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SNP arrays from FFPE

Monday 28 November 2011

Chromosomal imbalances are commonly seen in cancer and inherited genetic diseases. These imbalances may assist in the diagnosis, prognosis, and/or therapeutic management of certain neoplasms.

Several methods for detecting chromosomal imbalances, such as, fluorescent in situ hybridization, array comparative genomic hybridization, and single nucleotide polymorphism (SNP) arrays have proven useful in formalin-fixed paraffin-embedded (FFPE) tissues.

It has been reported the performance and reproducibility of virtual karyotyping of FFPE tissues with Affymetrix SNP arrays.

SNP arrays are a reliable, reproducible, and robust platform for the virtual karyotyping of FFPE tumor tissues with performance characteristics adequate for clinical application. Parameters that most significantly affected sample performance were sample age and storage conditions.


- Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues. Alvarez K, Kash SF, Lyons-Weiler MA, Kim HJ, Peterson LE, Mathai B, Hagenkord JM, Monzon FA. Diagn Mol Pathol. 2010 Sep;19(3):127-34. PMID: 20736741

- High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Oosting J, Lips EH, van Eijk R, Eilers PH, Szuhai K, Wijmenga C, Morreau H, van Wezel T. Genome Res. 2007 Mar;17(3):368-76. PMID: 17267813