Genomic analysis with array CGH


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1.    Speicher, M. R., Carter, N. P. The new cytogenetics: blurring the boundaries with molecular biology. Nature Rev. Genet. 6, 782–792 (2005).
2.    Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
3.    Jacobs, P.A., Baikie, A.G., Court Brown, W.M. and Strong, J.A. The somatic chromosomes in mongolism. Lancet 1, 710 (1959).
4.    Lucas, M., Kemp, N.H., Ellis, J.R., Marshall, R. A small autosomal ring chromosome in a female infant with congenital malformations. Ann. Hum. Genet. 27, 189-195 (1963).
5.    Rowley, J.D. A new consistent chromosomal abnormality in chronic myelogenous leukemia identified by quinacrine fluorescence and Giemsa staining. Nature 243, 290-293 (1973).
6.    Lubs, H.A. A marker X chromosome.Am. J. Hum. Genet. 21, 231–244 (1969).
7.    Florijn, R. J. et al. High-resolution DNA fiber-FISH forgenomic DNA mapping and colour bar-coding of largegenes. Hum. Mol. Genet. 4, 831–836 (1995).
8.    Knight, S. J., Fling, J. The use of subtelomeric probes to study mental retardation. Methods Cell Biol. 75, 799-831 (2004).
9.    Kallioniemi, A. et al. Comparative genomic hybridization formolecular cytogenetic analysis of solid tumors. Science258, 818–821 (1992).
10. Weiss M.M., Kuipers, E.J., Meuwissen, S.G., van Diest, P.J., Meijer, G.A. Comparative genomic hybridization as a supportive tool in diagnostic pathology. J. Clin. Pathol. 56, 522-527 (2003).
11. Barber, J.C.K., Joyce, C.A., Collinson, M.N., et al. Duplication of 8p23.1: A cytogenetic anomaly with no established clinical significance. J. Med. Genet. 35, 491–496 (1998).
12. Lin, H., Pizer, E., Morin, P.J. A frequent deletion polymorphism on chromosome 22q13 identified by representational difference analysis of ovarian cancer.Genomics 69, 391-394 (2000).
13. Carter, N.P. Methods and strategies for analyzing copy number variation using DNA microarrays. Nature 39, S16-S21 (2007).
14. Albertson, D. G., Collins, C., McCormick, F. & Gray, J. W. Chromosome aberrations in solid tumors. NatureGenet. 34, 369–376 (2003).
15. 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. 41, 241-248 (2004).
16. Rosenberg, C., Knijnenburg, J., Bakker, E. et al.Array‐CGH detection of micro rearrangements in mentally retarded individuals: clinical significance of imbalances present both in affected children and normal parents. J. Med. Genet.43, 180–186 (2006).
17. Menten, B. et al. Emerging patterns of crypticchromosomal imbalance in patients with idiopathicmental retardation and multiple congenital anomalies:a new series of 140 patients and review of publishedreports. J. Med. Genet. 43, 625–633 (2006).
18. Veltman, J. A. et al. High-throughput analysis ofsubtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am. J. Hum. Genet. 70, 1269–1276 (2002).
19. Lockwood, W.W., Chari, R., Chi, B., Lam, W.L.Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. European Journal of Human Genetics 14, 139–148 (2006).
20. Wenli, G., Zhang, F., Lupski, J.R. Mechanisms for human genomic rearrangements PathoGenetics 1(1), 4 (2008).
21. Feuk, L., Carson, A. R., Scherer, S. W. Structural variation in the human genome. Nature Rev. Genet. 7, 85-97 (2006).
22. Scherer, S.W., Lee, C., Birney, E., et al. Challenges and standards in integrating surveys of structural variation. Nature Genet. 39, S7-S15 (2006).
23. Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951 (2004).
24. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004).
25. Redon, R. et al. Global variation in copy number in the human genome. Nature 444,444–454 (2006).
26. Firth, H.V., Richards, S.M., Bevan, A.P., Clayton, S., Corpas, M., Rajan, D., Van Vooren, S., Moreau, Y., Pettett, R.M., Carter, N.P. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am. J. Hum. Genet.84, 524-533 (2009).
27. Ouahchi, K., Lindeman, N., Lee, C. Copy number variants and pharmacogenomics Pharmacogenomics 7, 25-29 (2006).
28. McCarroll , S.A., Hadnott, T.N., Perry, G.H., Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86-92 (2006).
29. Database of Genomic Variants -
30. Gonzalez, E., Kulkarni, H., Bolivar, H. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility.Science 307, 1434 -1440 (2005).
31. Kishawi, I. Agilent array technology and custom capabilities. [Internet] Agilent Technologies, published in 2008. Available from:
32. International Human Genome Sequencing Consortium. Initial sequencing andanalysis of the human genome. Nature 15, 860-921 (2001).
33. Bignell GR, Huang J, Greshock J et al: High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 14, 287-295 2004
34. Lucito, R. Et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res.13, 2291-2305 (2003).
35. LeProust, E. Agilent’s microarray platform: How high-fidelity DNA synthesis maximizes the dynamic range of gene expression measurements. [Internet] Agilent Technologies, published in 2008. Available from:…
36.  SurePrint technology. [Internet] Agilent technologies, updated in 2009. Available from:…
37.  Branham, W.S., Melvin, C.D., Han, T. et al. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements BMC Biotechnology 7, 8 (2007).
38. OG-500 Donor instructions.[Internet] DNA Genotek, updated in 2009. Available from…
39. Using saliva sponges to collect DNA samples from infants & young children. [Internet] DNA Genotek, published in 2006. Available from:…
40. Comparison of DNA purified with Oragene DNA and the QIAamp™ Mini Kit. [Internet] DNA Genotek, published in 2004. Available from:
41. Oragene™ DNA Self-Collection Kit. The new “gold standard” for DNA collection, stabilization and preparation.[Internet] DNA Genotek, published in 2008 Available from:…
42. International HapMap Consortium. The International HapMap Project.Nature 426, 789-96 (2003).
43. Cohen, J. Statistical power analysis for the behavioral sciences (2nd ed.). (1988). 
44. Finkelstein D, et al. Microarray data quality analysis: lessons from the AFGC project. Plant. Mol. Biol. 48, 119–131 (2002).
45. Dudoit, S., Yang, Y. H, Speed, T. P., Callow, M. J. Statistical methods for
identifying differentially expressed genes in replicated cDNA microarray experiments.
Statistica Sinica 12, 111-140 (2002).

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