$1,000 Genome No Good


Author: 
Theral Timpson

There comes a time when powerful memes that have become widespread begin to lose their value. Is it that time for ‘The $1,000 Genome?’ Mark Boguski thinks so. At the first annual Clinical Genome Conference in San Francisco this week, Dr. Boguski from Harvard Medical School said that the term is actually fallacious. The price of sequencing has come down. And now there are many other considerations, such as the fact that genome analysis will be done several times over the course of treatment he said in a talk entitled “Pathology and the Third Wave of Medical Genomics.” According to Dr. Boguski, the first wave was SNP detection and the second was GWAS studies. Now the clinical genome has its own conference.

Put on by the always capable CHI, the conference has evolved into its present form (last year it was called Beyond Sequencing), and I’d venture a guess that it will go by the new name for some time to come. The room was full. The speakers were top experts from the front lines. I mentioned Harvard Med above, the Mayo Clinic was also represented as well as the Medical College of Wisconsin--the institution which treated Nick Volker.

The conference was perhaps more tweeted than a Justin Bieber concert. I urge you to follow the hashtag #TCGC for a play by play account by the prolific @KevinDavies, who (I think) somehow manages to tweet for @BioITWorld, and @GholsonLyon and others who’ll give you notes from each of the talks.

We are now watching the labor pains and anticipating the delivery of this enormous, complicated fellow, the clinical genome. The conception came over a decade ago, and the baby has grown and grown in complexity and value. Is it already born? Some at this conference would say yes. Some say we’re still getting there. What no one says is that it won’t be.

Some notes I took on the first day included the talk by the bioinformatics star, Atul Butte. We had Atul on the program recently and he talked about how the environment is a big part of our health. “Genetics loads the gun,” he likes to say, “and environment pulls the trigger.” At the conference, Dr. Butte, who is an MD as well as PhD researcher, talked more about the importance of focusing on the environment than I remember from earlier presentations. “The environment can be a perscription,” he asserted, noting that once we know our genome we can seek out conditions that will be good for our genes. “Environmental factors still beat any odds ratios that we’re looking at for genotypes,” he reminded us.

The thought came to me as Atul talked that it would be great to have a conference dedicated to just this topic of genomics and the environment. I mentioned this to Kevin Davies and he directed me to the GET, or Genomes Environments and Traits, Conference started by George Church at Harvard Medical School.

Atul said that “teaching is the biggest challenge” for the clinical genome. There is so much work to be done educating doctors who know little about genomics.

Dr. Boguski from Harvard Med picked up on a comparison made by Atul between the number of clinical geneticists and the number of radiologists. There are 1,000 clinical geneticists and you can add 2,000 genetic counselors for a total of 3,000 experts on the clinical genome. And there are 30,000 radiologists in the country. More and more, radiology is used as the example for genomics. Many years ago experts had to be trained to read an Xray just as someone will have to learn what to do with gigabytes of personal genomic data. Dr. Boguski said that it’s the pathologists, not the medical geneticists who will do the interpretation of the genome.

Then there’s the matter of incidental findings. Should they be reported to the patient? Dr. Robert Green from Brigham and Women’s Hospital again used radiology for comparison. Let’s say a patient has a broken rib and goes to the clinic, he proposed. An Xray is taken and is analyzed by the radiologist. “Do you think if the radiologist sees a tumor or something wrong with the heart he’s not going to tell the patient?”

Dr. Green further provoked the crowd by saying that medicine is not an exact science. “We need to recognize what a mess this pseudo-scientific field of clinical medicine is. It’s complete horse shit!”

“Physicians are only going to learn this when they have to,” Dr. Green says. “We have to send them reports. Even though evidence is insufficient, the clinician must still provide advice, patients must make choices and policy makers must establish policies.”

Again I urge you to follow the hashtag #TCGC for more insight on an exciting field. “We’re watching an industry grow up right before our eyes,” beamed the exuberant editor of Bio-IT World.

Kevin and his colleagues are not just watching this industry grow, they’re doing their part to shepherd it along. Davies has profiled most of the new big data and analysis companies that are emerging at BioIT World.

He’s also the author of a book, “The $1,000 Genome.” It appears the industry is ready for a new title, Kevin.

Here’s a suggestion, “The Clinical Genome: Coming to a Hospital Near You.”



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