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PerkinElmer Launches Exome Resequencing Service on HiSeq 2000


By Julia Karow

made its debut in the next-gen sequencing market this week by launching a DNA sequencing and analysis service that will initially offer human and mouse exome sequencing.

Services are provided at PE's sequencing laboratory in Branford, Conn., on the Illumina HiSeq 2000 platform, and customers have a choice between the Agilent SureSelect, Illumina TruSeq, and Nimblegen EZ Exome methods for enriching exome DNA.

PerkinElmer is also employing its own platforms, in particular its Janus Automated Workstations and EnSpire Plate Readers, for sample and library preparation.

For data management and analysis, the service uses Geospiza's Lab Edition LIMS and Analysis Edition data analysis and visualization software.

Customers receive their data through a web-based portal that is hosted on site at PerkinElmer in a "private cloud" environment.

The team running PE's new service includes several 454 Life Sciences veterans, such as Dick Begley, president of emerging technologies at PE and former president and CEO of 454; Gerard Irzyk, senior director of operations for emerging technologies at PE and former director of 454's sequencing operations; Bill Spencer, senior director of emerging technologies at PE and a former business development manager at 454; and Edward Szekeres, director of bioinformatics and a former manager of production informatics at 454 (see Paired Ends, this issue).

Begley told In Sequence last month that the service received funding in May 2010 from an internal "new ventures" program that focuses on emerging technologies.

By the end of November, it was fully staffed and equipped, and as of December, it had "several dozen" currently undisclosed customers in North America and Europe. About half the exome sequencing projects to date involve inherited diseases — including neurological and mental disorders, kidney disorders, ALS, muscular dystrophy, and obesity — the other half cancer, he said. The plan is to expand the service to Asian-Pacific customers in the future.

The service, which aims to be profitable within 12 months, plans to attract large academic groups with disease-specific studies, core labs that want to outsource exome sequencing, and research units of pharmaceutical companies. The sequencing lab plans to become CLIA-certified in 2011 and HIPAA-compliant at a later stage.

Begley said the service is technology-agnostic and "will continue to look at both hardware and software" from other vendors.

The service might also expand in the future. "We are not prepared to tackle [full] human genomes yet," Begley said, "but we are working on that." So far, PE has seen the greatest demand for exome sequencing, but his team is also developing sequencing services for targets other than the exome.

Begley did not disclose pricing information for the service but said it is "very competitive." He also did not say how many Illumina sequencers PE currently has in place. In promotional material, PE promises a turnaround time of "as little as" four to six weeks.

PE's new service will compete with several existing exome sequencing services, for example from BGI, Illumina, and commercial service providers. Once it expands to human full-genome sequencing, it will also run into Complete Genomics, which specializes in this type of service.

But none of these, Begley said, offer the same complementary protein analysis and diagnostic services that PE does through its other businesses.

Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com.