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Broad Informatics Chief Says Institute Is Ready for 1M-SNP Genotyping Chips

The impending launch of 1-million-SNP genotyping arrays from Affymetrix and Illumina is welcomed at the Broad Institute, according to an institute official.
Jill Mesirov, chief informatics officer and the director of computational biology and bioinformatics at the Broad, told BioArray News last week that the institution, which provides access to both companies’ chips, has the infrastructure in place to handle the large amounts of data the arrays will produce.
“We are planning on offering [Illumina’s and Affy’s 1-million-SNP arrays] to our internal user community as well as to the external users who use our [National Center for Research Resources-funded] genotyping center services,” Mesirov wrote in an e-mail.
“They will be offered as soon as they are commercially released and in our production pipelines; generally this takes from two to six weeks of software development time past the commercial vendor release date,” she added.
Illumina and Affy expect to launch their chips in the second quarter.

Mesirov also wrote that the Broad’s lab information-management systems would require little additional enhancement because the institute upgraded its LIMS capabilities to handle earlier high-density genotyping chips from Affy and Illumina in 2005. In addition, the institute played a significant role in developing new whole-genome genotyping products for Affymetrix by helping to craft an algorithm that is essential to the higher-density arrays (see BAN 7/25/2006).

The production systems we have in place can already handle the data volume produced by these products,” Mesirov wrote. “We put a new design into production about a year and a half ago, originally to target the Affy 500K chipset. However, the design is extensible and enables us to plug in new vendor products and integrate them into our workflows quickly,” she wrote.
Mesirov’s comments echo those of other research centers that offer genotyping services. Fanny Chagnon, client manager of the McGill University and Génome Québec Innovation Center, which offers both Illumina and Affymetrix genotyping platforms to Canadian researchers, told BioArray News last month that the organization already made internal adjustments last year to handle Illumina and Affy’s 500,000-SNP products, and that those updates should suffice for the 1-million-SNP products (see BAN 1/23/2007).
“To use the Affy 500K [arrays], we’ve had to arrange our database so that it could handle such a body of data,” Chagnon told BioArray News last week. “But the way we’ve arranged it, we can handle much more data, so I think we’ll have no problem [with] a 1-million-SNP product.”
Chagnon also said that Génome Québec has decided to rely on its in-house team of informatics specialists rather than outsource the work to the companies or to software companies, a situation that Mesirov said is similar at the Broad.

“The production systems we have in place can already handle the data volume produced by these products.”

“All informatics work was performed in-house,” she wrote. “Because this large production system requires ongoing operational support, it would be very difficult to outsource the development, as ongoing support is a large part of the job,” Mesirov added. “Providing scientific and user support to the system without having had an intimate role in developing it would be problematic.”

In addition to being prepared to deal with data, Mesirov said that the Broad is doing all it can to be ready for the new chips based on the limited amount of information both Affy and Illumina have provided about the 1-million-SNP arrays.
Illumina has not publicly disclosed how it will help its customers transition from earlier whole-genome genotyping products, like its HumanHap550 BeadChip, to its Human 1M BeadChip.
According to Mesirov, the technical assistance Illumina and Affy have sent the institute so far has been “limited to basic information.” However, she said that “as we've previously implemented chip products from both vendors, we feel we are as prepared as we can be prior to receiving detailed technical information.”
Illumina has declined to discuss informatics issues related to the launch of its 1-million SNP chip. For Affy’s part, Steve Lincoln, the company’s vice president of informatics, said last month that the transition to the 1-million-SNP 6.0 array should be relatively easy.
“Our successive product updates are based on the same proven assay and same general informatics approach,” Lincoln wrote in an e-mail to BioArray News last month. “The new SNP 6.0 Array will be able to leverage the emerging best practices and most current systems for data management, data quality control, and data analysis that the 500K and SNP 5.0 arrays now use,” he wrote (see BAN 1/23/2007).

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