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PMID: 17267813 Published · ppublish English Comparative Study Journal Article

High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays.

Genome research ·Vol. 17 ·No. 3 ·2007-03-00 ·Pages 368-76

Oosting J, Lips EH, van Eijk R, Eilers PH, Szuhai K, Wijmenga C, Morreau H, van Wezel T

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.

MeSH Terms
Chromosome Mapping/methods Colorectal Neoplasms/genetics Evaluation Studies as Topic Female Gene Dosage/genetics Humans Loss of Heterozygosity/genetics Male Microarray Analysis/methods Microspheres Paraffin Embedding Polymorphism, Single Nucleotide Reproducibility of Results Sex Chromosomes/genetics Tissue Preservation
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Oosting Jan
Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands. [email protected]
Lips Esther H
van Eijk Ronald
Eilers Paul H C
Szuhai Károly
Wijmenga Cisca
Morreau Hans
van Wezel Tom
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.5686107
Email
[email protected]
Published
2007-03-00
Epub
2007-00-31
Pages
368-76
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1800928
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.5686107 PMC Full Text View journal details
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