Affymetrix this week launched its Axiom Custom Genotyping Arrays, the latest addition to its Axiom Genotyping platform.
Researchers can now use data in Affymetrix’s Axiom Genomic Database, which contains 7.4 million validated common and rare SNPs from the 1000 Genomes Project, the International HapMap Project, and other sources, to customize arrays containing 50,000 to 2.6 million SNPs. "This inherent flexibility allows researchers to conduct genome-wide association, replication, fine mapping, and candidate gene studies on a single platform," the company said in a statement.
"With more than 5 million validated SNPs, including more than 600,000 novel 1000 Genomes Project SNPs with a minor allele frequency (MAF) of less than 2.5 percent, the Axiom Genomic Database will enable researchers to study the role of rare variants in human disease by designing arrays with markers in specific MAF bins of their choice," the company said.
The custom genotyping arrays will also allow researchers to combine SNPs from their own sequencing projects with SNPs in Affy's database.
While currently the capacity of these arrays is 2.6 million SNPs, this will be expanded in the future to support more than 5 million SNPs, Affy said.
"As large-scale genotyping studies begin to leverage newly discovered content, a large number of researchers are now interested in low-frequency variants and genetic diversity in a variety of populations, particularly Africans," Affy said in a statement. "Both of these trends signal the need for higher-density arrays and the ability to customize content to maximize coverage in the population of interest."
The company noted that researchers can create arrays with 50,000 SNPs for focused or replication studies, multi-sample array plates with millions of low-frequency variants, or arrays tailored to a specific cohort being studied.
Affy said that its bioinformatics team will provide support to researchers designing Axiom Custom Genotyping Arrays to ensure that the design of the arrays meets the goals of their study.
Additionally, through Affy's Research Services Laboratory, researchers can also screen a subset of their sample cohort against approximately 5 million validated SNPs to assess linkage disequilibrium structure, minor allele frequency information, and assay performance, which will help them further customize their arrays. The screening services will allow researchers to base their customized design on "empirical data rather than speculative marker selection," the company said.