Single nucleotide polymorphism (SNP) genotyping is a method for determining genetic variation. As more and more SNPs have been identified from the genome in recent years, the power of this technique has steadily increased.

Affymetrix now offers the Genome-wide Human SNP Array 6.0 containing more than 1.8 million markers of genetic variation. Credit: AFFYMETRIX

Affymetrix, located in Santa Clara, California, is one company that is taking advantage of SNP-discovery projects, such as the International Hap Map effort, to generate SNP arrays for whole-genome association studies. In May, Affymetrix launched its next-generation array, called the Genome-wide Human SNP Array 6.0, or SNP6.0. “This chip allows us to look simultaneously at more than 1.8 million markers of genetic variation,” says Keith Jones, vice-president of assay and application product development at the company.

The SNP6.0 not only offers genome-wide SNP coverage, but also contains more than 900,000 probes that target copy-number variants (CNVs) in the genome. “When walking down the path in designing the SNP6.0, we took the biochemistry that we used to generate targets to hybridize to the arrays and empirically identified probes that responded in a dose-dependent manner to changes in copy number,” says Jones.

Other companies have also placed CNV probes onto their genotyping chips. Illumina, based in San Diego, California, now offers the Human 1M BeadChip, which boasts more than one million SNP and CNV probes, for whole-genome genotyping applications. Nimblegen, located in Madison, Wisconsin, and recently acquired by Roche Applied Sciences, also offers several whole-genome and custom-tiling array comparative genome hybridization products for examining copy-number variation across the entire genome. These arrays contain more than 385,000 probes at a median spacing of 6,000 base pairs. Agilent Technologies, located in Santa Clara, California, provides several array comparative genome hybridization products for analysis of copy-number variation in humans, mice and rats.

Illumina also offers several more-focused SNP arrays, including a cancer panel and one that targets the major histocompatibility complex, an area that Affymetrix also seems to be moving into. “I think it is also fair to say that you will see more application-specific SNP panels in the future,” says Jones.

N.B.