High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.
Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.
Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.
Yan P
YP
Yu
Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.
Amantha
A
Michalopoulos
Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.
Ying
Y
Ding
Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.
George
G
Tseng
Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.
Jian-Hua
JH
Luo
D002869:Chromosome Aberrations; D056915:DNA Copy Number Variations / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics; D005557:Formaldehyde / Q000737:chemistry*; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008223:Lymphoma / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding / Q000379:methods*; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D016707:Tissue Fixation; D015534:Trans-Activators / Q000235:genetics
C486381:CITED2 protein, human; D004273:DNA, Neoplasm; D012097:Repressor Proteins; D015534:Trans-Activators; D005557:Formaldehyde; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf