High-resolution SNP arrays in mental retardation diagnostics: How much do we gain

European Journal of Human Genetics

Volumn 18, Issue 2, 2010, Pages 178-185

  Bernardini, Laura ^a   Alesi, Viola ^a,b   Loddo, Sara ^a,b   Novelli, Antonio ^a   Bottillo, Irene ^a   Battaglia, Agatino ^c   Digilio, Maria Cristina ^d   Zampino, Giuseppe ^e   Ertel, Adam ^b   Fortina, Paolo ^b,f   Surrey, Saul ^b   Dallapiccola, Bruno ^a  

^a CASA SOLLIEVO DELLA SOFFERENZA HOSPITAL   (Italy)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c DEPARTMENT OF DEVELOPMENTAL NEUROSCIENCE   (Italy)

^d BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^e CATHOLIC UNIVERSITY   (Italy)

^f SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

GeneChip 6.0; Mental retardation; Pathogenic CNVs; SNP array

Indexed keywords

ADOLESCENT; ARTICLE; CHILD; CHROMOSOME 1; CHROMOSOME 11; CHROMOSOME 3; CHROMOSOME 5; CHROMOSOME 5Q; COMPARATIVE GENOMIC HYBRIDIZATION; CONGENITAL MALFORMATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DIAGNOSTIC VALUE; FALSE POSITIVE RESULT; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC ANALYSIS; HUMAN; KARYOTYPE 46,XX; KARYOTYPE 46,XY; MAJOR CLINICAL STUDY; MALE; MENTAL DEFICIENCY; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME INACTIVATION;

ALLELIC IMBALANCE; CHILD; CHILD, PRESCHOOL; COHORT STUDIES; FEMALE; GENETIC VARIATION; GENOTYPE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INFANT; KARYOTYPING; LOSS OF HETEROZYGOSITY; MALE; MENTAL RETARDATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 74449092827     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.154     Document Type: Article

References (44)

1. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 2006; 7: 85-97.
2. Chance PF, Abbas N, Lensch MW et al: Two autosomal dominant neuropathies result from reciprocal DNA duplication/deletion of a region on chromosome 17. Hum Mol Genet 1994; 3: 223-228.
3. Stankiewicz P, Lupski JR: Genome architecture, rearrangements and genomic disorders. Trends Genet 2002; 18: 74-82.
4. Cooper GM, Nickerson DA, Eichler EE: Mutational and selective effects on copy-number variants in the human genome. Nat Genet 2007; 39: S22-S29.
5. Perry GH, Tchinda J, McGrath SD et al: Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci USA 2006; 103: 8006-8011. (Pubitemid 43801043)
6. Sharp AJ, Locke DP, McGrath SD et al: Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005; 77: 78-88.
7. Shaw CJ, Bi W, Lupski JR: Genetic proof of unequal meiotic crossovers in reciprocal deletion and duplication of 17p11.2. Am J Hum Genet 2002; 71: 1072-1081.
8. Emanuel BS, Saitta SC: From microscopes to microarrays: dissecting recurrent chromosomal rearrangements. Nat Rev Genet 2007; 8: 869-883.
9. Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 2007; 39: S16-S21.
10. Fan YS, Jayakar P, Zhu H et al: Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization. Hum Mutat 2007; 28: 1124-1132.
11. Redon R, Ishikawa S, Fitch KR et al: Global variation in copy number in the human genome. Nature 2006; 444: 444-454. (Pubitemid 44809057)
12. Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjold M: Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J Med Genet 2005; 42: 699-705.
13. Sharp AJ, Cheng Z, Eichler EE: Structural variation of the human genome. Annu Rev Genomics Hum Genet 2006; 7: 407-442.
14. Trask BJ, Friedman C, Martin-Gallardo A et al: Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum Mol Genet 1998; 7: 13-26.
15. van Karnebeek CD, Scheper FY, Abeling NG et al: Etiology of mental retardation in children referred to a tertiary care center: a prospective study. Am J Ment Retard 2005; 110: 253-267.
16. Rauch A, Hoyer J, Guth S et al: Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation. Am J Med Genet A 2006; 140: 2063-2074.
17. Zahir F, Friedman JM: The impact of array genomic hybridization on mental retardation research: a review of current technologies and their clinical utility. Clin Genet 2007; 72: 271-287.
18. Shaikh TH: Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet Med 2007; 9: 617-625.
19. Rauch A, Ruschendorf F, Huang J et al: Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 2004; 41: 916-922.
20. Greshock J, Feng B, Nogueira C et al: A comparison of DNA copy number profiling platforms. Cancer Res 2007; 67: 10173-10180.
21. McCarroll SA, Kuruvilla FG, Korn JM et al: Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008; 40: 1166-1174.
22. Hehir-Kwa JY, Egmont-Petersen M, Janssen IM, Smeets D, van Kessel AG, Veltman JA: Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res 2007; 14: 1-11.
23. Wong KK, deLeeuw RJ, Dosanjh NS et al: A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 2007; 80: 91-104.
24. Koolen DA, Pfundt R, de Leeuw N et al: Genomic microarrays in mental retardation: a practical workflow for diagnostic applications. Hum Mutat 2009; 30: 283-292.
25. Korn JM, Kuruvilla FG, McCarroll SA et al: Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008; 40: 1253-1260.
26. Bernardini L, Castori M, Capalbo A et al: Syndromic craniosynostosis due to complex chromosome 5 rearrangement and MSX2 gene triplication. Am J Med Genet A 2007; 143A: 2937-2943.
27. Carbone A, Bernardini L, Valenzano F et al: Array-based comparative genomic hybridization in early-stage mycosis fungoides: recurrent deletion of tumor suppressor genes BCL7A, SMAC/DIABLO, and RHOF. Genes Chromosomes Cancer 2008; 47: 1067-1075.
28. Wagenstaller J, Spranger S, Lorenz-Depiereux B et al: Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation. Am J Hum Genet 2007; 81: 768-779.
29. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL: Resolving the resolution of array CGH. Genomics 2007; 89: 647-653.
30. Vermeesch JR, Fiegler H, de Leeuw N et al: Guidelines for molecular karyotyping in constitutional genetic diagnosis. Eur J Hum Genet 2007; 15: 1105-1114.
31. Lee C, Iafrate AJ, Brothman AR: Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007; 39: S48-S54. (Pubitemid 47014476)
32. Hernandez-Martin A, Gonzalez-Sarmiento R, De Unamuno P: X-linked ichthyosis: an update. Br J Dermatol 1999; 141: 617-627.
33. Shaw-Smith C, Redon R, Rickman L et al: Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004; 41: 241-248.
34. Battaglia A, Hoyme HE, Dallapiccola B et al: Further delineation of deletion 1p36 syndrome in 60 patients: a recognizable phenotype and common cause of developmental delay and mental retardation. Pediatrics 2008; 121: 404-410.
35. Heilstedt HA, Ballif BC, Howard LA et al: Physical map of 1p36, placement of breakpoints in monosomy 1p36, and clinical characterization of the syndrome. Am J Hum Genet 2003; 72: 1200-1212.
36. Ballif BC, Yu W, Shaw CA, Kashork CD, Shaffer LG: Monosomy 1p36 breakpoint junctions suggest pre-meiotic breakage-fusion-bridge cycles are involved in generating terminal deletions. Hum Mol Genet 2003; 12: 2153-2165.
37. Perry GH, Ben-Dor A, Tsalenko A et al: The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet 2008; 82: 685-695.
38. Froyen G, Van Esch H, Bauters M et al: Detection of genomic copy number changes in patients with idiopathic mental retardation by high-resolution X-array-CGH: important role for increased gene dosage of XLMR genes. Hum Mutat 2007; 28: 1034-1042.
39. Wolff DJ, Schwartz S, Carrel L: Molecular determination of X inactivation pattern correlates with phenotype in women with a structurally abnormal X chromosome. Genet Med 2000; 2: 136-141.
40. Vrijenhoek T, Buizer-Voskamp JE, van der Stelt I et al: Recurrent CNVs disrupt three candidate genes in schizophrenia patients. Am J Hum Genet 2008; 83: 504-510.
41. Sudo K, Ito H, Iwamoto I, Morishita R, Asano T, Nagata K: SEPT9 sequence alternations causing hereditary neuralgic amyotrophy are associated with altered interactions with SEPT4/SEPT11 and resistance to Rho/Rhotekin-signaling. Hum Mutat 2007; 28: 1005-1013.
42. Xie Y, Vessey JP, Konecna A, Dahm R, Macchi P, Kiebler MA: The GTP-binding protein Septin 7 is critical for dendrite branching and dendritic-spine morphology. Curr Biol 2007; 17: 1746-1751.
43. Buser AM, Erne B, Werner HB, Nave KA, Schaeren-Wiemers N: The septin cytoske-leton in myelinating glia. Mol Cell Neurosci 2009; 40: 156-166.
44. Zhang ZF, Ruivenkamp C, Staaf J et al: Detection of submicroscopic constitutional chromosome aberrations in clinical diagnostics: a validation of the practical performance of different array platforms. Eur J Hum Genet 2008; 16: 786-792.