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Strand Kicks Off EAP to Test Clinical Variant Interpretation and Reporting Software

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Strand Life Sciences began an early access program this week that will test a new platform it is currently developing to help diagnostic testing laboratories interpret the variants in genomic samples and generate reports listing candidates genes and variants likely responsible for the observed phenotype.

The Bangalore, India-based company demoed the platform — named StrandOmics — at the Association for Molecular Pathology annual meeting last week in Phoenix, Ariz. At the meeting, Strand offered clinicians and scientists from academic and commercial diagnostic labs a chance to test the platform and potentially sign up for the EAP, which officially began on Nov. 18 and will last for about six months.

The company is hoping to sign on participants that are developing sequencing-based diagnostic gene panels as well as those developing whole-exome and/or whole-genome sequence-based tests.

Dana Abramovitz, Strand's senior director for scientific and corporate strategy, told BioInform that EAP participants will have the opportunity to test the platform for three months — with freedom to generate a total of 100 reports — and give feedback that the company will use to improve the system ahead of the full launch planned for spring 2014.

According to the company's website, program participants will get discounted access to Avadis NGS, which they can use to generate the variant call files that serve as input to the interpretation platform. The website also states that once the program is completed and the software released, EAP participants will be offered a discount on the purchase price of the application for the first six months of use.

This product will be Strand's second offering for the clinical market. Earlier this year, the company — which has historically developed software for the research market and continues to do so — said that it planned to use the proceeds of a $10 million funding round to develop software applications and put infrastructure in place so that it could start offering NGS-based diagnostic services in India this year, with a plan to begin offering services globally in another year.

Since the company launched the Strand Centers for Genomics and Personalized Medicine in April, the lab through which it provides diagnostic testing and interpretation services to several hospitals in the India, its services offering has been "expanding exponentially," Abramovitz said. Its client list includes Max Hospital, Mazumdar-Shaw Cancer Center, St. Johns Medical College Hospital, and Kidwai Memorial Institute of Oncology.

While the interpretation solution that's about to be tested "stemmed from that service" — it was developed to help the company's lab analyze test data from sequencers and gene panels — the software is a separate product and will be marketed on its own, she said.

The platform is composed of internally developed workflows for interpreting disease-linked variants using a curated database of information from public repositories as well as scientific and medical literature that's updated with new information about variants as it becomes available. Once the system completes its analysis, it generates a ranked list of variants where the top listed variants are likely the most interesting in terms of disease.

Because the software was built from the ground up to support clinical laboratories, Strand also ensured that it meets all the necessary HIPAA, CLIA, and ACMG regulations and guidelines, Abramovitz said. She also noted that this is one of the selling points for the software. "We didn’t convert a tool that was used for research to be used for clinical [settings]. It is designed specifically for the clinical lab." Furthermore, "we developed it in collaboration with our lab so we actually know the needs of the labs and have built out for those needs," she added.

Initially, Abramovitz said, in collaboration with its EAP partners, Strand will focus on developing and tweaking a workflow that the company has created for identifying variants involved in Mendelian disease, but it will eventually make available a second oncology-specific workflow that'll let users compare somatic and germline mutations to identify cancer-linked variants.

The company is still discussing an appropriate business model and pricing for the software and it's hoping the next six months will bring some clarity to that decision process, according to Abramovitz. "We have some ideas but I think the early access program will help us define those better."

Qiagen is also moving into the clinical variant interpretation software arena, developing a web-based clinical variant interpretation and reporting solution to support next-generation sequence-based diagnostic testing that builds on intellectual property it obtained when it bought Ingenuity —renamed Qiagen Redwood City — earlier this year. The company began enrolling academic and commercial labs in its EAP after launching the program at AMP last week. Its list of testers includes Partners Healthcare, Emory Genetics Laboratory, and GeneDx.

Also, Philips Research is developing a prototype of tool called Platform for Personalized Analytics Applications, or PAPAyA, that is intended to help oncologists analyze, interpret, and report the results of NGS tests. In May, members of the development team told BioInform that the company planned a pilot study for the fourth quarter of this year to begin testing the software with an undisclosed cancer center.

Players on the services side include CollabRx and its recently launched Genetic Variant Annotation service, through which the company provides interpretation services to molecular diagnostics labs offering sequence-based tests; and Silicon Valley Biosystems, which emerged from stealth mode earlier this year and offers interpretation services for clinicians and healthcare providers as well as sequencing services provided by three partner labs.

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