Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells

Laboratory Investigation

Volumn 86, Issue 9, 2006, Pages 968-978

  Johnson, Nicola A ^a   Hamoudi, Rifat A ^a   Ichimura, Koichi ^a   Liu, Lu ^a   Pearson, Danita M ^a   Collins, V Peter ^a   Du, Ming Qing ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Archival fixed tissue; Array CGH; Astrocytic tumour; Microdissection; Whole genome amplification

Indexed keywords

DNA; DNA FRAGMENT; FORMALDEHYDE; HEMATOXYLIN; PARAFFIN;

ARTICLE; ASTROCYTE; CARCINOMA IN SITU; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENE AMPLIFICATION; GENOMICS; HISTOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; MICRODISSECTION; NECROSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TUMOR CELL;

ASTROCYTOMA; BIOLOGICAL SPECIMEN BANKS; DNA, NEOPLASM; FORMALDEHYDE; HUMANS; MICRODISSECTION; NECROSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; REPRODUCIBILITY OF RESULTS; TIME FACTORS; TISSUE PRESERVATION; TUMOR MARKERS, BIOLOGICAL;

EID: 33747622065     PISSN: 00236837     EISSN: 15300307     Source Type: Journal    
DOI: 10.1038/labinvest.3700441     Document Type: Article

References (18)

1. Ishkanian AS, Malloff CA, Watson SK, et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004;36:299-303.
2. Fiegler H, Carr P, Douglas EJ, et al. DNA microarrays for comparative genomic hybridisation based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003;36:361-374.
3. Seng TJ, Ichimura K, Liu L, et al. Complex chromosome 22 rearrangements in astrocytic tumors identified using microsatellite and chromosome 22 tile path array analysis. Genes Chromosomes Cancer 2005;43:181-193.
4. Ichimura K, Mungall AJ, Fiegler H, et al. Small regions of overlapping deletions on 6q26 in human astrocytic tumors identified using chromosome 6 tile path array-CGH. Oncogene 2006;25:1261-1271.
5. Gribble SM, Fiegler H, Burford DC, et al. Applications of combined DNA microarray and chromosome sorting technologies. Chromosome Res 2004;12:35-43.
6. Nessling M, Richter K, Schwaenen C, et al. Candidate genes in breast cancer revealed by microarray-based comparative genomic hybridization of archived tissue. Cancer Res 2005;65:439-447.
7. Harvell JD, Kohler S, Zhu S, et al. High-resolution array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas. Diagnost Mol Pathol 2004;13:22-25.
8. Ried T, Just K, Holtgreve-Grez H, et al. 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 1995;55:5415-5423.
9. Loo LWM, Grove DI, Williams EM, et al. Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 2004;64:8541-8549.
10. Bredel M, Bredel C, Juric D, et al. Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J Mol Diagn 2005;7:171-182.
11. Little SE, Vuononvirta R, Reis-Filho JS, et al. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics 2006;87:298-306.
12. Liu D, Liu C, DeVries S, et al. LM-PCR permits highly representative whole genome amplification of DNA isolated from small number of cells and paraffin-embedded tumor tissue sections. Diagnost Mol Pathol 2004;13:105-115.
13. Ichimura K, Schmidt EE, Goike HM, et al. Human glioblastomas with no alterations of the CDKN2A (p16INK4A, MTS1) and CDK4 genes have frequent mutations of the retinoblastoma gene. Oncogene 1996;13:1065-1072.
14. van Dongen JJ, Langerak AW, Bruggeman M, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 2003;17:2257-2317.
15. McCabe MG, Ichimura K, Liu L, et al. High resolution array-based comparative genomic hybridisation of medulloblastomas and supra-tentorial primitive neuro-ectodermal tumors. J Neuropathol Exp Neurol 2006 (in press).
16. Chen W, Houldsworth J, Olshen AB, et al. Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas. Blood 2005;107:2477-2485.
17. R Development Core Team. R: A language and environment for statistical computing. R Foundation for statistical computing: Vienna, Austria.
18. Liu J, Zabarovska VI, Braga E, et al. Loss of heterozygosity in tumor cells requires re-evaluation: the data are biased by the size-dependent differential sensitivity of allele detection. FEBS Lett 1999;462:121-128.