Bioinformatics will form the backbone of operations at First Genetic Trust, a recently launched “genetic bank” that plans to not only collect but also analyze genetic and genomic data from individuals.
Based in Chicago, the company then intends to sell privacy-protected patient data to pharmaceutical and genomics companies.
Andrea Califano, co-founder and chief technology officer of First Genetic Trust, told BioInform that the company plans to create databases of genomic information including whole-genome expression data and markers, such as single-nucleotide polymorphisms. Califano formed the company together with Arthur Holden, head of the SNP Consortium, and David Wang, who previously worked at Motorola, Bristol-Myers Squibb, and MIT’s Whitehead Institute.
Holden will serve as the company’s CEO, while Wang will be vice president in charge of strategy and planning.
With initial round funding of $13.5 million from Venrock Associates and Arch Venture Partners, the company began operating in August and currently has a staff of five. The company expects to have as many as 35 employees by the end of its first year.
As the company ramps up its capabilities, a longer term vision is to add value to raw data for pharma customers by doing linkage disequilibrium, haplotype, and association discovery studies between phenotype and genotype, eventually establishing relationships between genes, disease, and drug tolerance.
“Clearly the challenge is that even rather homogeneous populations seem to display a wide genetic heterogeneity. Therefore the requirement is to be able to use and integrate a vast array of complementary technologies to extract the information hidden in the databases,” said Califano, who is also in charge of hiring a team of computational biologists to analyze the data it expects to acquire.
First Genetic Trust will use a number of standard bioinformatics software packages although Califano declined to specify which ones would be installed. In addition, the company expects to develop new mathematical models and proprietary algorithms aimed at extracting information from its future databases. These tools will then be applied to come up with new predictive biology and medicine methods, said Califano.
“We definitely plan to sell the analytical services and tools to pharmaceutical companies but in a way that does not compromise the integrity and privacy of the individual genetic record of the patients,” said Califano.
He explained that the company would only analyze the genomes of participants in the studies if they approve the research through an informed consent procedure. First Genetic Trust’s customer base will be concentrated among pharmaceutical and genomics companies with whom the company founders have established relationships.
Besides the need for powerful association discovery algorithms, First Genetic Trust will also require non-computational techniques to understand the biology of the processes it will study, said Califano. The company will do some of this research internally and some will be done through collaborations with research centers, he added.
Califano, former director of the Computational Biology Center at IBM Research in Yorktown Heights, NY, said the new company would draw on his experience from his 15 years with Big Blue.
First Genetic Trust has already announced a strategic partnership with IBM for its computing, database, and security infrastructure. In about a year, when the working system is in place, the security of patient information will be assured, and clinical trials — and the informed consent system that they stand on — will be strengthened, Califano predicted.
Part of Califano’s experience is in the design and application of pattern discovery, pattern matching, and association discovery algorithms, which he said are critical for the study of disease-genotype relationship or for pharmacogenomic studies, especially those involving multi-gene interactions. The work he did at IBM involved directing the scientific program for a broad set of related computational biology and computational chemistry projects.
The time spent working with the multiple interrelated sides of these disciplines led him to take an integrative science approach, something that he said will be reflected in the bioinformatics infrastructure to be built at First Genetic Trust.
Califano is concentrating on the security issue by inventing database architectures and encryption schemes for patient data. He explained that First Genetic Trust will function like a Swiss bank, holding patient data instead of dollars, with the company acting as intermediary between patients, health providers and research groups, while concealing individual identities from all parties.
Paradoxically, at the most fundamental level the company’s first task entails understanding human relationships rather than technology. Wang explained that a successful bioinformatics system for the post-genomics era ultimately depends on understanding how patients and doctors interact.
“This is very subtle, and we need to proceed carefully as we translate this very personal information into an IT paradigm,” said Wang.