CGH array from FFPE

Open Access References

 Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis. Panzeri E, Conconi D, Antolini L, Redaelli S, Valsecchi MG, Bovo G, Pallotti F, Viganò P, Strada G, Dalprà L, Bentivegna A. PLoS One. 2011;6(9):e24237. PMID: 21909424 [Free] (Italy)

 DNA extraction from paraffin embedded material for genetic and epigenetic analyses. Pikor LA, Enfield KS, Cameron H, Lam WL. J Vis Exp. 2011 Mar 26;(49). PMID: 21490570 [Free] (Canada)

 Microarray-based CGH and copy number analysis of FFPE samples. Al-Mulla F. Methods Mol Biol. 2011;724:131-45. PMID: 21370011 (Koweit)

 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. de Jong D, Verbeke SLj, Meijer D, Hogendoorn PC, Bovee JV, Szuhai K. BMC Res Notes. 2011 Jan 4;4:1. PMID: 21205301 [Free] (Netherlands)

 Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity. Gunn S, Yeh IT, Lytvak I, Tirtorahardjo B, Dzidic N, Zadeh S, Kim J, McCaskill C, Lim L, Gorre M, Mohammed M. BMC Cancer. 2010 Jul 28;10:396. PMID: 20667129 [Free]

 Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Hostetter G, Kim SY, Savage S, Gooden GC, Barrett M, Zhang J, Alla L, Watanabe A, Einspahr J, Prasad A, Nickoloff BJ, Carpten J, Trent J, Alberts D, Bittner M. Nucleic Acids Res. 2010 Jan;38(2):e9. PMID: 19875416 [Free]

 Lennon PA, Zhuang Y, Pierson D, Zhang X, Williams C, Perez C, Lin P. Bacterial artificial chromosome array-based comparative genomic hybridization using paired formalin-fixed, paraffin-embedded and fresh frozen tissue specimens in multiple myeloma. Cancer. 2009;115:345–354. PMID: 19109814 (Free)

 High resolution oligonucleotide CGH using DNA from archived prostate tissue. Paris PL, Sridharan S, Scheffer A, Tsalenko A, Bruhn L, Collins C. Prostate. 2007 Sep 15;67(13):1447-55. PMID: 17654530 [Free]

 Limited tissue fixation times and whole genomic amplification do not impact array CGH profiles. Ghazani AA, Arneson NC, Warren K, Done SJ. J Clin Pathol. 2006 Mar;59(3):311-5. PMID: 16505285 [Free]

 High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schroder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H. Am J Pathol. 2003;162(3):763–770. (Free)

References

 Genomic aberrations in pediatric diffuse intrinsic pontine gliomas. Warren KE, Killian K, Suuriniemi M, Wang Y, Quezado M, Meltzer PS. Neuro Oncol. 2011 Nov 7. PMID: 22064882

 Homozygous loss of ADAM3A revealed by genome-wide analysis of pediatric high-grade glioma and diffuse intrinsic pontine gliomas. Barrow J, Adamowicz-Brice M, Cartmill M, MacArthur D, Lowe J, Robson K, Brundler MA, Walker DA, Coyle B, Grundy R. Neuro Oncol. 2011 Feb;13(2):212-22. PMID: 21138945

 Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for routine clinical use on formalin-fixed paraffin-embedded tissues. Lyons-Weiler M, Hagenkord J, Sciulli C, Dhir R, Monzon FA. Diagn Mol Pathol. 2008 Mar;17(1):3-13. PMID: 18303412

 Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles. Mc Sherry EA, Mc Goldrick A, Kay EW, Hopkins AM, Gallagher WM, Dervan PA. Clin Genet. 2007 Nov;72(5):441-7. PMID: 17935507

 Johnson NA, Hamoudi RA, Ichimura K, Liu L, Pearson DM, Collins VP, Du MQ. Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab. Invest. 2006;86:968–978. PMID: 16751780

 Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C. Genomics. 2006 Feb;87(2):298-306. PMID: 16271290

 Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C. Genomics. 2006 Feb;87(2):298-306. PMID: 16271290

 High-resolution cDNA microarray CGH mapping of genomic imbalances in osteosarcoma using formalin-fixed paraffin-embedded tissue. Zielenska M, Marrano P, Thorner P, Pei J, Beheshti B, Ho M, Bayani J, Liu Y, Sun BC, Squire JA, Hao XS. Cytogenet Genome Res. 2004;107(1-2):77-82. PMID: 15305059