Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis

Laboratory Investigation

Volumn 93, Issue 6, 2013, Pages 701-710

  Hosein, Abdel Nasser ^a   Song, Sarah ^b,c   McCart Reed, Amy E ^c   Jayanthan, Janani ^c   Reid, Lynne E ^c   Kutasovic, Jamie R ^c   Cummings, Margaret C ^c,d   Waddell, Nic ^b   Lakhani, Sunil R ^b,c,d   Chenevix Trench, Georgia ^a   Simpson, Peter T ^c  

^a QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d ROYAL BRISBANE AND WOMEN'S HOSPITAL   (Australia)

Author keywords

array CGH; breast cancer; DNA copy number alterations; DNA restoration; formalin fixed, paraffin embedded tissue; SNP array

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FORMALDEHYDE; PARAFFIN;

ALLELE; ARTICLE; AUTOPSY; CANCER TISSUE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA DAMAGE; DNA EXTRACTION; DNA REPAIR; DNA STRAND BREAKAGE; GENE; GENE AMPLIFICATION; GENE DOSAGE; GENE LOCUS; GENE MAPPING; HETEROZYGOTE; HOMOZYGOTE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

BREAST NEOPLASMS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA; DNA COPY NUMBER VARIATIONS; FEMALE; FIXATIVES; FORMALDEHYDE; HUMANS; PARAFFIN EMBEDDING; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN; TISSUE BANKS;

EID: 84878599846     PISSN: 00236837     EISSN: 15300307     Source Type: Journal    
DOI: 10.1038/labinvest.2013.54     Document Type: Article

References (35)

1. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818-821.
2. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005;37(Suppl):S11-S17.
3. Devries S, Nyante S, Korkola J, et al. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J Mol Diagn 2005;7:65-71.
4. Loo LW, Grove DI, Williams EM, et al. Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 2004;64:8541-8549.
5. Simpson PT, Reis-Filho JS, Lambros MB, et al. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas. J Pathol 2008;215:231-244.
6. Natrajan R, Lambros MB, Rodriguez-Pinilla SM, et al. Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin Cancer Res 2009;15:2711-2722.
7. Wicker N, Carles A, Mills IG, et al. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 2007;8:84.
8. Curtis C, Lynch AG, Dunning MJ, et al. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 2009;10:588.
9. Coe BP, Ylstra B, Carvalho B, et al. Resolving the resolution of array CGH. Genomics 2007;89:647-653.
10. Halper-Stromberg E, Frelin L, Ruczinski I, et al. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics 2011;27:1052-1060.
11. TCGA. Comprehensive molecular portraits of human breast tumors. Nature 2012;490:61-70.
12. Curtis C, Shah SP, Chin SF, et al. The genomic and transcriptomic architecture of 2,000 breast tumors reveals novel subgroups. Nature 2012;486:346-352.
13. Stephens PJ, Tarpey PS, Davies H, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 2012;486:400-404.
14. Thompson ER, Herbert SC, Forrest SM, et al. Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat 2005;26:384-389.
15. Jacobs S, Thompson ER, Nannya Y, et al. Genome-wide, highresolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Res 2007;67:2544-2551.
16. Tuefferd M, De Bondt A, Van Den Wyngaert I, et al. Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays. Genes Chromosomes Cancer 2008; 47:957-964.
17. Lips EH, Dierssen JW, van Eijk R, et al. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. Cancer Res 2005;65:10188-10191.
18. Oosting J, Lips EH, van Eijk R, et al. High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Res 2007;17:368-376.
19. Alvarez K, Kash SF, Lyons-Weiler MA, et al. Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffinembedded tissues. Diagn Mol Pathol 2010;19:127-134.
20. Nasri S, Anjomshoaa A, Song S, et al. Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. Cancer Genet Cytogenet 2010;198:1-6.
21. Hostetter G, Kim SY, Savage S, et al. Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Nucleic Acids Res 2010;38:e9.
22. van Beers EH, Joosse SA, Ligtenberg MJ, et al. A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 2006;94: 333-337.
23. Johnson CE, Gorringe KL, Thompson ER, et al. Identification of copy number alterations associated with the progression of DCIS to invasive ductal carcinoma. Breast Cancer Res Treat 2012;133: 889-898.
24. Krijgsman O, Israeli D, Haan JC, et al. CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosomes Cancer 2012;51:344-352.
25. Sun W, Wright FA, Tang Z, et al. Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res 2009;37:5365-5377.
26. Simpson PT, Gale T, Reis-Filho JS, et al. Columnar cell lesions of the breast: the missing link in breast cancer progression? A morphological and molecular analysis. Am J Surg Pathol 2005;29:734-746.
27. Hu Z, Fan C, Oh DS, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006;7:96.
28. Wood HM, Belvedere O, Conway C, et al. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 2010;38:e151.
29. Song S, Nones K, Miller D, et al. qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PloS ONE 2012;7:e45835.
30. Waddell N, Arnold J, Cocciardi S, et al. Subtypes of familial breast tumors revealed by expression and copy number profiling. Breast Cancer Res Treat 2010;123:661-677.
31. Jonsson G, Staaf J, Vallon-Christersson J, et al. The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer. Cancer Res 2012;72:4028-4036.
32. Schweiger MR, Kerick M, Timmermann B, et al. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutationanalysis. PloS ONE 2009;4:e5548.
33. Yost SE, Smith EN, Schwab RB, et al. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res 2012;40:e107.
34. Kerick M, Isau M, Timmermann B, et al. Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics 2011;4:68.
35. Lipson D, Capelletti M, Yelensky R, et al. Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies. Nat Med 2012;18:382-384.