Thursday, March 1, 2012

The $100 Genome: Preparing for the Personalized Medicine Revolution

DNA is the blue print of life, telling our cells what to become and when to become it.  Today we are making enormous progress in unlocking the health implications of genes but because of technological and economic barriers, we're looking with blinders on.  To account for our inability to read all 3.2 billion base pairs in the human genome we have concocted some pretty smart methods of looking at the parts that we think matter.  We look at specific markers that few people have (called single nucleotide polymorphisms or SNPs) or at a few of the areas that we believe are involved in processes related to specific diseases (gene-based microarray studies).  While these approaches have been fruitful, it is widely believed that affordable and accurate reads of the entire genome (i.e., whole genome sequencing) will open the door to a whole new level of diagnostic and therapeutic discovery.


Like the desktop computer, laptop, cell phones, and tablets, there is a tipping point where high enough quality and low enough price will cause payers and providers to switch from target-specific tests to whole genome sequencing.  Just as today's smart phones make it difficult to justify purchasing phones, cameras, and gaming devices, the whole genome contains specific targets (e.g., a BRCA 1 & BRCA 2 test for breast cancer) as well as everything else one might want to learn from the gene.  And because our genes do not change often, a single sequence can be referenced again and again as new diseases are suspected, new treatments considered, and new clinical findings discovered.  In other words, referencing our genome will become a routine aspect of patient care.

Many posit that $1000 represents the tipping point for whole genome sequencing.  It's quite an ambitious goal, considering that the first sequence of a whole human genome took 13 years and cost $3 billion.  Yet since that first sequence was published in 2001, prices have dropped in unprecedented fashion.  Today there are several companies claiming to be within a year of the $1000 genome including Life Technologies, Illumina, Oxford Nanopore Technologies, IBM, and Complete Genomics.  Telling of how quickly this field is advancing, there are companies reporting progress toward the $100 genome.  Most notably is Genia, a 10 person start-up that will use a semi-conductor or chip-based approach to provide highly accurate whole genome sequencing from $8000 machines that use $100 chips.  If they deliver as suggested, these machine and their chips will be in mass production within the year.

Ready or not, the tipping point is about to arrive.  No stakeholder of our healthcare system, from scientist, to nurse, to hospital CIO, to patient, will be unaffected by the change that will soon occur.  Now is the time to think carefully about what it will all mean so that we can make the most of the opportunities.  Entire books could be written about each of impending areas of change and by the time they're written they will likely be outdated.  To get the dialog started, here are just a few of the impacts that we need to start preparing for.  Working our way from bench to bedside, here's what I've got so far (more to follow):

Barrier to Personalized Medicine #1: The Free Rider Dilemma

Personalized Medicine's Next Frontier - Next Gen Phenotyping

Why Genome Sequencing Shouldn't Explain Disease - Understanding Discovery Work to Date





1 comment:

  1. The people (who will be patients) in particular, I think are on particularly shaky ground to take advantage of the new cool stuff. Which is unfortunate because it is their own genomic data. Not to say that everyone needs to understand sequencing, but some kind of agreed-upon explanation will soon be needed.

    For example, when I changed the dose of plavix for someone based on genotype, it is just one small piece in a meds list (no big deal). I can explain that based on "a blood test based on a single gene, I need to adjust this drug to match your body." I'm not sure I can use that pattern for more complicated issues.

    One of Medicine's prime ethics is "Patient Autonomy", which implies that a person needs to understand a situation enough to exert his/her own choices. It's hard enough now trying to explain screening tests and number-needed-to-treat vs number-needed-to-harm and relevance to populations. This is going to be a large problem for the clinical side to grapple with...how to explain this new information/world to each other AND to our patients.

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