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Bina Targets Whole-Genome Analysis in Hours with Hardware/Software Analysis Platform

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Bina Technologies this week launched its flagship genomic analysis platform, which it says can reduce the time required to analyze a whole human genome from several days to around four hours.

The Bina Genomic Analysis Platform includes specialized hardware and software for genomic sequence data alignment and variant calling. The underlying hardware, the Bina Box, has been engineered to analyze genomes 100 times faster than other options, according to the company.

Bina representatives told BioInform that they hope to secure clients in academic core labs, research institutions, universities, and health organizations who need tools to analyze whole-genome sequence data from Illumina's HiSeq and MiSeq systems.

"We've done our validating and benchmarking on the Illumina platform … and so today's customers will be those that are focused on whole genomes … and have one or more Illumina instruments that are in active use [and] working at high volume," Mark Sutherland, Bina's senior vice president of business development, told BioInform.

The company intends to begin supporting other sequencing platforms such as Life Technologies' Ion Proton, in the second half of this year, Narges Bani Asadi, Bina's founder and CEO, told BioInform.

Sutherland said that Bina's subscriptions cost about $12,500 per month. A subscription covers the installation of a standard 2U Bina box, which includes two alignment and variant calling pipelines — the first combines the Bina Aligner with the Genome Analysis Toolkit and the second is an accelerated version of the Burrows Wheeler Aligner and GATK.

The subscription fee also covers training and technical support, he said.

The price, which translates to $150,000 per year, is in line with another appliance-based genome analysis offering, Knome's KnoSys 100, which has a list price of $125,000. That system, which is geared more toward the clinical market than the research market, analyzes data from Illumina, Life Tech, and Complete Genomics sequencers.

It's likely that Bina will face some competition from Illumina itself, which offers the cloud-based BaseSpace platform for data storage and analysis. The first terabyte of storage on BaseSpace is free, and users can purchase additional storage in increments of one terabyte or 10 terabytes. One terabyte will cost $250 per month or $2,000 upfront for a full year, while 10 terabytes will be $1,500 per month or an annual up-front fee of $12,000.

However, Bina believes that having local hardware will be more attractive to customers than cloud-based offerings from the competition because they won't have to worry about uploading large datasets to the cloud, Asadi said. It's also good for researchers working in clinical and diagnostic settings who might be concerned about the security of their data, she said.

Redwood City, Calif.-based Bina debuted at the Bio-IT World conference last April. At the meeting it previewed SeqAlto, a variant analysis pipeline, and the Bina Box, a hardware system comprising graphics processing units, field programmable gate arrays, and multicore central processing units (BI 4/27/2012).

Since then, Asadi told BioInform, Bina has run three pilot projects with groups at academic and government institutions as well as a diagnostic company.

One of the pilots was a project that involved teams from the genetics department at Stanford University and the Veteran Affairs Hospital in Palo Alto.

They used Bina's system to analyze 500 genomes as part of a project funded by the US Department of Veterans Affairs that is studying a number of conditions including abdominal aortic aneurysm, Michael Snyder, a genetics professor and director of Stanford's center for genomics and personalized medicine, told BioInform.

Snyder said that using the Bina platform reduced the time required to process each genome down to about five hours compared to the 36 hours it took to analyze a single genome using Stanford's shared compute cluster and an internally developed bioinformatics pipeline. "That was a big advance for us," he said.

He also noted that Bina's platform is one of the few available that can process variants efficiently, which "was a good thing for us."

For its part, Bina benefitted from the pilots because it was able to validate the accuracy of its pipeline, Asadi told BioInform. For example, she said, the company found that its alignment tool maps more reads than BWA does and that it is also more accurate at calling insertions and deletions.

The company also discovered that a lot of its target customers, particularly those in pharma and clinics, prefer to have "local processing power," which is an advantage for Bina over cloud-based or software-only solutions.

Also, Bina has added new features to its platform based on its pilot experiences that improve its functionality, Asadi said. For example, the pipeline now includes a tool for analyzing structural variants so that users get a more comprehensive picture of genetic variation, she said.

The company also renamed its variant analysis pipeline, which used to be called SeqAlto. Now it's simply called the Bina Pipeline and Aligner to prevent confusion about the company's products, Asadi said.

Bina also incorporated the BWA/GATK pipeline in addition to its own so that users can see both sets of algorithms in action, she said.

Also, "BWA+GATK is one of the most popular frameworks for NGS analysis and we wanted to support that to lower the barrier of adoption for Bina Box," she explained.

Bina currently has 14 people on staff and is hiring, Asadi said. Specifically, it is looking for data scientists, high-performance computing experts, and sales people.

Besides increasing its headcount and wooing customers away from competitors such as DNANexus, Bina intends to form research partnership that will help it build specific kinds of applications — such as cancer analysis and newborn screening — that will run on its platform, Sutherland told BioInform.

"We are not doing any more pilots because that was designed specifically to provide us with product development feedback prior to launch and commercialization," he explained.

Instead, he said, Bina has kicked off a "scientific collaborations program" that will initially focus on cultivating relationships with groups working on using whole-genome sequencing in oncology and neonatal intensive care.

He would not disclose what the company's plans are on these fronts but said that it will announce two partnerships — one in each area — in the coming months.

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