March 07, 2012
The Transition To A DNA Data Rich Environment

A New York Times piece by John Markoff looks at the rapid rate of decline in DNA sequencing costs and the implications for the rate of progress in biomedical science.

“For all of human history, humans have not had the readout of the software that makes them alive,” said Larry Smarr, director of the California Institute of Telecommunications and Information Technology, a research center that is jointly operated by the University of California, San Diego, and the University of California, Irvine, who is a member of the Complete Genomics scientific advisory board. “Once you make the transition from a data poor to data rich environment, everything changes.”

We are living thru that transition. The flood of human genetic sequencing data is easily going to rise by 6 orders of magnitude in this decade and probably much higher that. Not only will a substantial portion of the population get themselves sequenced but also each person with certain diseases (notably cancers) will get many different biopsies sequenced.

As an important example of how everything changes in a data rich environment British researchers find that different samples from the same tumor have more different than shared genetic mutations.

They found around two third of genetic faults were not repeated across other biopsies from the same tumour. The research was published in the New England Journal of Medicine.

The ability to fully sequence a cancer cell's genome will allow sequencing of many different cells from the same cancer to identify all the mutations and then to figure out which of the mutations are important in enabling the spread of cancers. A cancer patient then could get a series of cancer treatments aimed at each cancer cell subpopulation that has specific mutations which require special handling.

Share |      Randall Parker, 2012 March 07 09:55 PM  Biotech Advance Rates

PacRim Jim said at March 8, 2012 1:32 AM:

Since it's not which genes you have, but which genes are turned on, it seems more important to monitor one's epigenome, preferably in real time, as impossible as that now sounds.

Schreal said at March 9, 2012 6:23 AM:

I suggest you read "The Creative Destruction of Medicine" by Dr Eric Topol, a prominent cardiologist. It's a very inspiring book, and he shares your concern about medical "gatekeepers," but feels access to information will ultimately be democratized.

As an example of the entrenchment of medical paternalism, he mentions that in 1960 90% of doctors would refuse to tell their own patients that they had cancer!

Randall Parker said at March 11, 2012 7:17 PM:

PacRim Jim,

With cancer genetic mutations turn on genes and turn off other genes to make cells grow uncontrolled. The ability to sequence hundreds of thousands or millions of tumor DNA samples will lead to the identification of which mutations enable cancer and how. That's extremely valuable.


Thanks. I'll add Topol's book to my Kindle.

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