OncoScan FFPE SNP Array

Overview

The Affymetrix OncoScan FFPE SNP array is a genome-wide copy-number and loss-of-heterozygosity (LOH) profiling platform optimised for formalin-fixed paraffin-embedded (FFPE) tumour material. It interrogates approximately 220,000 probes covering copy-number across the genome and roughly 900,000 SNP probes in cancer-relevant regions, enabling high-resolution allele-specific copy-number and LOH calls without a matched normal in many configurations.

Used by

• Applied via Affymetrix OncoScan FFPE SNP array to 15/16 NF2-loss unclassified renal cell carcinoma (uRCC) cases at MSKCC for genome-wide copy-number and LOH analysis, revealing 22q hemizygous loss and copy-neutral LOH as mechanisms of NF2 biallelic inactivation. PMID:27713405

Notes

• Designed for FFPE material where DNA quantity and quality are limiting; requires as little as 80 ng of DNA.
• Provides allele-specific copy-number information without a matched germline sample, though paired normal improves accuracy.
• Complementary to targeted panel sequencing (e.g., MSK-IMPACT) for detecting arm-level and focal copy-number alterations not captured by a gene panel alone.

Sources

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