Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms

The performance of a silica chip-based resequencing method, the Affymetrix HN PRT 440 assay (hereafter referred to as the Affymetrix assay), was evalu ated on a panel of well-characterized nonclade B viral isolates and on isol ates exhibiting length polymorphisms, Sequencing of human immunodeficiency virus type 1 (HIV-1) pol cDNAs from clades A, C, D, E, and F resulted in cl ade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spu rious resistance polymorphisms. The Affymetrix assay failed to detect the p resence of additional serine codons distal to reverse transcriptase (RT) co don 68 that are associated with multinucleoside RT inhibitor resistance. Th e increasing prevalence of non-clade B HIV-1 strains in the United States a nd Europe and the identification of clinically relevant pol gene length pol ymorphisms will impact the generalizability of the Affymetrix assay, emphas izing the need to accommodate this expanding pool of pol genotypes in futur e assay versions.