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Gene by Gene Acquires Arpeggi to Extend Genetic Testing and Diagnostic Offerings

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This week, commercial genetic testing firm Gene by Gene said that it has acquired Arpeggi, a bioinformatics startup that launched last year, for an undisclosed amount.

Under the terms of purchase agreement, all Arpeggi employees are expected to move to Gene by Gene's Houston offices in August. Additionally, Arpeggi's founders will join Gene by Gene’s management team, effective immediately. Nir Leibovich, Arpeggi's CEO, will now be Gene by Gene’s chief business officer, Jason Wang is now its chief technology officer, and David Mittelman will serve as chief scientific officer. Also, Arpeggi will not retain its name.

The companies intend to combine their respective offerings to build a suite of affordable genetic testing and diagnostic services that will be available to consumers, researchers, and healthcare providers. Arpeggi offers a free online resource called the Genome Comparison and Analytic Testing, or GCAT, tool that provides data and metrics for comparing the performance of alignment and variant calling tools. The company launched GCAT at the Bio-IT World conference earlier this year (BI 4/19/2013).

Arpeggi has also developed a variant calling tool, the Arpeggi engine, that it uses for internal projects.

For its part, Gene by Gene markets DNA testing services through its four divisions, which focus on ancestry, health, research, and paternity.

Mittelman, formerly Arpeggi's chief scientific adviser, described the purchase as a good fit for his firm because it gives it access to a fully equipped genetic testing laboratory that can be paired with Arpeggi's informatics capabilities to offer customers a one-stop testing service that spans the entire genetic testing process from sample collection to variant calling.

Arpeggi will also make improvements to the genetic testing pipelines Gene by Gene uses, he told BioInform. Since the companies have control over both lab protocols and software used for the analysis, they can optimize them to ensure more cost-effective testing and more accurate results, he said.

Meanwhile, Arpeggi's expertise in the next-generation sequence analysis market "fits in well" with Gene by Gene's efforts to move from Sanger- to NGS-based testing as well as with its plans to take advantage of new opportunities in the genomics market in the future, according to Bennett Greenspan, a founder and managing partner at Gene by Gene.

"My expectation is that in the weeks and months ahead we are going to be able to announce products and new initiatives," he told BioInform. The company isn't disclosing details about these new offerings at present.

GCAT will continue to be free for all users, Mittelman said. Arpeggi will continue to incorporate new features into the tool such as benchmarks for somatic variant callers. Recently, it included in GCAT a set of "highly confident" variant calls for the NA12878 genome that they built in collaboration with the Genome in a Bottle consortium, he said. Researchers can use this data as a benchmark with which to measure the performance of their variant callers.

Arpeggi had said previously that it intended to launch the Arpeggi engine this summer. However, the merger with Gene by Gene changes things ,making it unclear if the company will release the tool as planned, Mittelman told BioInform.

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