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High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using affymetrix cytoscan HD chip

Yu, YP and Michalopoulos, A and Ding, Y and Tseng, G and Luo, JH (2014) High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using affymetrix cytoscan HD chip. PLoS ONE, 9 (4).

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Abstract

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. © 2014 Yu et al.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Yu, YPypyu@pitt.eduYPYU
Michalopoulos, A
Ding, Y
Tseng, G
Luo, JHLUOJH@pitt.eduLUOJH
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorFranco, RenatoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 3 April 2014
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 9
Number: 4
DOI or Unique Handle: 10.1371/journal.pone.0092820
Schools and Programs: Dietrich School of Arts and Sciences > Statistics
School of Medicine > Pathology
Refereed: Yes
Date Deposited: 30 Jun 2014 15:43
Last Modified: 31 Jul 2020 15:55
URI: http://d-scholarship.pitt.edu/id/eprint/21968

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