Application of metaphase HR-CGH and targeted chromosomal microarray analyses to genomic characterization of 116 patients with mental retardation and dysmorphic features

American Journal of Medical Genetics, Part A

Volumn 146, Issue 18, 2008, Pages 2361-2369

  Nowakowska, B ^a,b   Stankiewicz, P ^a,b   Obersztyn, E ^a   Ou, Z ^b   Li, J ^b   Chinault, A C ^b   Smyk, M ^a   Borg, K ^a   Mazurczak, T ^a   Cheung, S W ^b   Bocian, E ^a  

^a INSTITUTE OF MOTHER AND CHILD   (Poland)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Array CGH; Chromosomal abnormalities; Mental retardation; Metaphase HR CGH

Indexed keywords

ARTICLE; CHROMOSOME 16P; CHROMOSOME 8Q; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHROMOSOME DELETION; CHROMOSOME POLYMORPHISM; CLINICAL FEATURE; COMPARATIVE STUDY; CONTROLLED STUDY; DYSMORPHISM; FEMALE; GENETIC DISORDER; GENOMICS; HUMAN; KARYOTYPE; MAJOR CLINICAL STUDY; MALE; MENTAL DEFICIENCY; METAPHASE HIGH RESOLUTION COMPARATIVE GENOMIC HYBRIDIZATION; MICROARRAY ANALYSIS; PRIORITY JOURNAL; TARGETED CHROMOSOMAL MICROARRAY ANALYSIS; DEVELOPMENTAL DISORDER; DNA MICROARRAY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DELETION; GENE DUPLICATION; GENETICS; KARYOTYPING; METAPHASE; METHODOLOGY; MULTIPLE MALFORMATION SYNDROME; PRESCHOOL CHILD;

ABNORMALITIES, MULTIPLE; CHILD, PRESCHOOL; DEVELOPMENTAL DISABILITIES; FEMALE; GENE DELETION; GENE DUPLICATION; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; MALE; MENTAL RETARDATION; METAPHASE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 51449121623     PISSN: 15524825     EISSN: 15524833     Source Type: Journal    
DOI: 10.1002/ajmg.a.32475     Document Type: Article

References (52)

1. Bejjani BA, Shaffer LG. 2006. Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 8:528-533.
2. Bejjani BA, Theisen AP, Ballif BC, Shaffer LG. 2005a. Array-based comparative genomic hybridization in clinical diagnosis. Expert Rev Mol Diagn 5:421-428.
3. Bejjani BA, Saleki R, Ballif BC, Rorem EA, Sundin K, Theisen A, Kashork CD, Shaffer LG. 2005b. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am J Med Genet Part A 134A:259-267.
4. Bisgaard AM, Kirchhoff M, Turner Z, Jepsen B, Brøndum-Nielsen K, Cohen M, Hamborg-Petersen B, Bryndorf T, Tommerup N, Skovby F. 2006. Additional chromosomal abnormalities in patients with a previously detected abnormal karyotype, mental retardation, and dysmorphic features. Am J Med Genet Part A 140A:2180-2187.
5. Borg K, Nowakowska B, Obersztyn E, Cheung SW, Mazurczak T, Stankiewicz P, Bocian E. 2007. Complex balanced translocation t(1;5;7)(p32.1;q14.3;p21.3) and two microdeletions del(1)(p31.1p31.1) and del(7)(p14.1p14.1) in a patient with features of Greig cephalopolysyndactyly and mental retardation. Am J Med Genet Part A 143A:2738-2743.
6. Bruder CE, Hirvelä C, Tapia-Paez I, Fransson I, Segraves R, Hamilton G, Zhang XX, Evans DG, Wallace AJ, Baser ME, Zucman-Rossi J, Hergersberg M, Boltshauser E, Papi L, Rouleau GA, Poptodorov G, Jordanova A, Rask-Andersen H, Kluwe L, Mautner V, Sainio M, Hung G, Mathiesen T, Möller C, Pulst SM, Harder H, Heiberg A, Honda M, Niimura M, Sahlén S, Blennow E, Albertson DG, Pinkel D, Dumanski JP. 2001. High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarrayCGH. Hum Mol Genet 3:271-282.
7. Cheung SW, Shaw CA, Yu W, Li J, Ou Z, Patel A, Yatsenko SA, Cooper ML, Furman P, Stankiewicz P, Lupski JR, Chinault AC, Beaudet AL. 2005. Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med 7:422-432.
8. Ciccone R, Giorda R, Gregato G, Guerrini R, Giglio S, Carrozzo R, Bonaglia MC, Priolo E, Lagana C, Tenconi R, Rocchi M, Prampraro T, Zuffardi O, Rossi E. 2005. Reciprocal translocations; A trap for cytogenetists? Hum Genet 117:571-582.
9. de Vries BB, Pfundt R, Leisink M, Koolen DA, Vissers LE, Janssen IM, Reijmersdal S, Nillesen WM, Huys EH, Leeuw N, Smeets D, Sistermans EA, Feuth T, van Ravenswaaij-Arts CM, van Kessel AG, Schoenmakers EF, Brunner HG, Veltman JA. 2005. Diagnostic genome profiling in mental retardation. Am J Hum Genet 77:606-616.
10. Gribble SM, Prigmore E, Burford DC, Porter KM, Ng BL, Douglas EJ, Fiegler H, Carr P, Kalaitzopoulos D, Clegg S, Sandstrom R, Temple IK, Youings SA, Thomas NS, Dennis NR, Jacobs PA, Crolla JA, Carter NP. 2005. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet 42:8-16.
11. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951.
12. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299-303.
13. Joly G, Lapierre J-M, Ozilou C, Gosset P, Aurias A, de Blois M-C, Prieur M, Raoul O, Colleaux L, Munnich A, Romana SP, Vekemans M, Turleau C. 2001. Comparative genomic hybridisation in mentally retarded patients with dysmorphic features and a normal karyotype. Clin Genet 60:212-219.
14. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1992. Comparative genomic hybridization for molecular analysis of solid tumors. Science 258:818-821.
15. Kallioniemi OP, Kallioniemi A, Sudar D, Rutovitz D, Gray JW, Walkman F, Pinkel D. 1993. Comparative genomic hybridization: A rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4:41-46.
16. Kirchhoff M, Gerdes T, Maahr J, Rose H, Lundsteen C. 1997. Automatic correction of the interfering effect of unsuppressed interspersed repetitive sequences in comparative genomic hybridization analysis. Cytometry 28:130-134.
17. Kirchhoff M, Gerdes T, Rose H, Maahr J, Ottesen AM, Lundsteen C. 1998. Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry: 31:163-173.
18. Kirchhoff M, Rose H, Petersen BL, Maahr J, Gerdes T, Lundsteen C, Bryndorf T, Kryger-Baggesen N, Christensen L, Engelholm SA, Philip J. 1999a. Comparative genomic hybridization reveals a recurrent pattern of chromosomal aberrations in severe dysplasia/carcinoma in situ of the cervix and in advanced-stage cervical carcinoma. Genes Chromosomes Cancer 24:144-150.
19. Kirchhoff M, Gerdes T, Maahr J, Rose H, Bentz M, Döhner H, Lundsteen C. 1999b. Deletion below 10 Megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chromosomes Cancer 25:410-413.
20. Kirchhoff M, Rose H, Maahr J, Gerdes T, Bugge M, Tommerup N, Tümer Z, Lespinasse J, Jensen PKA, Wirth J, Lundsteen C. 2000. High resolution comparative genomic hybridization reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes. Eur J Hum Genet 8:661-668.
21. Kirchhoff M, Rose H, Lundsteen C. 2001. High resolution comparative genomic hybridization in clinical cytogenetics. J Med Genet 38:740-744.
22. Kirchhoff M, Pedersen S, Kjeldsen E, Rose H, Dunø M, Kølvraa S. 2004. Prospective study comparing HR-CGH and subtelomeric FISH for investigation of individuals with mental retardation and dysmorphic features and an update of study using only HR-CGH. Am J Med Genet Part A 127A:111-117.
23. Knight SJ, Regan R, Nicod A, Horsley SW, Kearney L, Homfray T, Winter RM, Bolton P, Flint J. 1999. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 354:1676-1681.
24. Lapierre JM, Cacheux V, Collot N, Silva FD, Hervy N, Rivet D, Romana S, Wiss J, Benzaken B, Aurias A, Tachdjian G. 1998. Comparison of comparative genomic hybridization with conventional karyotype and classical fluorescence in situ hybridization for prenatal and postnatal diagnosis of unbalanced chromosome abnormalities. Ann Genet 41:133-140.
25. Lockwood WW, Chari R, Chi B, Lam WL. 2006. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 14:139-148.
26. Lu X, Shaw CA, Patel A, Li J, Cooper ML, Wells WR, Sullivan CM, Sahoo T, Yatsenko SA, Bacino CA, Stankiewicz P, Ou Z, Chinault AC, Beaudet AL, Lupski JR, Cheung SW, Ward PA. 2007. Clinical implementation of chromosomal microarray analysis: Summary of 2513 postnatal cases. PLoS ONE 2:e327.
27. Ness GO, Lybæk H, Houge G. 2002. Usefulness of high-resolution comparative genomic hybridization (CGH) for detecting and characterizing constitutional chromosome abnormalities. Am J Med Genet 113:125-136.
28. Ou Z, Kang SH, Shaw CA, Carmack CE, White LD, Patel A, Beaudet AL, Cheung SW, Chinault AC. 2008. Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses. Genet Med 10:278-289.
29. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207-211.
30. Poss AF, Goldenberg PC, Rehder CW, Kearney HM, Melvin EC, Koeberl DD, McDonald MT. 2006. Clinical experience with array CGH: Case presentations from nine months of practice. Am J Med Genet Part A 140A:2050-2056.
31. Ravnan JB, Tepperberg JH, Papenhausen P, Lamb AN, Hedrick J, Eash D, Ledbetter DH, Martin CL. 2006. Subtelomere FISH analysis of 11 688 cases: An evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J Med Genet 43:478-489.
32. Redon R, Rio M, Gregory SG, Cooper RA, Fiegler H, Sanlaville D, Banerjee R, Scott C, Carr P, Langford C, Cormier-Daire V, Munnich A, Carter NP. Colleaux L. 2005. Tiling path resolution mapping of constitutional 1p36 deletions by array-CGH: Contiguous gene deletion or "deletion with positional effect" syndrome? J Med Genet 42:166-171.
33. Reclon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. 2006. Global variation in copy number in the human genome. Nature 444:444-454.
34. Rooney PH, Stevenson DA, Marsh S, Johnston PG, Haites NE, Cassidy J, McLeod HL. 1998. Comparative genomic hybridization analysis of chromosomal alterations induced by the development of resistance to thymidylate synthase inhibitors. Cancer Res 58:5042-5045.
35. Schaeffer AJ, Chung J, Heretis K, Wong A, Ledbetter DH, Lese Martin C. 2004. Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am J Hum Genet 74:1168-1174.
36. Schoumans J, Nielsen K, Jeppesen I, Anderlind B-M, Blennow E, Brondum-Nielsen K, Nordenskjöld M. 2004. A comparison of different metaphase CGH method for the detection of cryptic chromosome aberrations of defined size. Eur J Hum Genet 12:447-454.
37. Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjöld M. 2005. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridization (arrayCGH). J Med Genet 42:699-705.
38. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science 305:525-528.
39. Shaffer LG, Kennedy GM, Spikes AS, Lupski JR. 1997. Diagnosis of CMTlA duplications and HNPP deletions by interphase FISH: Implications for testing in the cytogenetics laboratory. Am J Med Genet 69:325-331.
40. Shaffer LG, Kashork CD, Saleki R, Rorem E, Sundin K, Ballif BC, Bejjani BA. 2006. Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr 149:98-102.
41. Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE. 2006. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet 38:1038-1042.
42. Shaw CJ, Shaw CA, Yu W, Stankiewicz P, White LD, Beaudet AL, Lupski JR. 2004. Comparative genomic hybridization using a proximal 17p BAC/PAC array detects rearrangements responsible for four genomic disorders. J Med Genet 41:113-119.
43. Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, Firth H, Sanlaville D, Winter R, Colleaux L, Bobrow M, Carter NP. 2004. Microarray based comparative genomic hybridization (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 41:241-248.
44. Shevell M, Ashwal S, Donley D, Flint J, Gingold M, Hirtz D, Majnermer A, Noetzel M, Sheth RD. 2003. Practice parameter: Evaluation of the child with global developmental delay: Report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology 60:367-380.
45. Stankiewicz P, Beaudet AL. 2007. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev 17:182-192.
46. Stankiewicz P, Lupski JR. 2002. Genome architecture, rearrangements and genomic disorders. Trends Genet 18:74-82.
47. Veltman JA, Schoenmakers EF, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG. 2002. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 70:1269-1276.
48. Veltman JA, Jonkers Y, Nuijten I, Janssen I, van der Vliet W, Huys E, Vermeesch J, Van Buggenhout G, Fryns JP, Admiraal R, Terhal P, Lacombe D, van Kessel AG, Smeets D, Schoenmakers EF, van Ravenswaaij-Arts CM. 2003. Definition of a critical region on chromosome 18 for congenital aural atresia by arrayCGH. Am J Hum Genet 72:1578-1584.
49. Veyver I, Beaudet AL. 2006. Comparative genomic hybridization and prenatal diagnosis. Curr Opin Obstet Gynecol 18:185-191.
50. Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, Choy CO, Straatman H, van der Vliet W, Huys EH, van Rijk A, Smeets D, van Ravenswaaij-Arts CM, Knoers NV, van der Burgt I, de Jong PJ, Brunner HG, van Kessel AG, Schoenmakers EF, Veltman JA. 2003. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 73:1261-1270.
51. Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB, Janssen IM, van der Vliet WA, Huys EH, de Jong PJ, Hamel BC, Schoenmakers EF, Brunner HG, Veltman JA, van Kessel AG. 2004. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet 36:955-957.
52. Yu W, Ballif BC, Kashork CD, Heilstedt HA, Howard LA, Cai WW, White LD, Liu W, Beaudet AL, Bejjani BA, Shaw CA, Shaffer LG. 2003. Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 wellcharacterized 1p36 deletions. Hum Mol Genet 12:214.