Sequencing: how clinically relevant is it?

July 29, 2012 Leave a comment

In the interview that I participated in February (gosh it’s been so long already!), the following question showed up:

  • Many critics of sequencing cite that cost (reagents and analytics) and clinical relevance are the two major shortcomings of sequencing. Now that the equipment manufacturers have brought down costs significantly, how about the clinical relevance?

Here are some thoughts. First of all, on the cost side, there still needs to be major innovation in both sequencing chemistry and assembly/annotation infrastructure. The cost needs to go down further, and the analysis needs to be much simpler to have major clinical adoption. Now about the clinical relevance, clinical data are being generated at massive scale already. There are more than 10,000 genomes sequenced in year 2011. At such pace (and growing exponentially, too!), it won’t take much time to pass the inflection point. After all, the clinical relevance scarcity today is mostly due to the lack of data, which sounds ironic cause no prior data has been as massive as WGS data! Of course, you know what I mean: the lack of data stems from the lack of understanding of links between genotypes and clinical features. When you have WGS scale genotype data in hand, all of the factors that act to shape phenotype are to be considered in order to decipher the links, which is why we say we need a lot more data (and smart analysis). The most short-term clinically relevant use of WGS data is the link between genotype and drug response, but just as importantly, it’ll enable new drug-able targets to be defined, and novel therapeutic regimes to be invented. For major cancer types, as fast as 2-5 years later, I believe we will witness sequencing to be adopted as the first line diagnosis test that physicians will order, which will then help to further scale data collection and expansion of WGS utility. In areas where the regulatory burden is much lower (e.g. post-natal, carrier screening, etc.), the adoption of WGS can be even within the next 1-3 years especially if sequencing cost were to keep the decreasing trend.

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What’s the core value of a genomics based diagnostic company?

April 11, 2012 Leave a comment

A blog with no update is dead. I figured that I need to make it a habit to post thoughts in order to keep it alive. So, for today, before I get more time to elaborate more of my previous points about how to apply genomics and sequencing to the clinical world, let me post a question that I have been debating with myself these days.

To a biotech company, which mode works better:

  1. The company is based on a core technology. Markets are addressed by developing applications from the core technology;
  2. The company lives by its commercial set up, network and sales channels in a specific market. Applications are developed eitherbased on the company’s own technology or, more likely, by leveraging existing technologies that some other companies have developed.

One can, of course, find examples of companies living with either mode, or even a combination. There are pros and cons to both modes, apparently. Now, the real question is, for genomics based and clinically focused molecular diagnostic applications, what is the best choice? Strategy precedes tactics, and one should have a clear vision going into the business.

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What’s your vision of the future of genomics medicine

February 16, 2012 Leave a comment

I see the future of genomics medicine to lie in, eventually, health screening. This is the most proactive way to Lee Hood’s vision of P4 medicine. In responsive medicine (which is where we are today), often, patients experience frustrations of having presented internal or even external symptoms but can’t get a clear diagnosis for a long time. With the help of sequencing, physicians will be empowered by genome and transcriptome level abnormalities to better guide diagnosis. But that’s not enough. The future of medicine will aim at preventing any abnormalities from accumulating and eventually leading to symptoms. That’s why sequencing will have to go to the health screening level, and that’s when it’s realizing the true value of preventive healthcare which comes with dramatic care cost savings compared to responsive healthcare.

How would it be done? Whole genome sequencing may only need to be done once or a few times in one’s life time. Transcriptome wise, one can imagine it being used with the same frequency as the routine physicals according to age: every 2-3 years for young adults, annually for middle aged and maybe twice a year for elderly. The main aim of transcriptome sequencing is to catch early signs of abnormal growth. Whole genome sequencing will be done when physicians see the need from symptoms. One can even imagine it replacing many of the routine tests we’re getting today that, for example, measures blood protein/antigen levels as indications of diseases. The cost of such tests compared to regular sequencing will make it a no-brainer when sequencing cost is below $1000 for clinical grade genomes, and below $100 for transcriptomes. At a minimum, sequencing can help to limit those biochemical tests to only serve as confirmatory tools.

How do we get there?

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Moving forward into the clinics: not exactly WGS but it’s getting there!

February 13, 2012 Leave a comment

http://www.bloomberg.com/news/2012-02-12/high-speed-dna-scans-help-most-lung-cancer-patients-study-finds.html

This is very positive. Now we have both Foundation Medicine and Ambry Genetics offering sequencing for cancer care, be it selected sets or Exomes. It’s apparent that discoveries will come mostly from whole genome sequencing, but the use of the more targeted or enriched sequencing in the clinics where costs are lower, speed is faster, and coverage can be even deeper is likely our intermediate solution towards getting the benefits of sequencing.

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Can we make medicine SIMPLE, eventually?

February 12, 2012 Leave a comment

I watched the documentary of Steve Jobs today. I have to admit that even though I have never been an Apple fan, his story made me understood the reason why there are so many of them out there.

What really provoked me into thinking was his philosophy.

The first one is, as a marketing genius, he tossed the traditional mode of product development. As developers, we were taught to get customer requirements first, and to fulfill those requirements with our product design. What Jobs did was bypassing the whole user requirement phase: I know what you want even before you know it. I’ll make a product and you’ll fall in love with it because you’ll come to the realization that this has been what you’ve always wanted but didn’t know clearly what to request.

The second one is, his belief in branding is one word: trust. People have an almost blind trust in that everything that Apple makes is good, and they would buy simply because of that. At the same time, he made sure that Apple delivers to people’s expectation in the trust, and then some.

The third one is, his design ideas are concentrated into two: elegant, and simple. Elegant design makes the product appealing, and simple user experience lowers customer transition hurdle to zero.

I can’t help but to think: can we, in the biotech/biomedical field, make medicine SIMPLE? People have a natural fear for hospitals, for medicine, for doctors, for medical devices, everything. If we want our future medicine to be “participatory” as Lee Hood visioned, can we change people’s fear for our products? Can we, one day, make medicine simple and lovable?

He/She who can solve that may just be the next Jobs.

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An interview about the future of genomics medicine

February 11, 2012 Leave a comment

Recently, I had the chance to participate in an interview with a leading consulting firm who’s conducting market research for their client. With a list of very thought provoking questions, I thought jotting down some points would be helpful for both the interview and for myself to collect and clean up my thoughts. I’ll be posting a few of those interesting ones over the next few weeks as I get more time to clean them up. It turns out that such practices are indeed useful. We Chinese have an old saying that roughly translates into “good memory always lose against clumsy hands”, highlighting the importance of jotting down your thoughts as they pop up 🙂

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What’s Driving Roche’s $5.7 Billion Bid for Illumina – 01/27/2012 – The Burrill Report

January 30, 2012 Leave a comment

What’s Driving Roche’s $5.7 Billion Bid for Illumina – 01/27/2012 – The Burrill Report.

Interesting read (or ‘hear’, since it’s an audio report). What’s your take on Roche’s move? Is it just another merger (think 454 and ion torrent), or is it a turn-point of some sort for the sequencing industry?

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