NEW YORK (GenomeWeb) — Austin, Texas-based Genformatic is hoping to make its bread and butter by providing various bioinformatics services to support genetic scientists in clinical and research contexts and developing bespoke software solutions that are tailored to customers' specifications.
Genformatic, launched in late 2011, provides whole genome and exome sequence analysis and interpretation services to physicians and patients to identify underlying disease-causing mutations, assess disease risks, and personalize treatments ; and to scientists who are analyzing genetic data as part of research studies.
"We are a small company but we try to provide concierge bioinformatics services for research and clinical communities," Genformatic CEO Daniel Weaver told BioInform. That means, he explained, that its emphasis is on providing high quality services to customers and tuning its solutions where necessary to fit with their requirements.
The company believes that this approach to doing business will help it stand out in the crowded landscape that is the bioinformatics industry. "We do more with the data" than researchers would receive from running a standard analysis using the Broad's Genome Analysis Toolkit, for example, "and try to deliver more individualized and refined datasets that are accurate and informative for whatever the researcher might be interested in," Weaver said. "Because we are smaller and more nimble, we can provide the sort of custom analyses that other [companies] might not be able to provide," he added.
Furthermore, Genformatic's services cover many of the analysis needs in the genetics community and it believes that the performance of its tools is on par with existing solutions in the market. "We hope that we can compete effectively against companies like Qiagen" which has been buying up informatics companies in a bid to offer solutions that span the research and clinical markets, he said. "We got an early start … and have done so without the same sort of upfront costs that … competitors may have faced, so at some point we might be able to compete effectively on price although that's not our main angle."
Genformatic partners with an unnamed CLIA lab to provide sequencing services for customers who don't already have their data in hand and analyzes the data using bespoke pipelines composed of open source and propriety algorithms and databases. Its pipelines detect and return lists of single nucleotide polymorphisms, copy number variants, and small insertions and deletions. According to its website, clients receive lists of known and novel mutations found in submitted samples including information on genomic position; links to read files that show the reads that cover each variant position; and access to supporting information from public literature. Clients can also visualize their data in genome browsers developed by the University of California, Santa Cruz and the National Center for Biotechnology Information. The company also compiles and returns known information on drug-variant associations.
On the clinical side, the company uses its pipeline to help physicians identify mutations associated with genetic disease, predict disease risk and drug response, and compare tumor and normal samples in oncology cases. Results from Genformatic's clinically-focused analysis are returned in a so-called Genformed report, which is updated as new information becomes available in the scientific literature — the company updates these health risk reports once during the first year for free and afterwards it will continue to do so for an undisclosed subscription fee. Physicians and their patients can use the information it provides to personalize health plans by taking into account health risks and drug responses identified by genetic testing.
Genoformatic's underlying infrastructure includes the Bayesian Integrated Caller (BAYSIC) which integrates calls made using different software such as the Genome Analysis Toolkit and SamTools to improve the sensitivity and specificity of its own calls. The company published a paper last month in BMC Bioinformatics where it describes the method and compares its performance to existing variant detection methods. It ran the study in collaboration with researchers at the Baylor Institute for Immunology Research, MD Anderson Cancer Center, and the University of Virginia School of Medicine.
Its system also includes VarIANT, an interpretation and analysis tool that combines information from various genomic databases to interpret variants found in genetic data. Other applications include some sample management software and an application called Genmate which lets users share and compare genomic information. Genformatic uses an internally developed encryption system called GENIE to encrypt the genomic data before it's shared, with appropriate consent, between providers, patients, institutions, and other entities.
Pricing for Genformatic's services varies depending on the customer, sequencing depth, and number of samples. For customers from the clinical segment of the market, the company charges $999 to analyze a standard exome sequenced at a depth of 50x. If customers want to run the company's variant calling pipeline, the price goes up to $1,099; and to include variant interpretations, the price goes up to $1,699. For a 100x exome and to receive a Genformed report, the company charges $5,499; and to receive a 200x exome and a Genformed report costs $6,599. For a trio of exomes sequenced at 200x and 100x, the cost is $14,999 and $7,599 respectively. To sequence tumor-normal pairs at 200x costs $12,599
For research customers, pricing starts at $999 per exome for the standard 50x sequence data. To include variant call data, the price goes up to $1,099 per exome; and to include interpretation costs $1,699. Pricing for whole genomes for research use cases sequenced at 50x and 200x costs $4,499 and $25,599 respectively. The company offers special pricing for larger projects that involve multiple samples. It does not disclose these costs publicly.
Genformatic also offers custom bioinformatics services as part of its portfolio. According to its website, its custom services list includes software development in Perl, C, Java, Python and Ruby, and more; database design and development; web application development; and pipeline development for RNA-seq and differential expression analyses. The company also offers services for microbiome and metagenomic analysis projects. Standard microbiome sequencing and analysis start at about $150 per sample.
The company has customers at a number of research and academic institutions as well as some business from the pharmaceutical industry. One of its clients is the Dell Pediatric Research Institute, a collaborator that has worked with Genoformatic on analyzing amplified DNA from archived newborn blood spots. The partners plan to publish a paper describing the study this year.