Monday, October 20, 2008

The Personal Genome Project

Today at 4pm, my genome will be released publicly at the Personal Genome Project (PGP) Site.

As part of the PGP's first 10 participants, I contributed my entire medical record, phenotype, and genotype in the hope that this data will support research to enhance personalized medicine for future patients.

The first analysis of my genome reveals:

1. I carry a mutation for Hereditary Motor and Sensory Neuropathy with Optic Atrophy (HMSN VI), also known as Charcot Marie-Tooth disease. Specifically, the base pair change is

Chromosome 1, MFN2 (mitofusin 2 protein)

My father has had Multiple Sclerosis for 18 years and thus my family has had many discussions about neurological disorders. HMSN typically affects patients in their childhood and thus far, no one in my family or me has been directly affected.

2. I'm heterozygous for Severe Combined Immunodeficiency Disease (Boy in a Bubble Syndrome)

Other than 2 episodes of Lyme disease, I've not had any infections requiring treatment nor has my daughter.

3. I have 2.23 times average risk for Prostate Cancer.

The papers about this particular mutation studied two simultaneous mutations and I only have one. Thus, it's unclear if a single mutation has the same risk as two.

4. I have a no Kell antigen which could have implications for future blood transfusions. If I was ever transfused, I could develop antibodies against Kell antigens that could cause a transfusion reaction upon a second transfusion.

5. I have several mutations which put me at increased risk for Tuberculosis.

During residency, I led the TB service at Harbor UCLA Medical Center. Several of my fellow residents developed positive PPD's, but I did not seroconvert. Thus, after extensive exposure, I've remained PPD negative, so I appear to be doing well despite the genetic risk.

What does all this mean?

1. I will certainly be aware of any neurological or ocular findings in any family member

2. My PSA is .4 and my prostate exam is completely normal. I will take any changes in prostate health more seriously than before.

3. I've encouraged other members of my family to get involved as future PGP subjects. Is there any relationship between my father's MS and the mutation I carry which causes Hereditary Motor and Sensory Neuropathy? Is there any relationship between the mutation for Severe Combined Immunodeficiency Disease and my mother's Celiac disease? These and other research questions will be possible as more people, including those in my family, contribute their lifetime medical records and genomes to PGP.

I'll share all my experiences with the Personal Genome Project and the release of my genome via my blog. You'll also find a podcast on the BIDMC website.


mxganse said...

After seeing you at the Red Hat conference this past summer and keeping up on the genome project, I am looking forward to reading the report. I'm not a doctor, so I hope the project releases results in a easy to read language.

I work for a major medical diagnostic company, and I have been encouraging our business to invest in this sort of technology to drive certain growth in something that I imagine will be VERY popular.

Austin said...

My question is this: How do you get your genetic makeup tested? I've looked at services such as but $399 is out of this college student's budget.

John Halamka said...

The price of testing is falling rapidly from $300 million from Craig Ventner, to $1 million for Jim Watson, to $10,000 for the PGP participants. Hopefully in another a year it will be under $1000. For now, total genome sequencing is limited to research such as PGP.

Mark Boxshus "Cookie Doctor" said...


You should be commended for your participation. I developed CMT later in life, and having this technology 10 years ago, might have resulted in a significant change in my day to day health care as well as physician input. But then again, the medical community is still learning about CMT and all of it's nuances, so it might have been a bit of a crap shoot at best. Keep up the great work. BIDMC is leading the way with some very cutting edge research as well as offering support and facility accommodations to medical non-profit associations seeking a home for members to congregate. I thank you and everyone else at BIDMC for taking a supportive, as well as a personal role in aggressively pursuing new technologies and embracing those that require additional help.


Mark P Boxshus
New England Support Group Leader
Charcot Marie Tooth Association

Unknown said...

I'd be very careful about believing that you've got alleles that predispose you to one thing or another.

What happens a LOT of the time is researchers find what they think is a correlation, and then other people repeat the experiment, on a larger scale, and don't see the correlation. But you tend not to hear about that second experiment.

So unless researchers have a proven mechanism down for why that mutation causes that predisposition, take those assesments with a huge grain of salt. I heard a presentation where the researcher suggetsed that 90% of such correlations aren't borne out in larger tests, so that prostate mutation may not be as worrisome as you think.

John Halamka said...

Thanks for all these comments. It is certainly true that the technology is nascent and there may not be a direct relationship between a mutation and a known mechanism of disease. However, I will continue to report everything that is learned about my genome transparently via this blog. Since my cell lines and genome are now available to the world, I expect that many new interesting findings will be circulated.