Genome-wide Oligonucleotide Array Comparative Genomic Hybridization for Etiological Diagnosis of Mental Retardation: a Multicenter Experience of 1499 Clinical Cases

Overview

Journal J Mol Diagn

Publisher Elsevier

Specialties Molecular Biology
Pathology

Date 2010 Jan 23

PMID 20093387

Citations 33

Authors

Bixia Xiang

Hongbo Zhu

Yiping Shen

David T Miller

Kangmo Lu

Xiaofeng Hu

Hans C Andersson

Tarachandra M Narumanchi

Yueying Wang

Jose E Martinez

Bai-Lin Wu

Peining Li

Marilyn M Li

Tian-Jian Chen

Yao-Shan Fan

Affiliations

Soon will be listed here.

Abstract

To assess the clinical utility of genome-wide oligonucleotide arrays in diagnosis of mental retardation and to address issues relating to interpretation of copy number changes (CNCs), we collected results on a total of 1499 proband patients from five academic diagnostic laboratories where the same 44K array platform has been used. Three of the five laboratories achieved a diagnostic yield of 14% and the other two had a yield of 11 and 7%, respectively. Approximately 80% of the abnormal cases had a single segment deletion or duplication, whereas the remaining 20% had a compound genomic imbalance involving two or more DNA segments. Deletion of 16p11.2 is a common microdeletion syndrome associated with mental retardation. We classified pathogenic CNCs into six groups according to the structural changes. Our data have demonstrated that the 44K platform provides a reasonable resolution for clinical use and a size of 300 kb can be used as a practical cutoff for further investigations of the clinical relevance of a CNC detected with this platform. We have discussed in depth the issues associated with the clinical use of array CGH and provided guidance for interpretation, reporting, and counseling of test results based on our experience.

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References

Wagenstaller J, Spranger S, Lorenz-Depiereux B, Kazmierczak B, Nathrath M, Wahl D . Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation. Am J Hum Genet. 2007; 81(4):768-79. PMC: 2227926. DOI: 10.1086/521274. View

Mefford H, Sharp A, Baker C, Itsara A, Jiang Z, Buysse K . Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008; 359(16):1685-99. PMC: 2703742. DOI: 10.1056/NEJMoa0805384. View

Roeleveld N, Zielhuis G, Gabreels F . The prevalence of mental retardation: a critical review of recent literature. Dev Med Child Neurol. 1997; 39(2):125-32. DOI: 10.1111/j.1469-8749.1997.tb07395.x. View

Koolen D, Pfundt R, de Leeuw N, Hehir-Kwa J, Nillesen W, Neefs I . Genomic microarrays in mental retardation: a practical workflow for diagnostic applications. Hum Mutat. 2008; 30(3):283-92. DOI: 10.1002/humu.20883. View

Ledbetter D . Cytogenetic technology--genotype and phenotype. N Engl J Med. 2008; 359(16):1728-30. DOI: 10.1056/NEJMe0806570. View

Shen Y, Wu B . Microarray-based genomic DNA profiling technologies in clinical molecular diagnostics. Clin Chem. 2009; 55(4):659-69. DOI: 10.1373/clinchem.2008.112821. View

Shevell M, Majnemer A, Morin I . Etiologic yield of cerebral palsy: a contemporary case series. Pediatr Neurol. 2003; 28(5):352-9. DOI: 10.1016/s0887-8994(03)00006-7. View

Shaffer L, Theisen A, Bejjani B, Ballif B, Aylsworth A, Lim C . The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet Med. 2007; 9(9):607-16. DOI: 10.1097/gim.0b013e3181484b49. View

Friedman J, Baross A, Delaney A, Ally A, Arbour L, Armstrong L . Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006; 79(3):500-13. PMC: 1559542. DOI: 10.1086/507471. View

10.

Baldwin E, Lee J, Blake D, Bunke B, Alexander C, Kogan A . Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med. 2008; 10(6):415-29. DOI: 10.1097/GIM.0b013e318177015c. View

11.

Aradhya S, Cherry A . Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med. 2007; 9(9):553-9. DOI: 10.1097/gim.0b013e318149e354. View

12.

Redon R, Ishikawa S, Fitch K, Feuk L, Perry G, Andrews T . Global variation in copy number in the human genome. Nature. 2006; 444(7118):444-54. PMC: 2669898. DOI: 10.1038/nature05329. View

13.

Pickering D, Eudy J, Olney A, Dave B, Golden D, Stevens J . Array-based comparative genomic hybridization analysis of 1176 consecutive clinical genetics investigations. Genet Med. 2008; 10(4):262-6. DOI: 10.1097/GIM.0b013e31816b64ad. View

14.

Cushman L, Torres-Martinez W, Cherry A, Manning M, Abdul-Rahman O, Anderson C . A report of three patients with an interstitial deletion of chromosome 15q24. Am J Med Genet A. 2005; 137(1):65-71. DOI: 10.1002/ajmg.a.30836. View

15.

Shaw-Smith C, Pittman A, Willatt L, Martin H, Rickman L, Gribble S . Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat Genet. 2006; 38(9):1032-7. DOI: 10.1038/ng1858. View

16.

Koolen D, Vissers L, Pfundt R, de Leeuw N, Knight S, Regan R . A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet. 2006; 38(9):999-1001. DOI: 10.1038/ng1853. View

17.

Lee C, Iafrate A, Brothman A . Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet. 2007; 39(7 Suppl):S48-54. DOI: 10.1038/ng2092. View

18.

Shen Y, Miller D, Cheung S, Lip V, Sheng X, Tomaszewicz K . Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin Chem. 2007; 53(12):2051-9. DOI: 10.1373/clinchem.2007.090290. View

19.

de Vries B, Pfundt R, Leisink M, Koolen D, Vissers L, Janssen I . Diagnostic genome profiling in mental retardation. Am J Hum Genet. 2005; 77(4):606-16. PMC: 1275609. DOI: 10.1086/491719. View

20.

Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P . Large-scale copy number polymorphism in the human genome. Science. 2004; 305(5683):525-8. DOI: 10.1126/science.1098918. View