Whole-genome single nucleotide polymorphism array analysis is complementary to classical cytogenetic analysis in the evaluation of lymphoid proliferations

Objectives: To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. Methods: Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA). Results: Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. Conclusions: The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.