DNA quality assessment for array CGH by isothermal whole genome amplification

Cellular Oncology

Volumn 29, Issue 4, 2007, Pages 351-359

  Buffart, Tineke E ^a   Tijssen, Marianne ^a   Krugers, Thijs ^a   Carvalho, Beatriz ^a   Smeets, Serge J ^a   Brakenhoff, Ruud H ^a   Grabsch, Heike ^b   Meijer, Gerrit A ^a   Sadowski, Henry B ^c   Ylstra, Bauke ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c Enzo Life Sciences Inc   (United States)

Author keywords

Array CGH; DNA quality; FFPE; Isothermal amplification

Indexed keywords

DNA; FORMALDEHYDE;

ARRAY COMPARATIVE GENOMIC HYBRIDIZATION; ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; DNA DETERMINATION; DNA HYBRIDIZATION; FROZEN SECTION; GENE AMPLIFICATION; HISTOLOGY; HUMAN; HUMAN CELL; ISOTHERM; PALATE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STOMACH CANCER;

DNA; GENOME, HUMAN; HUMANS; NEOPLASMS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; PARAFFIN EMBEDDING; TISSUE FIXATION;

EID: 34447136841     PISSN: 15705870     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (19)

1. D.G. Albertson and D. Pinkel, Genomic microarrays in human genetic disease and cancer, Hum. Mol. Genet. 12(Spec No. 2) (2003), R145-R152.
2. M.T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P.S. Meltzer, Z. Yakhini, L. Bruhn and S. Laderman, Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA, Proc. Natl. Acad. Sci. USA 101 (2004), 17765-17770.
3. T. Buffart, B. Carvalho, E. Hopmans, V. Brehm, E. Klein Kranenbarg, T. Schaaij-Visser, P. Eijk, N. van Grieken, B. Ylstra, C.J. van de Velde and G. Meijer, Gastric cancers in young and elderly patients show different genomic profiles, J. Pathol. 211 (2007), 45-51.
4. B. Carvalho, T.E. Buffart, R.M. Reis, T. Mons, C. Moutinho, P. Silva, N.C. van Grieken, H. Grabsch, C.J.H. van de Velde, B. Ylstra, G.A. Meijer and F. Carneiro, Mixed gastric carcinomas show similar chromosomal aberrations in both their diffuse and glandular components, Cell Oncol. 28 (2006), 283-294.
5. S. Devries, S. Nyante, J. Korkola, R. Segraves, K. Nakao, D. Moore, H. Bae, M. Wilhelm, S. Hwang and F. Waldman, Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors, J. Mol. Diagn. 7 (2005), 65-71.
6. J. Fridlyand, A.M. Snijders, B. Ylstra, H. Li, A. Olshen, R. Segraves, S. Dairkee, T. Tokuyasu, B.M. Ljung, A.N. Jain, J. McLennan, J. Ziegler, K. Chin, S. Devries, H. Feiler, J.W. Gray, F. Waldman, D. Pinkel and D.G. Albertson, Breast tumor copy number aberration phenotypes and genomic instability, BMC Cancer 6 (2006), 96.
7. B. Fritz, F. Schubert, G. Wrobel, C. Schwaenen, S. Wessendorf, M. Nessling, C. Korz, R.J. Rieker, K. Montgomery, R. Kucherlapati, G. Mechtersheimer, R. Eils, S. Joos and P. Lichter, Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma, Cancer Res. 62 (2002), 2993-2998.
8. K. Jong, E. Marchiori, G. Meijer, A.V. Vaart and B. Ylstra, Breakpoint identification and smoothing of array comparative genomic hybridization data, Bioinformatics 20 (2004), 3636-3637.
9. D. Pinkel and D.G. Albertson, Array comparative genomic hybridization and its applications in cancer, Nat. Genet. 37(Suppl.) (2005), S11-S17.
10. T. Ried, K.E. Just, H. Holtgreve-Grez, S. du Manoir, M.R. Speicher, E. Schrock, C. Latham, H. Blegen, A. Zetterberg, T. Cremer and G. Auer, Comparative genomic hybridization of formalin-fixed, paraffin-embedded breast tumors reveals different patterns of chromosomal gains and losses in fibroadenomas and diploid and aneuploid carcinomas, Cancer Res. 55 (1995), 5415-5423.
11. M.W. Schreurs, M.A. Hermsen, R.I. Geltink, K.B. Scholten, A.A. Brink, E.W. Kueter, M. Tijssen, C.J. Meijer, B. Ylstra, G.A. Meijer and E. Hooijberg, Genomic stability and functional activity may be lost in telomerase-transduced human CD8+ T lymphocytes, Blood 106 (2005), 2663-2670.
12. M.P. Tabor, R.H. Brakenhoff, V.M.M. van Houten, J.A. Kummer, M.H. Snel, P.J. Snijders, G.B. Snow, C.R. Leemans and B.J. Braakhuis, Persistence of genetically altered fields in head and neck cancer patients: biological and clinical implications, Clin. Cancer Res. 7 (2001), 1523-1532.
13. E.H. van Beers, S.A. Joosse, M.J. Ligtenberg, R. Fles, F.B. Hogervorst, S. Verhoef and P.M. Nederlof, A multiplex PCR predictor for aCGH success of FFPE samples, Br. J. Cancer 94 (2006), 333-337.
14. P. van den IJssel, M. Tijssen, S.F. Chin, P. Eijk, B. Carvalho, E. Hopmans, H. Holstege, D.K. Bangarusamy, J. Jonkers, G.A. Meijer, C. Caldas and B. Ylstra, Human and mouse oligonucleotide-based array CGH, Nucleic Acids Res. 33 (2005), e192.
15. M.M. Weiss, E.J. Kuipers, C. Postma, A.M. Snijders, D. Pinkel, S.G. Meuwissen, D. Albertson and G.A. Meijer, Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival, Cell Oncol. 26 (2004), 307-317.
16. M.M. Weiss, E.J. Kuipers, C. Postma, A.M. Snijders, I. Siccama, D. Pinkel, J. Westerga, S.G. Meuwissen, D.G. Albertson and G.A. Meijer, Genomic profiling of gastric cancer predicts lymph node status and survival, Oncogene 22 (2003), 1872-1879.
17. M.M. Weiss, M.A. Hermsen, G.A. Meijer, N.C. van Grieken, J.P. Baak, E.J. Kuipers and P.J. van Diest, Comparative genomic hybridization, Mol. Pathol. 52 (1999), 243-251.
18. M. Wilhelm, J.A. Veltman, A.B. Olshen, A.N. Jain, D.H. Moore, J.C. Presti, Jr., G. Kovacs and F.M. Waldman, Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer, Cancer Res. 62 (2002), 957-960.
19. B. Ylstra, P. van den IJssel, B. Carvalho, R.H. Brakenhoff and G.A. Meijer, BAC to the future! or oligonucleotides: A perspective for micro array comparative genomic hybridization (array CGH), Nucleic Acids Res. 34 (2006), 445-450.