Affymetrix 250K SNP Array

Overview

The Affymetrix 250K SNP Array is a high-density oligonucleotide microarray platform that simultaneously genotypes ~250,000 single nucleotide polymorphisms (SNPs) across the genome. It is used for genome-wide somatic copy-number alteration (SCNA) profiling and loss-of-heterozygosity (LOH) analysis in tumor samples.

Used by

• Used to profile somatic copy-number alterations (n=207 samples) and LOH (n=200 samples) across seven high-grade soft tissue sarcoma subtypes; data analyzed with GISTIC and RAE to identify significantly altered regions PMID:20601955.
• Applied to 383 primary LUAD tumours (Affymetrix 250K StyI chip) for genome-wide somatic copy-number alteration profiling, supporting discovery of copy-number changes associated with EGFR, KRAS, and TP53 mutations PMID:18948947.
• Used on 22 ESCC tumors (18 from Discovery Cohort) for somatic copy-number variation (SCNV) analysis; combined with array-CGH and three public SNP-array datasets for a total of 184 analyzable primary ESCC samples PMID:24686850

Notes

• Raw data from the sarcoma study deposited in NCBI GEO under accession GSE21124 PMID:20601955.
• Copy-number profiling revealed ~90% frequency of chromosome 12q amplification in dedifferentiated liposarcoma (DDLS) and complex karyotypes in DDLS, PLLS, LMS, and MFS PMID:20601955.

Sources

• PMID:20601955
• PMID:18948947

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