The Personal Genome
We are on the verge of being able to have our genomes sequenced and analyzed. Today in the article “Gene Map Becomes a Luxury Item”, by Amy Harmon of the New York Times, Ms. Harmon describes how wealthy people are beginning to sign up to have their genomes sequenced and analyzed by Harvard Professor George M. Church’s company Knome at a price starting at $350,000. (Knome is pronounced “know me”, and the company’s web site proclaims “know thyself”, a play on the company’s name.)
University of California—Davis Professor Jonathan A. Eisen, on his The Tree of Life blog, jokingly complained that Ms. Harmon had interviewed him but had discarded his quotes. Ms. Harmon, good sport that she is, responded in the comments by contributing outtakes of the article that included discarded quotes from Dr. Eisen and from J. Craig Venter.
Dr. Venter, of course, has already had his genome sequenced and analyzed by his institute, the J. Craig Venter Institute in Rockville, Maryland. The paper describing Dr. Venter’s genome was published in PLoS Biology. Dr. Venter has written a book, A Life Decoded: My Genome: My Life, and a good review is available on Dr. Jonathan Badger’s T. taxus blog.
Dr. James Watson, one of the co-discoverers of the structure of DNA, has had his genome sequenced; the data are available at the James Watson’s Personal Genome Sequence Browser web site at Cold Spring Harbor Laboratory.
Dr. Church has also organized the Personal Genome Project. This project will sequence and analyze the genomes of volunteers, who will share their medical records, making the data much more useful. I wrote eight days ago about the 1000 Genomes Project, for which medical records will not be available. A blog about the Personal Genome Project, named The Personal Genome, is written by Jason Bobe.
Another company that is providing personal genome data is 23andMe, which provides a blog named The Spittoon. For about $1000, 23andMe obtains data on nearly 600,000 single nucleotide polymorphisms (SNPs) and provides a genetic analysis of the data. Andrew Scheidecker had his genome analyzed by 23andMe in December, 2007, and wrote software called Personal Genome Explorer that made his data available to everyone.
The goal of inexpensively obtaining a genome analysis was deemed important enough for the Archon X Prize for Genomics to promise an award of $10 million for the successful sequencing of 100 genomes in 10 days at a cost of less than $10,000 per genome. See “$10 Million Prize Set Up for Speedy DNA Decoding”, by Nicholas Wade of The New York Times.
Other companies that have developed high-throughput sequencing technologies that might make the relatively inexpensive genome within reach are 454 Life Sciences, Helicos BioSciences, and Pacific Biosciences. Dr. Eisen saw a talk about the Pacific Biosciences technology and came away enthusiastic, writing in his blog:
But it was the last talk of the whole meeting that really did blow my mind. It was from Steve Turner from Pacific Biosciences. He presented an overview of their sequencing technology as well as a tiny bit of data. Now, normally I am uninterested in marketing talks where little data is presented. But this talk was different. First, their technology clearly has enormous potential for revolutionizing the sequencing field. Basically, what they are doing is reading the activity of a DNA polymerase as it replicates a single DNA molecule and they do it in real time. He referred to this as using the DNA polymerase as a sequencing engine and then he took the crowd through the details of the technology and some of the modifications they have made to make it work better.
Ms. Harmon’s article is one of a series in the New York Times named The DNA Age; another good article written by Ms. Harmon is My Genome, Myself: Seeking Clues in DNA. Other good articles at the New York Times on personal genomes and high throughput sequence are “The Race to Read Genomes on a Shoestring, Relatively Speaking” and “Working by Eavesdropping on DNA Doing Its Work”, both by Andrew Pollack.
In a few years, it will be routine for everyone to have their genome sequenced and analyzed. It will take a long time to get the quality of the predictions up to a useful level, however. How much of the genome needs to be sequenced to obtain an accurate analysis, 600,000 SNPs (23andMe) or the full genome (Knome, Personal Genome Project)? I personally am interested in having my genome analyzed because, as a scientist, I am always interested in data. However, I would consider the genetic analysis to be speculative until many more genomes have been analyzed.
Notes added on 6 March 2008:
The Genetic Future blog has a post from 22 January 2008 about negative reaction to 23andMe.
I learned from GenomeWeb today that on 8 February 2008, Helicos BioSciences announced that it had sold its first sequencer. Yesterday, Expression Analysis confirmed that they were the purchaser. Expression Analysis said they will use the sequencer for “de novo sequencing, candidate gene sequencing, and digital gene expression.”
March 04 2008 10:48 pm | Biology
