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New Product Watch: Jul 26, 2011


Illumina has begun shipping its HumanOmni5-Quad DNA Analysis BeadChip. The San Diego firm in a statement called the chip the "new flagship array" of its Omni family of whole-genome genotyping microarrays for association studies.

The Omni5 features more than 4.3 million variants per sample selected from the International HapMap Project and the 1000 Genomes Project. Users also have the option to add up to 500,000 custom markers.

The Omni5 is available in a four-plex format, allowing users to run four samples on four 5-million-marker arrays per BeadChip. The company said that its customers now have the capacity to survey nearly 20 million variants per assay at throughput of more than 460 samples per week using its HiScan or iScan systems.

According to Illumina, the Omni5 provides coverage of human variation down to 1 percent minor allele frequency, and also offers coverage of high-value regions of the genome associated with disease, including genic regions, the major histocompatibility complex region, and nonsynonymous SNPs. The array also features almost 5,000 insertion/deletion and multi-base substitution markers selected by the 1000 Genomes Project, which Illumina claimed can help researchers "elucidate a better understanding of how structural variants affect traits and diseases."

Illumina first announced its intention to launch the Omni5 in 2009. A 2010 launch date was later postponed to 2011 as the firm awaited the generation of rare variant content from the 1000 Genomes Project (BAN 11/2/2010).

Affymetrix has launched its CytoScan HD Cytogenetics Solution. The new offering consists of Affy's CytoScan HD array, reagent kit, Chromosome Analysis Suite software, and GeneChip instrument system.

Affy claims that CytoScanHD provides the "broadest coverage" of SNPs for detecting human chromosomal aberrations associated with genes related to constitutional and cancer cytogenetics. The array includes more than 2.6 million copy number markers, of which 750,000 are genotypeable SNPs and 1.9 million are non-polymorphic probes.

The array enables accurate breakpoint estimation, high-resolution loss of heterozygosity determination, detection of uniparental isodisomy and regions identical-by-descent, as well as low-level mosaicism visualization and heterogeneity measurements, the firm said.

The reagent kit includes all reagents required for the array, aside from ethanol and Clontech's Titanium DNA Amplification Kit. The CytoScan protocol can be accomplished in two and a half days with seven hours of hands-on time, according to the firm.

Affy designed the array in accordance with new recommendations from the American College of Medical Genetics concerning chromosomal microarrays. The firm discussed the new offering with (BioArray News) earlier this year (BAN 5/10/2011).

Golden Helix this week announced the availability of version 7.5 of its SNP & Variation Suite. The software tools included in the suite can be used to analyze, visualize, and manage large-scale sequence and array-based genomic data.

Golden Helix's latest offering expands on the software's sequence analysis module by offering new methods for sequence analysis, such as the Kernel-Based Adaptive Cluster test and the Combined Multivariate and Collapsing method. These statistical methods can be applied to detect associations between complex disease phenotypes and rare variants while correcting for confounding variables, according to the firm.

SVS 7.5 also features support for variant classification, including support for insertions and deletions regardless of format and a new bi-allelic expansion feature for coding resequencing data for SNP analysis. These new tools can be used to analyze both data from next-generation sequencing platforms and microarrays, a Golden Helix official said.

"Most of the new rare variant analysis and association functionality added in 7.5 can be employed on any data set containing genotypes regardless of where the genotypes came from," Josh Forsythe, Golden Helix's vice president of sales and marketing, told BioArray News this week. "For example, the newer Illumina [Omni2.5 and 5M] and Affymetrix Axiom arrays contain rare variants in addition to common variants," he said. "The improved CMC and new KBAC collapsing methods released in 7.5 can be used to assess rare variant burden based on the content on these newer arrays."

Single nucleotide variants and indels can be further visualized with the Variant Map feature included in SVS 7.5. Variant Maps present color representations of SNVs, indels, and mix substitution variants by analyzing each marker in the source spreadsheet, comparing alleles to a reference base.

SVS 7.5 also includes an upgraded genome browser, developed to provide gene and genetic position context information through the incorporation of data repositories.