Single chip for SNPs and copy number variations

Affymetrix has officially released its new single-chip SNP 5.0 Array, which allows both single nucleotide polymorphism (SNP) and copy number variation testing on the one chip.

The new array features SNPs from the original two-chip 500K array set, as well as 500,000 additional probes that can measure other genetic differences, such as copy number variation.

The company said the SNP 5.0 Array gives researchers a significant increase in information above the original 500K array set for the same price, while reducing the array processing time.

The SNP 5.0 was developed in collaboration with the Broad Institute of Harvard and the Massachusetts Institute of Technology to better identify and understand the genetic variations associated with complex diseases such as autism, autoimmunity, bipolar disease, cancer, diabetes and heart disease. Scientists from the Autism Consortium and the Broad Institute are using the SNP 5.0 array to study the genetics of autism.

"To understand the causes of complex genetic diseases, our investigators want simultaneously to test both SNPs and copy number variants, all in the same experiment," the Broad Institute's program director for medical and population genetics, Dr David Alshuler, said.

"The SNP 5.0 array not only draws on the most current data from the International HapMap Project to guide SNP assay design, but also from the rapidly emerging database of common copy number variants to direct placement of additional probes."

Affymetrix is working with scientists from the Broad to develop additional software tools for data analysis for the SNP 5.0 Array, as well as add additional SNPs to the next-generation SNP 6.0 array that is scheduled to launch later this year.

Late last year, scientists using Affymetrix's 500K array announced the first comprehensive copy number variation (CNV) map of the human genome. The study, published in the November 23, 2006 issue of Nature, was the first publication to demonstrate the performance of whole-genome SNP arrays in detecting CNVs in the general population.

Researchers in the study discovered that CNVs are much more prevalent than previously thought. CNV regions were found to comprise about 360 megabases, or around 12 per cent of the human genome.

The researchers constructed the CNV map of the human genome by analysing samples from 270 people of European, Asian or African descent, who were originally included in the International HapMap Project. The DNA from these individuals was scanned using Affymetrix's 500K Array and a BAC array platform developed by the Wellcome Trust Sanger Institute.

Using this combination of techniques on these samples, the researchers discovered 1447 CNV regions containing hundreds of genes, disease loci, functional elements and segmental duplications.

The SNP 5.0 Array is available in Australia from Millennium Science. Call 1800 678 242 for more information.