Virtual Children, Genome Sequencing for Everyone, and Forget Genetic Privacy

Chris Dwan, acting senior vice-president of IT at the new New York Genome Center, discussed how to handle the Big Data issues involving whole genome sequencing. Dwan was essentially optimistic that most of the infrastructure for storing and “slinging” vast quantities of genomic information already exists. For most purposes, Dwan argued that researchers and genomic data consumer services companies can store their information in the “cloud” with Amazon and the like and current high-speed internet connections are sufficient for getting data from one place to another.

Referencing Mount Sinai Medical School geneticist Eric Schadt’s recent commentary in Nature, Dwan argued that as whole genome sequencing costs fall to near zero, trying to keep genomic information private will be futile. Unfortunately, our unsettled political climate could result in laws and regulations with regard to handling genomic information written in response to fear, uncertainty, and doubt. Such ill-advised privacy regulations would severely slow progress in turning genomic discoveries into effective treatments. Although I am far from persuaded by his argument, Dwan suggested that since genetic privacy will simply not be possible, laws against genetic discrimination similar to the Americans with Disabilities Act might be necessary.

The next panel dealt with a lot exciting developments in molecular diagnostics, but I will single out Sequenom’s non-invasive test for Down’s syndrome and other similar diseases. Typically everyone has 23 pairs of chromosomes for a total of 46. Down’s syndrome occurs when there are 3 versions of chromosome 21. The new Sequenom test takes advantage of the fact that fetal cells shed into a woman’s bloodstream where they can be removed and tested to see if the fetus she is carrying has Down’s syndrome at about 10 weeks into her pregnancy. The new test is 99 percent accurate.

What’s the Best Way to Sequence a Genome?

The next panel was the battle of the sequencers featuring presenters from Life Technologies, Complete Genomics Inc., Nabsys, Inc., and GnuBio. It’s pretty clear that there’s far more than one way to skin a genome. Life Technologies uses the Ion Torrent chip reader and will release its Proton chip next year which can decipher 1.2 billion DNA base pairs in hours. “The $1,000 genome is actually already here,” declared Life Technologies vice-president John Stark. Rival sequencer Complete Genomics has built a sequencing factory that can decode 1,000 genomes per month. The company has already sequenced more than 7,000, according to chief business development officer Robert Klein. Klein just got his complete genome last week and has been delving into it. He admitted to being a bit disturbed when he uncovered a variant that looked like it might confer some risk of Huntington-like disease. Fortunately, further research suggested that his variant was not pathogenic.

Amusingly, Barrett Bready, CEO of Nabsys, Inc. began by citing a 2010 Reuters article, the headline of which asked, “Did the Failure of Genomics Doom the U.S. Economy?” Probably not, but perhaps new developments in genomics will pull us out. The Nabsys sequencing technology can read 1 million DNA base pairs per second. Finally, John Boyce, the CEO of GnuBio described how his company sequencing system based on emulsions using standardized cartridges can undertake 100,000 reactions per second. However, mentioned by many in the hallway discussions and hovering over the panel was the specter of the absent Oxford Nanopore which promises to sequence an entire human genome of 3 billion base pairs in 15 minutes.

Archon X Genomics $10 Million Prize Announcement

The first day’s sessions closed with a keynote by Harvard University genetics guru George Church. He forcefully argues that everyone needs whole genome sequencing now! After all, there are 2,700 highly predictive actionable tests implicating 6,000 different gene variants already available.

Church announced during his talk that he and Harvard’s Wyss Institute were formally entering the competition for the $10 million Archon Genomics X Prize. The goal is to sequence 100 genomes donated by people who are 100 years old or older between September 5 and October 5, 2013 for less than $10,000 each. The search is on for rare gene variants that protect against disease and enhance longevity. Among many other worthy projects, Church is behind the Personal Genome Project which aims to get 100,000 participants to voluntarily reveal their genetic and medical information so that researchers can begin to link gene combinations more firmly to disease onsets and outcomes.*

Day 2: Friday I will report on the Thursday sessions dealing with designer babies, interpreting the genomic information of healthy people, and what the venture capital world thinks of personal genomics.

*Disclosure: I am a participant in the Personal Genome Project.