Kaiser’s Massive Genetic Database Leverages Its Patient Population (But It’s A One Way Street)
This week MIT’s Technology Review featured a story about Kaiser Permanente and its plans to use its Northern California patients to construct an enormous genetic database. The acronym-unfriendly Research Program on Genes, Environment, & Health, or RPGEH is funded in large part by a $25 million NIH research grant courtesy of February’s stimulus bill. The program will genotype 100,000 patients using SNP array technology from Affymetrix. If all goes well, the project will expand to as many as 500,000 patients by 2013.
What makes the RPGEH proposal so exciting, from a research perspective, is not just the 700,000 SNPs that will be genotyped for 100,000 patients, although that alone would represent one of the largest genetic research databases currently in existence. The real value lies in the marrying of genetic information with robust medical, environmental and other phenotypic data that Kaiser already maintains as a health care provider. From the RPGEH’s official description:
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The Genome In Silico and the Future of Whole-Genome Sequencing
In my previous post summarizing last weekend’s conference on Genetics and Ethics in the 21st Century I briefly mentioned Professor John Robertson’s discussion of the “genome in silico.” Using Illumina’s recently announced $48,000 whole-genome sequencing service as an example, Robertson wondered whether the future of whole-genome sequencing lies in converting the genome to silicon storage (in silico) or whether on-demand sequencing of short genetic segments (or even whole genomes) will continue to be done as and when patients present with specific clinical conditions (in vivo). To put it another way, will the patient of the future present his doctor with the equivalent of Illumina’s concept iPhone app or Knome’s USB drive, or will she come prepared to undergo a more traditional blood draw or tissue biopsy.
Following Illumina’s announcement at the Consumer Genetics Show, Daniel MacArthur at Genetic Future speculated that Illumina, in focusing “on the sequence generation side…[was] restricting itself to the least attractive segment of the personal genomics market.” And I agreed, arguing that the bioinformatics portion of the genome sequencing market — interpreting and functionalizing raw sequence data — appeared to be both larger and less well-developed, thus presenting a more promising commercial opportunity.
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