Premium
Unlocking the Archives: Genomic Analysis of Formalin‐Fixed Paraffin Embedded Tissue
Author(s) -
Monzon Federico Alberto,
Alvarez Karla,
LyonsWeiler Maureen A,
Kash Shera,
Kim HyunJung,
Hagenkord Jill M
Publication year - 2009
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.23.1_supplement.72.1
Subject(s) - snp array , biology , karyotype , snp , dna microarray , tissue microarray , dna extraction , comparative genomic hybridization , computational biology , microbiology and biotechnology , genetics , single nucleotide polymorphism , chromosome , genotype , polymerase chain reaction , gene , gene expression , cancer
Background Virtual karyotypes derived from SNP microarrays can be performed on formalin‐fixed paraffin embedded (FFPE) tissue samples. Methods 284 archival FFPE human tissue samples (tumor and normal) were processed to obtain virtual karyotypes with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays. Tissue was macro‐dissected from 10µm sections and DNA extraction was performed. Data analysis was performed with the CNAG 3.0 software. Results 226 samples (79.6%) yielded adequate virtual karyotypes for interpretation. Importantly, 43% of failed samples belong to one specific source where tissue blocks were subject to extreme temperature variation. Parameters for selecting samples for hybridization based on PCR product size range for the 10K 2.0 arrays were developed which obtained 80‐90% success rate on hybridizations. 37 samples were repeated (2 to 4 times) and in all instances results from all successful repeats from one sample showed identical virtual karyotypes. In 15 samples two or more tumor regions were assayed separately and in 53% of these, tumor heterogeneity in chromosomal imbalances was observed. Conclusion Virtual karyotyping with SNP microarrays is a robust technique that shows good performance and excellent reproducibility when applied to the analysis of FFPE tissues.