SNP array analysis in constitutional and cancer genome diagnostics - Copy number variants, genotyping and quality control

Cytogenetic and Genome Research

Volumn 135, Issue 3-4, 2011, Pages 212-221

  De Leeuw, N ^a   Hehir Kwa, J Y ^a   Simons, A ^a   Geurts Van Kessel, A ^a   Smeets, D F ^a   Faas, B H W ^a   Pfundt, R ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Cancer genome diagnostics; Constitutional genome diagnostics; Genotype analysis; Intellectual disability; Molecular karyotyping; Quality control; SNP array; Uniparental disomy

Indexed keywords

ACUTE LYMPHOBLASTIC LEUKEMIA; ANEUPLOIDY; ARTICLE; CANCER DIAGNOSIS; CANCER GENETICS; COPY NUMBER VARIATION; GENETIC ANALYSIS; GENOTYPE; HOMOZYGOSITY; HUMAN; KARYOTYPING; LABORATORY DIAGNOSIS; PARENT; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; QUALITY CONTROL; RECESSIVE GENE; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY;

COMPARATIVE GENOMIC HYBRIDIZATION; CONGENITAL ABNORMALITIES; DATA INTERPRETATION, STATISTICAL; DNA COPY NUMBER VARIATIONS; FEMALE; GENOTYPE; HOMOZYGOTE; HUMANS; INTELLECTUAL DISABILITY; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PREGNANCY; PRENATAL DIAGNOSIS; REFERENCE VALUES;

EID: 83455246303     PISSN: 14248581     EISSN: 14219794     Source Type: Journal    
DOI: 10.1159/000331273     Document Type: Article

References (58)

1. Brunetti-Pierri N, Berg JS, Scaglia F, Belmont J, Bacino CA, et al: Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat Genet 40: 1466-1471 (2008).
2. Buysse K, Delle Chiaie B, Van Coster R, Loeys B, De Paepe A, et al: Challenges for CNV interpretation in clinical molecular karyotyping: lessons learned from a 1001 sample experience. Eur J Med Genet 52: 398-403 (2009).
3. Collin RW, van den Born LI, Klevering BJ, de Castro-Miró M, Littink KW, et al: High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population. Invest Ophthalmol Vis Sci 52: 2227-2239 (2011).
4. Collins-Underwood JR, Mullighan CG: Genomic profiling of high-risk acute lymphoblastic leukemia. Leukemia 24: 1676-1685 (2010).
5. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38: 75-81 (2006). (Pubitemid 43011885)
6. de Leeuw N, Pfundt R, Koolen DA, Neefs I, Scheltinga I, et al: A newly recognised microdeletion syndrome involving 2p15p16.1: narrowing down the critical region by adding another patient detected by genome wide tiling path array comparative genomic hybridisation analysis. J Med Genet 45: 122-124 (2008). (Pubitemid 351252877)
7. de Vries BB, Pfundt R, Leisink M, Koolen DA, Vissers LE, et al: Diagnostic genome profiling in mental retardation. Am J Hum Genet 77: 606-616 (2005). (Pubitemid 41361607)
8. Faas BH, van der Burgt I, Kooper AJ, Pfundt R, Hehir-Kwa JY, et al: Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250k SNP array analysis. J Med Genet 47: 586-594 (2010).
9. Feenstra I, Fang J, Koolen DA, Siezen A, Evans C, et al: European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations (ECARUCA); an online database for rare chromosome abnormalities. Eur J Med Genet 49: 279-291 (2006). (Pubitemid 43994552)
10. Friedman J, Adam S, Arbour L, Armstrong L, Baross A, et al: Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization. BMC Genomics 10: 526 (2009).
11. Gijsbers AC, Lew JY, Bosch CA, Schuurs-Hoeijmakers JH, van Haeringen A, et al: A new diagnostic workflow for patients with mental retardation and/or multiple congenital abnormalities: test arrays first. Eur J Hum Genet 17: 1394-1402 (2009).
12. Hagenkord JM, Chang CC: The rewards and challenges of array-based karyotyping for clinical oncology applications. Leukemia 23: 829-833 (2009).
13. Hagenkord JM, Monzon FA, Kash SF, Lilleberg S, Xie Q, Kant JA: Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia. Performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. J Mol Diagn 12: 184-196 (2010).
14. Hannes FD, Sharp AJ, Mefford HC, de Ravel T, Ruivenkamp CA, et al: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant. J Med Genet 46: 223-232 (2009).
15. Hehir-Kwa J, Egmont-Petersen M, Janssen I, Smeets D, van Kessel A, et al: 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 14: 1-11 (2007).
16. Hehir-Kwa JY, Wieskamp N, Webber C, Pfundt R, Brunner HG, et al: Accurate distinction of pathogenic from benign CNVs in mental retardation. PLoS Comput Biol 6:e1000752 (2010).
17. Heinrichs S, Li C, Look AT: SNP array analysis in hematologic malignancies: avoiding false discoveries. Blood 115: 4157-4161 (2010).
18. Hildebrandt F, Heeringa SF, Rüschendorf F, Attanasio M, Nürnberg G, et al: A systematic approach to mapping recessive disease genes in individuals from outbred populations. PLoS Genet 5:e1000353 (2009).
19. Hochstenbach R, van Binsbergen E, Engelen J, Nieuwint A, Polstra A, et al: Array analysis and karyotyping: workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands. Eur J Med Genet 52: 161-169 (2009).
20. Huang J, Wei W, Zhang J, Liu G, Bignell GR, et al: Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics1: 287-299 (2004).
21. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al: Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64 (2008). (Pubitemid 351630326)
22. Koolen DA, Vissers LE, Pfundt R, de Leeuw N, Knight SJ, et al: A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet 38: 999-1001 (2006). (Pubitemid 44325923)
23. Koolen DA, Pfundt R, de Leeuw N, Hehir-Kwa JY, Nillesen WM, et al: Genomic microarrays in mental retardation: a practical workflow for diagnostic applications. Hum Mutat 30: 283-292 (2009).
24. Kuiper RP, Schoenmakers EF, van Reijmersdal SV, Hehir-Kwa JY, Geurts van Kessel A, et al: High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia 21: 1258-1266 (2007). (Pubitemid 46831815)
25. Kuiper RP, Waanders E, van der Velden VH, van Reijmersdal SV, Venkatachalam R, et al: IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia 24: 1258-1264 (2010).
26. Langemeijer SM, Kuiper RP, Berends M, Knops R, Aslanyan MG, et al: Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 41: 838-842 (2009).
27. Lee C, Iafrate AJ, Brothman AR: Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 39:S48-S54 (2007). (Pubitemid 47014476)
28. McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, et al: Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet 41: 1223-1227 (2009).
29. McMullan DJ, Bonin M, Hehir-Kwa JY, de Vries BB, Dufke A, et al: Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study. Hum Mutat 30: 1082-1092 (2009).
30. Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, et al: Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med 359: 1685-1699 (2008).
31. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, et al: 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 (2010).
32. Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, et al: Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446: 758-764 (2007). (Pubitemid 46582031)
33. Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, et al: Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 360: 470-480 (2009).
34. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, et al: A robust algorithm for copy number detection using high-density oligonucleotide single-nucleotide polymorphism genotyping arrays. Cancer Res 65: 6071-6079 (2005). (Pubitemid 40994391)
35. Nowakowska B, de Leeuw N, Ruivenkamp CA, Sikkema-Raddatz B, Crolla JA, et al: Parental insertional balanced translocations are an important cause of apparently de novo CNVs in patients with developmental anomalies. Eur J Hum Genet, in press (2011).
36. Patel A, Kang SH, Lennon PA, Li YF, Rao PN, et al: Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia. Am J Hematol 83: 540-546 (2008). (Pubitemid 351874869)
37. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, et al: Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci USA 103: 8006-8011 (2006). (Pubitemid 43801043)
38. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al: PLINK: a tool set for whole-genome association and populationbased linkage analyses. Am J Hum Genet 81: 559-575 (2007). (Pubitemid 47330214)
39. Rauch A, Hoyer J, Guth S, Zweier C, Kraus C, et al: Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation. Am J Med Genet A 140A:2063-2074 (2006). (Pubitemid 44522453)
40. Raymond FL, Tarpey P: The genetics of mental retardation. Hum Mol Genet 15 Spec No 2:R110-R116 (2006). (Pubitemid 44446783)
41. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al: Global variation in copy number in the human genome. Nature 444: 444-454 (2006). (Pubitemid 44809057)
42. Schuurs-Hoeijmakers JH, Hehir-Kwa JY, Pfundt R, van Bon BW, de Leeuw N, et al: Homozygosity mapping in outbred families with mental retardation. Eur J Hum Genet 19: 597-601 (2011).
43. Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, et al: A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet 40: 322-328 (2008). (Pubitemid 351311774)
44. Shinawi M, Liu P, Kang SH, Shen J, Belmont JW, et al: Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioural problems, dysmorphism, epilepsy, and abnormal head size. J Med Genet 47: 332-341 (2010).
45. Simons A, Stevens-Kroef M, El Idrissi-Zaynoun N, van Gessel S, Olde Weghuis D, et al: Microarray-based genomic profiling as a diagnostic tool in acute lymphoblastic leukemia. Genes, Chromosomes and Cancer, 2011 Aug 31. doi: 10.1002/gcc.20919 PMID:21882283 (2011).
46. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, et al: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29: 263-264 (2001). (Pubitemid 33096449)
47. Stankiewicz P, Beaudet AL: Use of genome-wide array analysis in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev 17: 182-192 (2007). (Pubitemid 46843553)
48. Stefansson H, Rujescu D, Cichon S, Pietiläinen OP, Ingason A, et al: Large recurrent microdeletions associated with schizophrenia. Nature 455: 232-236 (2008).
49. Stegelmann F, Bullinger L, Griesshammer M, Holzmann K, Habdank M, et al: High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations. Haematologica 95: 666-669 (2010).
50. Ting JC, Roberson ED, Miller ND, Lysholm-Bernacchi A, Stephan DA, et al: Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio. Hum Mutat 28: 1225-1235 (2007). (Pubitemid 350250387)
51. Tyreman M, Abbott KM, Willatt LR, Nash R, Lees C, et al: High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings. J Med Genet 46: 531-541 (2009).
52. Ullmann R, Turner G, Kirchhoff M, Chen W, Tonge B, et al: Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation. Hum Mutat 28: 674-682 (2007). (Pubitemid 47047294)
53. van Bon BW, Mefford HC, Menten B, Koolen DA, Sharp AJ, et al: Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome. J Med Genet 46: 511-523 (2009).
54. van Bon BW, Balciuniene J, Fruhman G, Nagamani SC, Broome DL, et al: The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 19: 400-408 (2011).
55. Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, et al: Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. J Hum Genet 73: 1261-1270 (2003). (Pubitemid 38037420)
56. Vissers LE, de Vries BB, Veltman JA: Genomic microarrays in mental retardation: from copy number variation to gene, from research to diagnosis. J Med Genet 47: 289-297 (2010).
57. Weiss LA, Shen Y, Korn JM, Arking DE, Miller DT, et al: Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med 358: 667-675 (2008). (Pubitemid 351240746)
58. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW: 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 (2006). (Pubitemid 44832022)