Detection limits of DNA copy number alterations in heterogeneous cell populations

Cellular Oncology

Volumn 36, Issue 1, 2013, Pages 27-36

  Krijgsman, Oscar ^a   Israeli, Daniëlle ^a   Van Essen, Hendrik F ^a   Eijk, Paul P ^a   Berens, Michel L M ^b   Mellink, Clemens H M ^b   Nieuwint, Aggie W ^a   Weiss, Marjan M ^a   Steenbergen, Renske D M ^a   Meijer, Gerrit A ^a   Ylstra, Bauke ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b ACADEMIC MEDICAL CENTER   (Netherlands)

Author keywords

aCGH; Clinical genetics; Microarray; Mosaicism; Tumor heterogeneity

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; CELL POPULATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA ISOLATION; FEMALE; GENE DOSAGE; HUMAN; HUMAN CELL; INTELLECTUAL IMPAIRMENT; LIMIT OF DETECTION; MAJOR CLINICAL STUDY; MALE; MOSAICISM; PRIORITY JOURNAL; TUMOR CELL LINE;

BREAST NEOPLASMS; CELL LINE, TUMOR; CHROMOSOME ABERRATIONS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA; DNA COPY NUMBER VARIATIONS; FEMALE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INTELLECTUAL DISABILITY; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 84877072617     PISSN: 22113428     EISSN: 22113436     Source Type: Journal    
DOI: 10.1007/s13402-012-0108-2     Document Type: Article

References (38)

1. A.E. Oostlander, G.A. Meijer, B. Ylstra, Microarray-based comparative genomic hybridization and its applications in human genetics. Clin. Genet. 66, 488-495 (2004)
2. L.E. Vissers, B.B. de Vries, J.A. Veltman, Genomic microarrays in mental retardation: from copy number variation to gene, from research to diagnosis. J Med Genet. 47(5), 289-297 (2010)
3. D. Pinkel, D.G. Albertson, Array comparative genomic hybridization and its applications in cancer. Nat. Genet. 37(Suppl), S11-S17 (2005)
4. K. Wang, J. Li, S. Li, L. Bolund, C. Wiuf, Estimation of tumor heterogeneity using CGH array data. BMC Bioinforma. 10, 12 (2009)
5. C. Curtis, A.G. Lynch, M.J. Dunning, I. Spiteri, J.C. Marioni, J. Hadfield, S.F. Chin, J.D. Brenton, S. Tavaré, C. Caldas, The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics. 10, 588 (2009)
6. B.C. Ballif, E.A. Rorem, K. Sundin, M. Lincicum, S. Gaskin, J. Coppinger, C.D. Kashork, L.G. Shaffer, B.A. Bejjani, Detection of low-level mosaicism by array CGH in routine diagnostic specimens. Am J Med Genet Part A 140A, 2757-2767 (2006)
7. S.W. Cheung, C.A. Shaw, D.A. Scott, A. Patel, T. Sahoo, C.A. Bacino, A. Pursley, J. Li, R. Erickson, A.L. Gropman, D.T. Miller, M.R. Seashore, A.M. Summers, P. Stankiewicz, A.C. Chinault, J.R. Lupski, A.L. Beaudet, V.R. Sutton et al., Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics. Am J Med Genet Part A 143A, 1679-1686 (2007)
8. C. Garnis, B.P. Coe, S.L. Lam, C. MacAulay, W.L. Lam, High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics 85(6), 790-793 (2005)
9. N.A. Johnson, R.A. Hamoudi, K. Ichimura, L. Liu, D.M. Pearson, V.P. Collins, M.Q. Du, Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab Invest 86, 968-978 (2006)
10. J.R. Vermeesch, C. Melotte, G. Froyen, V.S. Van, B. Dutta, N. Maas, S. Vermeulen, B. Menten, F. Speleman, M.B. De, H.P. Van, P. Marynen, J.P. Fryns, K. Devriendt, Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J. Histochem. Cytochem. 53, 413-422 (2005)
11. B. Ylstra, P. van den Ijssel, B. Carvalho, R.H. Brakenhoff, G.A. Meijer, BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34(2), 445-450 (2006)
12. D. Pinto, K. Darvishi, X. Shi, D. Rajan, D. Rigler, T. Fitzgerald, A.C. Lionel, B. Thiruvahindrapuram, J.R. Macdonald, R. Mills, A. Prasad, K. Noonan, S. Gribble, E. Prigmore, P.K. Donahoe, R.S. Smith, J.H. Park, M.E. Hurles, N.P. Carter, C. Lee, S.W. Scherer, L. Feuk, Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat. Biotechnol. 29(6), 512-520 (2011)
13. J.R. González, B. Rodríguez-Santiago, A. Cáceres, R. Pique-Regi, N. Rothman, S.J. Chanock, L. Armengol, L.A. Pérez-Jurado, A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data. BMC Bioinforma. 12, 166 (2011)
14. S.A. Scott, N. Cohen, T. Brandt, G. Toruner, R.J. Desnick, L. Edelmann, Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med. 12(2), 85-92 (2010)
15. R. Valli, C. Marletta, B. Pressato, G. Montalbano, F. Lo Curto, F. Pasquali, E. Maserati, Comparative genomic hybridization on microarray (a-CGH) in constitutional and acquired mosaicism may detect as low as 8% abnormal cells. Mol. Cytogenet. 4, 13 (2011)
16. K. Szuhai, I. Jennes, D. de Jong, J.V. Bovée, M. Wiweger, W. Wuyts, P.C. Hogendoorn, Tiling resolution array-CGH shows that somatic mosaic deletion of the EXT gene is causative in EXT gene mutation negative multiple osteochondromas patients. Hum. Mutat. 32(2), E2036-E2049 (2011). doi: 10.1002/humu.21423
17. E.S. Venkatraman, A.B. Olshen, A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6), 657-663 (2007)
18. O. Krijgsman, D. Israeli, J.C. Haan, H.F. van Essen, S.J. Smeets, P.P. Eijk, M. Steenbergen RD, K. Kok, S. Tejpar, G.A. Meijer, B. Ylstra, CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Gene. Chromosome. Canc. 51(4), 344-352 (2012). doi: 10.1002/gcc.21920
19. T.E. Buffart, D. Israeli, M. Tijssen, S.J. Vosse, A. Mrsić, G.A. Meijer, B. Ylstra, Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations. Gene. Chromosome. Canc. 47(11), 994-1004 (2008)
20. K. Jong, E. Marchiori, A. van der Vaart, S.F. Chin, B. Carvalho, M. Tijssen, P.P. Eijk, P. van den Ijssel, H. Grabsch, P. Quirke, J.J. Oudejans, G.A. Meijer, C. Caldas, B. Ylstra, Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 26(10), 1499-1506 (2007)
21. D.J. Venter, S.J. Ramus, F.M. Hammet, M. de Silva, A.M. Hutchins, V. Petrovic, G. Price, J.E. Armes, Complex CGH alterations on chromosome arm 8p at candidate tumor suppressor gene loci in breast cancer cell lines. Canc. Genet. Cytogenet. 160(2), 134-140 (2005)
22. D. Pinkel, R. Segraves, D. Sudar, S. Clark, I. Poole, D. Kowbel, C. Collins, W.L. Kuo, C. Chen, Y. Zhai, S.H. Dairkee, B.M. Ljung, J.W. Gray, D.G. Albertson, High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20(2), 207-211 (1998)
23. M.A. van de Wiel, K.I. Kim, S.J. Vosse, W.N. van Wieringen, S.M. Wilting, B. Ylstra, CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23(7), 892-894 (2007)
24. B.P. Coe, B. Ylstra, B. Carvalho, G.A. Meijer, C. Macaulay, W.L. Lam, Resolving the resolution of array CGH. Genomics 89(5), 647-653 (2007)
25. N.P. Carter, Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet. 39(7 Suppl), S16-S21 (2007)
26. R. Beroukhim, C.H. Mermel, D. Porter, G. Wei, S. Raychaudhuri, J. Donovan, J. Barretina, J.S. Boehm, J. Dobson, M. Urashima, K.T. Mc Henry, R.M. Pinchback, A.H. Ligon, Y.J. Cho, L. Haery, H. Greulich, M. Reich, W. Winckler, M.S. Lawrence, B.A. Weir, K.E. Tanaka, D.Y. Chiang, A.J. Bass, A. Loo, C. Hoffman, J. Prensner, T. Liefeld, Q. Gao, D. Yecies, S. Signoretti, E. Maher, F.J. Kaye, H. Sasaki, J.E. Tepper, J.A. Fletcher, J. Tabernero, J. Baselga, M.S. Tsao, F. Demichelis, M.A. Rubin, P.A. Janne, M.J. Daly, C. Nucera, R.L. Levine, B.L. Ebert, S. Gabriel, A.K. Rustgi, C.R. Antonescu, M. Ladanyi, A. Letai, L.A. Garraway, M. Loda, D.G. Beer, L.D. True, A. Okamoto, S.L. Pomeroy, S. Singer, T.R. Golub, E.S. Lander, G. Getz, W.R. Sellers, M. Meyerson, The landscape of somatic copy-number alteration across human cancers. Nature 463(7283), 899-905 (2010)
27. R.J. Leary, J.C. Lin, J. Cummins, S. Boca, L.D. Wood, D.W. Parsons, S. Jones, T. Sjöblom, B.H. Park, R. Parsons, J. Willis, D. Dawson, J.K. Willson, T. Nikolskaya, Y. Nikolsky, L. Kopelovich, N. Papadopoulos, L.A. Pennacchio, T.L. Wang, S.D. Markowitz, G. Parmigiani, K.W. Kinzler, B. Vogelstein, V.E. Velculescu, Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc. Natl. Acad. Sci. U. S. A. 105(42), 16224-16229 (2008)
28. R. Redon, S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, T.D. Andrews, H. Fiegler, M.H. Shapero, A.R. Carson, W. Chen, E.K. Cho, S. Dallaire, J.L. Freeman, J.R. González, M. Gratacòs, J. Huang, D. Kalaitzopoulos, D. Komura, J.R. MacDonald, C.R. Marshall, R. Mei, L. Montgomery, K. Nishimura, K. Okamura, F. Shen, M.J. Somerville, J. Tchinda, A. Valsesia, C. Woodwark, F. Yang, J. Zhang, T. Zerjal, J. Zhang, L. Armengol, D.F. Conrad, X. Estivill, C. Tyler-Smith, N.P. Carter, H. Aburatani, C. Lee, K.W. Jones, S.W. Scherer, M.E. Hurles, Global variation in copy number in the human genome. Nature 444(7118), 444-454 (2006)
29. S.J. Smeets, U. Harjes, W.N. van Wieringen, D. Sie, R.H. Brakenhoff, G.A. Meijer, B. Ylstra, To DNA or not to DNA? That is the question, when it comes to molecular subtyping for the clinic!Clin. Cancer Res. 17(15), 4959-4964 (2011)
30. T.E. Buffart, B. Carvalho, T. Mons, R.M. Reis, C. Moutinho, P. Silva, N.C. van Grieken, M. Vieth, M. Stolte, C.J. van de Velde, E. Schrock, A. Matthaei, B. Ylstra, F. Carneiro, G.A. Meijer, DNA copy number profiles of gastric cancer precursor lesions. BMC Genomics. 8, 345 (2007)
31. X.Y. Goh, J.R. Rees, A.L. Paterson, S.F. Chin, J.C. Marioni, V. Save, M. O'Donovan, P.P. Eijk, D. Alderson, B. Ylstra, C. Caldas, R.C. Fitzgerald, Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma. Gut 60(10), 1317-1326 (2011)
32. H.F. van Essen, B. Ylstra, High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues. Meth. Mol. Biol. 838, 329-341 (2012)
33. O. De Wever, M. Mareel, Role of tissue stroma in cancer cell invasion. J. Pathol. 200(4), 429-447 (2003)
34. N.P. West, M. Dattani, P. McShane, G. Hutchins, J. Grabsch, W. Mueller, D. Treanor, P. Quirke, H. Grabsch, The proportion of tumour cells is an independent predictor for survival in colorectal cancer patients. Br. J. Cancer 102(10), 1519-1523 (2010)
35. W.E. Mesker, J.M. Junggeburt, K. Szuhai, P. de Heer, H. Morreau, H.J. Tanke, R.A. Tollenaar, The carcinoma-stromal ratio of colon carcinoma is an independent factor for survival compared to lymph node status and tumor stage. Cell. Oncol. 29(5), 387-398 (2007)
36. K. Tanaka, D. Yamamoto, M. Yamada, H. Okugawa, Influence of cellularity in human breast carcinoma. Breast 13(4), 334-340 (2004)
37. Y. Wu, H. Grabsch, T. Ivanova, I.B. Tan, J. Murray, C. H. Ooi, A. I. Wright, N. P. West, G. G. Hutchins, J. Wu, M. Lee, J. Lee, J. H. Koo, K. G. Yeoh, N. van Grieken, B. Ylstra, S. Y. Rha, J. A. Ajani, J.H. Cheong, S.H. Noh, K.H. Lim, A. Boussioutas, J.S. Lee, P. Tan. Comprehensive genomic meta-analysis identifies intra-tumoural stroma as a predictor of survival in patients with gastric cancer. Gut. (2012 Jun 26). [Epub ahead of print]
38. S.F. Chin, A.E. Teschendorff, J.C. Marioni, Y. Wang, N.L. Barbosa-Morais, N.P. Thorne, J.L. Costa, S.E. Pinder, M.A. van de Wiel, A.R. Green, I.O. Ellis, P.L. Porter, S. Tavaré, J.D. Brenton, B. Ylstra, C. Caldas, High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol. 8(10), R215 (2007)