High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Salawu, Abdulazeez ^a   Ul Hassan, Aliya ^a   Hammond, David ^a   Fernando, Malee ^b   Reed, Malcolm ^a   Sisley, Karen ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b ROYAL HALLAMSHIRE HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE; PARAFFIN;

ARTICLE; CANCER CELL CULTURE; CHEMICAL LABELING; CLINICAL PROTOCOL; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA DEGRADATION; DNA DETERMINATION; DNA MICROARRAY; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DOSAGE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; LEIOMYOSARCOMA; MOLECULAR WEIGHT; PROCESS OPTIMIZATION; TISSUE CHARACTERIZATION; UNIVERSAL LINKAGE SYSTEM LABELLING;

ALGORITHMS; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; DNA; ELECTROPHORESIS, AGAR GEL; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC TECHNIQUES; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; LEIOMYOSARCOMA; MODELS, GENETIC; PARAFFIN; REPRODUCIBILITY OF RESULTS; RETROSPECTIVE STUDIES; SPECIMEN HANDLING;

EID: 84870531863     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050415     Document Type: Article

References (29)

1. Hanahan D, Weinberg RA, (2011) Hallmarks of cancer: the next generation. Cell 144: 646-674.
2. Taylor BS, Barretina J, Maki RG, Antonescu CR, Singer S, et al. (2011) Advances in sarcoma genomics and new therapeutic targets. Nature Reviews Cancer 11: 541-557.
3. Kwek SS, Roy R, Zhou H, Climent J, Martinez-Climent JA, et al. (2009) Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis. Oncogene 28: 1892-1903.
4. Italiano A, Bianchini L, Keslair F, Bonnafous S, Cardot-Leccia N, et al. (2008) HMGA2 is the partner of MDM2 in well-differentiated and dedifferentiated liposarcomas whereas CDK4 belongs to a distinct inconsistent amplicon. Int J Cancer 122: 2233-2241.
5. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, et al. (2004) Comparative genomic hybridisation using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A 101: 17765-17770.
6. Tan DSP, Lambros MBK, Natrajan R, Reis-Filho JS, (2007) Getting it right: designing microarray (and not 'microawry') comparative genomic hybridisation studies for cancer research. Laboratory Investigation 87: 737-754.
7. Srinivasan M, Sedmak D, Jewell S, (2002) Effect of Fixatives and Tissue Processing on the Content and Integrity of Nucleic Acids. The American Journal of Pathology 161: 1961-1971.
8. van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FBL, et al. (2005) A multiplex PCR predictor for aCGH success of FFPE samples. British Journal of Cancer 94: 333-337.
9. Mc Sherry EA, Mc Goldrick A, Kay EW, Hopkins AM, Gallagher WM, et al. (2007) Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles. Clin Genet 72: 441-447.
10. Alers JC, Rochat J, Krijtenburg P-J, van Dekken H, Raap AK, et al. (1999) Universal linkage system: An improved method for labelling archival DNA for comparative genomic hybridisation. Genes, Chromosomes and Cancer 25: 301-305.
11. Hostetter G, Kim SY, Savage S, Gooden GC, Barrett M, et al. (2010) Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Nucleic Acids Research 38: e9.
12. Szponar A, Yusenko MV, Kovacs G, (2010) High-resolution array CGH of metanephric adenomas: lack of DNA copy number changes. Histopathology 56: 212-216.
13. Chen Z, Liu Z, Li W, Qu K, Deng X, et al. (2011) Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer. Genes Chromosomes Cancer 50: 689-699.
14. Rossi E, Klersy C, Manca R, Zuffardi O, Solcia E, (2011) Correlation between genomic alterations assessed by array comparative genomic hybridisation, prognostically informative histologic subtype, stage, and patient survival in gastric cancer. Hum Pathol 42: 1937-1945.
15. Oikawa M, Yoshiura K, Kondo H, Miura S, Nagayasu T, et al. (2011) Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridisation. Radiat Oncol 6: 168.
16. Braggio E, McPhail ER, Macon W, Lopes MB, Schiff D, et al. (2011) Primary Central Nervous System Lymphomas: A Validation Study of Array-Based Comparative Genomic Hybridisation in Formalin-Fixed Paraffin-Embedded Tumor Specimens. Clinical Cancer Research 17: 4245-4253.
17. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104: 20007-20012.
18. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
19. Ul-Hassan A, Sisley K, Hughes D, Hammond DW, Robinson MH, et al. (2009) Common genetic changes in leiomyosarcoma and gastrointestinal stromal tumour: implication for ataxia telangiectasia mutated involvement. International Journal of Experimental Pathology 90: 549-557.
20. The Cancer Genome Atlas, (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
21. Mankoo PK, Shen R, Schultz N, Levine DA, Sander C, (2011) Time to Recurrence and Survival in Serous Ovarian Tumors Predicted from Integrated Genomic Profiles. PLoS ONE 6: e24709.
22. de Jong D, Verbeke S, Meijer D, Hogendoorn P, Bovee J, et al. (2011) Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples. BMC Research Notes 4: 1.
23. Hirsch D, Camps J, Varma S, Kemmerling R, Stapleton M, et al. (2012) A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps. Genes Chromosomes Cancer 51: 490-500.
24. Derre J, Lagace R, Nicolas A, Mairal A, Chibon F, et al. (2001) Leiomyosarcomas and most malignant fibrous histiocytomas share very similar comparative genomic hybridisation imbalances: an analysis of a series of 27 leiomyosarcomas. Lab Invest 81: 211-215.
25. Ylipää A, Hunt KK, Yang J, Lazar AJF, Torres KE, et al. (2011) Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors. Cancer 117: 308-309.
26. Hu J, Rao UNM, Jasani S, Khanna V, Yaw K, et al. (2005) Loss of DNA copy number of 10q is associated with aggressive behavior of leiomyosarcomas: A comparative genomic hybridisation study. Cancer Genetics and Cytogenetics 161: 20-27.
27. Larramendy ML, Kaur S, Svarvar C, Böhling T, Knuutila S, (2006) Gene copy number profiling of soft-tissue leiomyosarcomas by array-comparative genomic hybridisation. Cancer Genetics and Cytogenetics 169: 94-101.
28. Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, et al. (2010) Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet.
29. Perot G, Derre J, Coindre JM, Tirode F, Lucchesi C, et al. (2009) Strong smooth muscle differentiation is dependent on myocardin gene amplification in most human retroperitoneal leiomyosarcomas. Cancer Res 69: 2269-2278.