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Topol on Genomics

Getting My Whole Genome Sequence

etopol, MD, Genomic Medicine, 11:24PM Dec 14, 2012

Eric Topol, MD: Director, Scripps Translational Science Inst.


In this segment, I describe the experience of seeing the 3.3 million variants in my genome compared with the 3 billion bases in the reference human genome on my iPad via the 99-cent "My Genome" app. This comes after participating on the faculty at Illumina's inaugural "Understanding My Genome" conference and is of particular interest considering a review paper we just published on the role of pharmacogenomics in clinical practice.

Harper AR, Topol EJ. Pharmacogenomics in clinical practice and drug development. Nat Biotechnol. 2012;30:1117-1124.


Below is a transcript of Dr. Topol's post "Getting My Whole Genome Sequence." We look forward to your feedback.

This segment is about consumer genomics, and I'm going to talk a little about my experience with having my whole genome sequenced.

This is something that I've been looking forward to for quite a long time, but now I have my full report and my whole genome and its variants are loaded on my iPad, so I can look up, at any time, matters of interest.

For example, if I wanted to look up drug interaction variants that I'm particularly interested in, whether it’s cardiovascular or neurologic, or susceptibility to a particular cancer mutation types, whatever, this is pretty remarkable. After you get your sequence done, you can view the data via a MyGenome App, available for $0.99, and it displays the data on your iPad – and it can keep you busy. I actually had 3.3 million variants compared with the reference genome, and about 22,000 of these were in my exome, in the coding elements.

That's a lot of variants. I can spend literally the next several months, perhaps years, looking up each variant. There's pretty nice graphics here – you have the capability of going right into the actual base change.

I’ll pick out a condition to go over with you and see what it looks like. Let's say I go into Alzheimer disease and the various variants that I have in that region here at Alzheimer: PSEN1/2, APP, and APOE1 are all here. You just tap on a gene. I wish I had that APP variant, which is protective from Alzheimer disease with cognitive decline through the 9th and 10th decades, but, unfortunately, I don’t have that.

If I go into one of these genes, I can go right to the actual change in base. I can look at the region and just pinch around on the iPad, and I can go in directly and hyperlink to the articles written about it. I can get all of the information about that particular variant that exists today through the iPad. Pretty nice, it can keep you busy.

At the moment, has it changed my life? No, obviously not. But it might when a few million people are sequenced with various conditions and have phenotype matching of rare low frequency variants that we've recently reviewed in segments in the last few months with susceptibility variants, particularly in the area of pharmacogenomics.

I want to call your attention to an article that my colleague Andrew Harper, a medical student, and I, published in Nature Biotechology, reviewing pharmacogenomics. These variants are so powerful – they are relatively high in frequency and have high odds ratios and high penetrance – very different from most disease susceptibility variants, so we're going to learn a lot more about those.

Going back to consumer genomics, you can get the 23andMe service now for $99, and with that has a panel of genes about 21 drugs – including caffeine, which has an important association with myocardial infarction for those who are slow metabolizers. You can get information on all these other drugs that are in common use. $99 is a pretty good bargain – it would probably cost a few hundred dollars if one were to send out for separate results on each particular drug. This is a particularly interesting development, to see consumer genomic panels go that low. That's, of course, for genome-wide scanning, which gives a lot more information than just pharmacogenomics.

What I'd like to summarize here is that we're hitting a new kind of enhanced phase of consumer genomics. The price has come down for genome-wide scans and pharmacogenomic panels. Take a look at the data that we summarized in that recent review article, and you'll see there's a really striking difference between the common variants in the genome that are associated with drug response, be it efficacy or major side effects, as compared to disease susceptibility variants, which typically have only a small very modest risk increment.

Now, we have whole genome sequencing, which you can get and put on your iPad, at least all the variants that are relevant, so this is moving fast. I actually am impressed that you can graphically look at the data – and someone uninitiated in genomics can really get a pretty handle and look up relevant articles. Sure, this could induce anxiety, but on the other hand, this is an extraordinary amount of information. When used for the right purposes, it could help drive the field of genomics and hopefully will help the physician community embrace and get more accustomed to and assimilated into the era of genomic medicine that lies before us.

I'll be interested in your thoughts about whether you'd like to get whole genome sequencing and I put a poll up for that if it were affordable. I should note that an NPR recent survey said that over 90% would, of about 650 people who were asked. They're NPR listeners so they are, of course, a special skewed audience, so I'll be interested to see what our physician audience on the Genomic Medicine site has to say about that one.

Thanks for tuning in to another segment here. I look forward to bringing you more perspectives and interesting developments in genomic medicine on Medscape.

Poll: Would you have your whole genome sequenced if this was available for <$1000? Yes|No, waiting for it to be even < $200|No, waiting for millions of people to be sequenced so it is more informative|No, waiting for randomized trials to show this information improves outcomes|Never; this is not ever going to be helpful|
About This Blog

Disclosure: Eric J. Topol, MD, has disclosed he is on the scientific advisory board of Gilead Sciences and an advisor to Quest Diagnostics.

The content of this blog does not necessarily reflect the viewpoints of Medscape.
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