The Genome In Silico and the Future of Whole-Genome Sequencing

silicon waferIn 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.

If there’s anybody who should know where the future commercial value of whole-genome sequencing resides it is Jorge Conde, CEO of Knome, the only commercial genomics company (at this time) that will both sequence and interpret an entire genome. In a recent article by Emily Singer in MIT’s Technology Review, Conde weighed in on the future of whole-genome sequencing:

Analysis of the meaning of the human genome is proving to be more much more complicated than the sequencing itself. “In the long-term, that will be a big driver of value,” says Conde. “We will see the high price point go away, and the real value for both individuals and companies will be to provide an ongoing narrative.”

Although some companies (Complete Genomics) and research (the Human Microbiome Project) have focused on sequencing projects that look beyond the human genome, I continue to believe that the bioinformatics and interpretive components of whole-genome sequencing services are likely to be the key drivers of value for both consumers and companies as the industry develops. After all, no matter where and how often sequencing occurs, it’s only as useful as the interpretation afforded it.

But even as the interpretation of genomes inevitably improves, the question remains whether that interpretation will be performed on genomic data that reaches the clinic in silico or in vivo. The standard story of personal genomics is that a few years hence, once the cost has dropped to $1,000 (or lower), genomic sequencing will become a once-in-a-lifetime event, with the genome in silico taking its rightful place in the typical patient’s (electronic) health record. Yet after my conversations at Breckenridge this weekend — along with last week’s announcement by scientists at McGill University that suggests the genetic sequence may vary between an individual’s blood and tissue cells — I’m wondering if it’s time to reexamine the inevitability of the genome in silico and to consider the possibility that, even in an age of personal genomics and personalized medicine, patients may continue to carry their genomic sequences into the doctor’s office the old-fashioned way: under their skin.

Filed under: Biobanking, Bioinformatics/IT, Direct-to-Consumer Services, Genetic Testing/Screening, Genomic Sequencing, Genomics & Society, Informed Consent, Legal & Regulatory
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