High-resolution Copy Number Analysis of Paraffin-embedded Archival Tissue Using SNP BeadArrays

Overview

Journal Genome Res

Specialty Genetics

Date 2007 Feb 3

PMID 17267813

Citations 28

Authors

Jan Oosting

Esther H Lips

Ronald van Eijk

Paul H C Eilers

Karoly Szuhai

Cisca Wijmenga

Hans Morreau

Tom van Wezel

Affiliations

Soon will be listed here.

Abstract

High-density SNP microarrays provide insight into the genomic events that occur in diseases like cancer through their capability to measure both LOH and genomic copy numbers. Where currently available methods are restricted to the use of fresh frozen tissue, we now describe the design and validation of copy number measurements using the Illumina BeadArray platform and the application of this technique to formalin-fixed, paraffin-embedded (FFPE) tissue. In fresh frozen tissue from a set of colorectal tumors with numerous chromosomal aberrations, our method measures copy number patterns that are comparable to values from established platforms, like Affymetrix GeneChip and BAC array-CGH. Moreover, paired comparisons of fresh frozen and FFPE tissues showed nearly identical patterns of genomic change. We conclude that this method enables the use of paraffin-embedded material for research into both LOH and numerical chromosomal abnormalities. These findings make the large pathological archives available for genomic analysis, which could be especially relevant for hereditary disease where fresh material from affected relatives is rarely available.

Citing Articles

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Allelic Switching of , , and during Colorectal Cancer Tumorigenesis.

Boot A, Oosting J, Doorn S, Ouahoud S, Ventayol Garcia M, Ruano D Int J Genomics. 2019; 2019:1287671.

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Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies.

Carlsson J, Davidsson S, Fridfeldt J, Giunchi F, Fiano V, Grasso C BMC Med Res Methodol. 2018; 18(1):161.

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Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

Iddawela M, Rueda O, Eremin J, Eremin O, Cowley J, Earl H BMC Genomics. 2017; 18(1):526.

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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.

Zhang P, Lehmann B, Shyr Y, Guo Y Int J Genomics. 2017; 2017:1926304.

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