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Affy, Illumina Arrays Remain Platforms of Choice for Consumer Genomics Firms


By Justin Petrone

Direct-to-consumer genomics firms continue to prefer high-density genotyping microarrays manufactured by Affymetrix and Illumina over rival technologies, according to a recent survey by BioArray News.

According to results of the survey, nearly all DTC genomic service providers are using either custom or catalog chips made by the two West Coast array vendors. Some companies also vowed to integrate next-generation sequencing into their services when cost and reliability issues improve, but were not willing to provide an estimate of when that might be.

The first three firms in the space, Decode Genetics, Navigenics, and 23andMe, launched their services in 2007 with back-to-back entries. While Decode and 23andMe have used Illumina BeadArrays in their services, Navigenics has relied on Affymetrix GeneChips.

"We have been mainly using Illumina chips for what we do, but we have used all kinds of different methods to establish alleles and variants in [the] context of comprehensive genetic profiling," Kári Stefánsson, Decode's president of research, told BioArray News this week.

He said Reykjavik, Iceland-based Decode has been using catalog Illumina arrays as a "backbone" in its service and then adds onto that "genotyping of individual SNPs and individual variants." It is "not unlikely that we will switch over to a custom-made chip at one point," he said.

Stressing that Decode is "not wedded to any technology platform," Stefánsson said the firm continues to rely mostly on Illumina for its service because Decode had used the platform in its discovery work with "good and reliable" results.

He added that though Decode was reorganized after filing for bankruptcy protection last year (see BAN 1/26/2010), there have been "no changes" in the DeCodeMe service and there are "no plans to make any dramatic changes in DeCodeMe in the near future."

Also sticking with the Illumina platform is Mountain View, Calif.-based 23andMe, which relies on an Illumina HumanHap550 BeadChip along with a custom array of about 30,000 SNPs for its service.

Andru Hsu, the firm's science and policy liaison, told BioArray News via e-mail last week that 23andMe has used the HumanHap550 since the shop debuted in 2007. However, the firm is now on the second version of its custom array, and is "always looking for ways to improve coverage of the genome or particular genetic markers of interest."

Navigenics, the third firm to debut a consumer genomics service, continues to use a custom Affymetrix SNP 6.0 array in its service. The Redwood Shores, Calif.-based company also acquired its Clinical Laboratory Improvement Amendments-compliant lab in Sacramento from Affy last year (see BAN 3/17/2009).

Company representatives did not reply to questions in time for this publication.

Lastly, Houston-based Seqwright launched its personal genomics service on the Affy SNP 6.0 Array in January 2008. An e-mail to the firm seeking comment was not returned.

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Other DTC genomics firms to enter the space in the past year have also opted for arrays as their primary technology platform. They are mostly split on their choice of vendor: One, San Diego-based Pathway Genomics has used Illumina's chips since debuting its service in June 2009; while another, Redwood City, Calif.-based Counsyl, which launched its service last month, relies on the Affymetrix platform.

David Becker, chief scientific officer at Pathway, told BioArray News via e-mail this week that the company has used a custom Illumina microarray to generate the genotypic information required for its genetic health and ancestry reports.

"Most of the useful or actionable information in the genome is currently contained within a few thousand markers," Becker said. "This makes a microarray the most cost-effective method for scanning the informative content in the genome."

He added that "it's important to note that in addition to Illumina, we have also validated other genetic analysis technologies including standard [and] targeted DNA sequencing, qPCR probes, mass spectrometry, and other types of manufacturer’s microarrays. We use multiple technologies to cross-validate our markers, and to develop specific test panels."

Counsyl, meantime, uses an Affymetrix array that it has customized in order to test the mutations involved in rare inherited diseases.

Representatives for Counsyl did not return phone calls and e-mails seeking comment in time for this publication.

Whole-Genome Sequencing

While all companies interviewed for this article continue to use arrays in their services, others have begun offering whole-genome sequencing to those who can afford it, including Illumina, which in June 2009 unveiled its personal genome sequencing service; and Cambridge, Mass.-based Knome.

According to Decode's Stefánsson, it is "likely that people will go to complete genome sequencing at one point in time." He noted, however, that customers will benefit more from whole-genome sequencing in the future when more is known of the correlation between variation and human disease.

"We and others will probably transition to complete genome sequencing gradually as knowledge increases and the price of sequencing drops," he said. Decode's service currently costs $985, while Illumina's personal whole-genome sequencing service, for instance, costs $48,000.

23andMe's Hsu said that the firm keeps "apprised of developing technology offerings, including next-gen sequencing," and will consider including them in its service "if and when whole-genome sequencing becomes affordable and reliable for consumers."

Meantime, Pathway's Becker said that the firm sees the increased adoption of next-gen sequencing tools as a means to place "high-quality genetic information into the hands of the patient and physician, to inform and to improve medical treatment and the quality of life."

Overall, Decode's Stefánsson noted that the DTC genomics market, which contains a variety of players with different offerings, has "developed more slowly than predicted." He said that eventually market demand will spike as consumers and physicians realize the usefulness of having their genomic profile.

"It is so inevitable that profiles like these will become omnipresent and there won't be anyone in 10 years' time that won't have a profile like this," Stefánsson said.

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