in patients with developmental delay and/or multiple congenital anomalies in a clinical setting. Clin Genet 79:147-157.
40. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW. 2006. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115:205-214.