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"Personal" Genomics...Part 2

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Cancer Research 101: "Personal" Genomics...Part 2

Monday, April 2, 2012

"Personal" Genomics...Part 2

Rather than amend or append my post on "personal genomics" from earlier today, I thought I would provide a new one that expands on the "personal" genomics thread.

But this time, it is not about privacy, confidentiality or other kinds of ethical concerns, per se. Instead it goes right to the heart of the matter of "just how useful will this information be to the average person", average meaning a person at 'average' or 'slightly above average' risk for a disease.

Some details of a very interesting study were released today at the Annual Meeting of the American Association for Cancer Research (AACR) in Chicago (meeting website here), and published simultaneously in the journal Science Translational Medicine. Authored by a team at Johns Hopkins in Baltimore and led by world-famous researcher Dr. Bert Vogelstein, the study, entitled The Predictive Capacity of Personal Genome Sequencing suggests that the information that might be provided could actually be of limited usefulness.

Rather than me trying to paraphrase the whole thing, I refer you to an excellent article by Gina Kolata in the New York Times today (Study Says DNA’s Power to Predict Illness Is Limited) that offers an excellent recap.

For a second viewpoint, but same conclusions, you can check out this column from  Robert Bazell entitled "Gene tests: Your DNA blueprint may disappoint, scientists say" online also today at

Bottom line, it seems to me, is that we really have to be more careful than ever about exposing ourselves to privacy, confidentiality, insurabililty and other legal and ethical dilemmas, especially if the risks might outweigh the gains in many, if not most, cases.

Clearly there is no definitive pronouncement to be made one way or the other yet - it is far too early days for that. But it is good to have these debates with our eyes wide open.

Sure beats the alternative...

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At April 5, 2012 at 11:57 AM , Anonymous Jim Woodgett said...

A few recent thoughts I posted on this issue of tumour heterogeneity:

Are these findings surprising given the well understood nature of the instability of tumour genetic integrity? Once tumours have sufficiently compromised their DNA repair processes, their rates of mutation are significantly elevated and heterogeneity is bound to increase. We also know that selective pressure (acquisition of drug resistance) can cause watershed shifts in cell populations, allowing new populations to emerge and dominate. Tracking these shifts should yield important prognostic information, unless genomic integrity is shot, at which point using precision tools is likely a wasted effort. Expansion of deep sequencing of genetically unstable tumours will undoubtedly generate reams of data. However, documenting the precise shapes of clouds on one day does not help predict the shapes the following day, or the next.

Why is this important? Answer the amount of money that is being flushed into cancer resequencing. I see little justification for doing this for genetically unstable tumours beyond the initial work that was very informative as a means to tell us about basic properties and similarities between a tumour and a metastasis (e.g. the work of people like Sam Apericio in Vancouver). Next generation sequencing is incredibly powerful and is providing great insights into other diseases, including some genetically stable forms of cancer. But the tool is so powerful a hammer than seemingly to some people, every tumour looks like a nail.

At April 5, 2012 at 2:53 PM , Blogger Dr. Michael A. Wosnick said...


I missed your more recent post in Nature so thanks for linking and expanding on it here.

On March 20, 2012 I posted some similar misgivings in an article entitled: Personalized Medicine [Part 2]- Time for a Reality Check? (link -

In part, very similarly to your comment, I said:

"The second area stems (no pun intended) from the reality that cancer is, at its heart, a set of diseases marked by tremendous genetic instability. The reason that so many cancers are hard to treat is because every time you think you have it pinned down, it morphs into something a bit different.

For example, when a number of the first Gleevec patients started to relapse, the sound of people jumping OFF the bandwagon was an audible thud. Skeptics said "see, we knew it couldn't really work so easily!" Subsequent studies showed, however, that Gleevec indeed worked exactly as advertised, but in the interim, the cancers had “evolved” – they developed some secondary mutations that essentially allowed the Gleevec roadblock to be bypassed. If you put roadblocks up on the main highways, cancer will find a way to take a side road to get out of town. If you block the side roads, cancer often will find some other route."

But the Vogelstein paper at AACR has really started a conversation about the value of whole genome sequencing. That was what I was putting out there in the current post.

But as you no doubt are aware, there has been a huge reaction, pro and con, and I think that some of the sequelae of the Vogelstein et al paper needs to be further documented so I plan to post a new note later today to address the other side of the coin.

At April 5, 2012 at 5:00 PM , Anonymous Jim Woodgett said...

The fundamental problem in cancer therapy is that we tend to treat it in a serial manner (or with drugs that have similar mechanisms of action). Cancer is inherently mutable and if we blow the first shot, it is [teleologically] "warned", making subsequent shots less effective. HIV is also an inherently mutable virus, albeit with far fewer genes, but virologists learned through triple cocktail approaches that even it could be tamed if triangulated from the beginning. I realise there is still a dearth of effective molecular treatments, but if we are to make a significant leap forward, it is going to be through such triangulation rather than reliance on the mythical magic bullet.


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