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Response to “The hype for DTC Genome scans is waning”

From Steve Murphy: http://thegenesherpa.blogspot.com/2009/04/genome-app-store.html

I was reading an article in the economist the other day, a good article mind you. It turns out that Drew Yates was correct. It appears that the hype for DTC Genome scans is waning……

Well, there’s no direct reference on Think Gene about how the media’s enthusiasm for DTC Genomics would wane, so I’ve posted the following two emails from my gmail account which were mailed to a small private mailing list of some of Steven Murphy’s medical friends.

These are my emails, and the list is dead (it never went anywhere), so I’ve scrubbed any names and quotes from private emails and posted my letters here with their attachments appended as images. Yah, it’s blog fodder, but I have else nothing interesting to write about genetics right now other than that law in congressional hearings about regulating genetic tests —but I’d assume people who care or matter already know about it.

Thu, Dec 4, 2008 at 1:32 AM

[#],

[email quote]

[response to quote, not interesting without quote]

[email quote]

Extending the Britney Spears idea, the only thing America loves more than its heroes —is to tear them down.

SNP chip testing is in a hype cycle, and both the peak and the trough are irrational and destructive. The Times #1 invention was probably the apex of this period, and we already know that the industry is in for hard times regarding Navigenics, deCODE, and continued economic difficulties.

As for foxing:

The cycle is predictable. Here’s how it will go:

  1. Something new and futuristic! Wow, DNA and mutations, just like in comic books!
  2. 23andMe is the most important invention in the world.
    [we're about here, 03/12/08]
  3. “Have we gone too far?”
  4. [DNA company hero] stumbles: A prosaic, hard-hitting piece about serious doubts.
  5. Genetic testing is a bunch of bollocks and everybody involved is a greedy hack. We’re wasting money on astrology and astrologists. Back to basics!
  6. [some very good study] reports application of genomics with obviously positive results
  7. Genomic medicine is another ordinary tool with it’s own applications. People trust it for what it is, and media coverage dims to mean neutral hum.

The prosaic medical truth can’t compete with hype like “What if my son could be a pro football player and I don’t know it?” (yes, that is a direct quote from the NYTs about ACTN3) However, it does compete quite well when everybody is cynically scrambling for The Black And White Truth.

We know that will happen, so our strategy is simple: Be honest, be transparent, be available, be consistent. No hype. Just responsible medical professionals reliably providing respectable medical advice and best-effort expert opinions —except from a genomic specialty perspective. The public will find you when the truth is fasionable again, and you won’t have to spend millions of dollars to win the hype game.

Sure, we’ll eventually apply cool technology like http://www.justin.tv/claudian to medicine (instead of watching people play World of Warcraft video games), but so what? It’s the trust and the truth that matters, and that’s what will have lasting value to you and others.

Conveniently, in addition to a winning strategy, this is also The Right Thing to do.

Since the public is conditioned to forget everything since Last Thursday, the entire history of the cycle is forgotten, and the cycle repeats. The last hype cycle was HGP; the next one will be full sequencing. So while it’s going to easy to be the voice of reason while hype trajectory is negative these next couple years, the challenge will be when some VPBIZDEV! or silverspoon VC flashes millions of dollars in your face to launch the next hype wave or front some huckster company’s reputation when fashions change. Say no; they find some other yahoo; they pay to make that yahoo look like Time’s #1 Innovator; you’ll be made to feel like a curmudgeonly has-been.

Remember Dr. Michael Nierenberg.

You can’t pay people to honestly care about what they do. The truth isn’t a marketing expense.

-drew

the-hype-cycle

Sun, Dec 14, 2008 at 8:10 PM

[#] and [#],

I disagree that it’s better that Navigenics is trying to include doctors while 23andMe is trying to market itself as a consumer product. Both companies provide similar, medically questionable tests to the public, both companies launder accountability for their claims through clever marketing and the press, and neither company assumes any responsibility for the consequences of their reports. But I believe that 23andMe is on the line of what is permissible, while Navigenics has crossed that line. Thus, I propose that the medical community direct 23andMe by example to eventual responsible preventative medicine by punishing Navigenics and promoting Coriell PMC. This is the pragmatic path to produce the most good, as I will elaborate.

Note I have attached relevant evidence for any statement I have made regarding the claims of any company. These attachments are sized to be used as PowerPoint slides for your convenience. All original documents are freely available online.

Also, feel free to forward this along to whomever this may be interesting

Navigenics

As the physician, it’s your responsibility to act in the best interest of the patent. However, Navigenics clearly states that it accepts no responsibility in all contexts —including medical advice. Thus, no responsible physician can promote Navigenics.

Yet, Navigenics continues to promote themselves as “partnering with physicians” to provide their “Health Compass” service to “ensure state-of-the-art medical advice” and to “help you make informed, personal health decisions.” Left unchallenged, these statements will continue until they are assumed true. Thus, no responsible physician may practice non-participation.

I have yet to see one single actionable medical claim about Navigenics —a fact explicitly expresses in their Terms and Conditions (excerpts attached) and never contradicted by Navigenics‘ medical director, Michael Nierenberg. Thus, in a “partnership” between Navigenics and a physician, Navigenics gets all the money and the credit, the patent gets to pay more for less care, and the physician gets all the liability and the work of producing the medical advice. This is your roll in the “medical revolution” pledged to you by your bleached-out BIZDEV! “friends.” Participate, and you’re either a sucker or a sellout —not a responsible physician.

Worst of all, Navigenics thinks that they can sell “medicine that’s not medicine” through clever marketing and physician partnerships, enriching Navigenics now while they dodge the liability of medical responsibility later. For the same reasons that credit-swapping “insurance that’s not insurance” should have never been tolerated, this kind of “is isn’t” sophistry sets an industry precedent by which one may sell  a promise now without accepting any of the expected future value of liability already built into the system to prevent abuse. Like insurance, since preventive medical advice is an abstract promise, once the precedent of accepting no liability has been set and successfully tested, non-liable preventive medical advice can be infinitely created and sold with no physical limits… until the system breaks. Understandably, some people will be less likely to trust non-liable advice. The solution is to package non-liable advice with liable, trusted medical institutions until the public is so confused that it is unable to sort reality from fiction. Finally, once the business model of selling free and infinite non-liable medical assets by packaging them with and laundering them through trusted medical advice has been sufficiently demonstrated to the investment community, responsible ventures will not be competitive for investment capital.

Thus begins the great genomic industry sellout race to zero trust. At the end, disposable start-up companies like Navigenics cash out and collapse (or just collapse), and surviving trusted institutions of medicine get stuck with the loss.

Navigenics is an unprofitable venture-funded web start up created by Silicon Valley investors to test the limits of the personalized medicine market. I propose that the physician community compose the results of that test. Those results should be this message:

* A market for responsible, actionable, honest preventative medicine exists and holds great promise for patients, investors, physicians, and scientists.
* This new market is not accessible to irresponsible, inactionable, dishonest companies.

While my case makes promoting Navigenics in the medical community quite difficult to justify, non-promotion through inaction is not acceptable, either. If Navigenics fails without the message above promoted by a clear and unified leadership in the medical community, Navigenics will be free to compose its own history. That history will be that “market forces” made personalized medicine non-viable and non-applicable, that Navigenics was “ahead of its time,” and that Navigenics‘ failure itself is proof that “the market is not ready for personalized medicine.” In addition to being false (as long as people die, there will always be a market for demonstrably better health care), the immediate consequence will be a freeze of investment capital in anything claiming to be personalized medicine and a widespread, enduring skepticism towards the preventative medical community. Since “the market” was blamed, nothing will be learned, and the same irresponsible practices will be tested again in different market conditions.

Thus, for the case I make above, I propose a unified attack on Navigenics to promote the message that non-liable medicine by marketing is fraud and will not be tolerated.

23andMe

The pragmatic, political reality is that 23andMe is the public pet project of a billionaire’s wife. It’s not going to die, it’s not going to be thwarted by institutional disapproval, and it has to go somewhere.

Thus, I propose to let 23andMe have their novelty consumer web service “data democracy,” but firmly block any implied medical application until the accountability and clinical application demands of the medical community are met. It’s wholly appropriate to have no medical opinion about an inactionable novelty consumer product so long as that product is not marketed otherwise.

Maintain state control: you want to know what 23andMe is going to do and why. Do this by blocking where you don’t want them (irresponsible preventative medicine) and making it easy for them to be somewhere that’s not valuable to you (novelty consumer web services). Don’t unilaterally block them with weak ideas like “your feelings as a doctor” because that offers 23andMe no acceptable response. Again, 23andMe has to go somewhere, so offering no acceptable response forces 23andMe to behave unpredictably (and in your offered context, unacceptably) without achieving any useful objective. Worse, sloppy, disorganized attacks brand you as uncooperative partisan to be mitigated —not a as leader. That will be a problem for you in Silicon Valley as the medical application of informatics and the internet continues to advance. Maybe impulsive attacks once helped galvanize the medical community when 23andMe was first announced —and maybe that was necessary at the time— but these impulsive attacks are now counter-productive and should be discouraged.

Further, unlike Navigenics, 23andMe is far more transparent regarding the scientific data justifying its reports and openly engages the scientific community. This transparency should be rewarded, not punished, and using this transparency to justify impulsive attacks will set a president that transparency is an untenable liability in preventative medicine. This helps nobody. Again, while scientific transparency may not be appropriate to include in medical advice, it is absolutely appropriate to include in novelty consumer web services.

Thus, for the case I make above, while both Navigenics and 23andMe are guilty of irresponsible medicine by marketing, I propose that the medical community permits 23andMe to exist as a novelty consumer product only with no medical insinuations until 23andMe chooses to practice medicine responsibly. That choice will be made when the publicly stated criteria to earn the acceptance of the medical community have been met:

* Declare the demonstrable clinical utility of the test as backed by falsifiable, actionable medical claims.
* Fully accept the appropriate medical liability and responsibility for providing those medical claims.

deCODEme

deCODEme has blundered into the same “medicine that’s not medicine” fraudulent territory as Navigenics, but they do not make as good of a negative example as Navigenics does because deCODEme is not the DTC genomics leader. If deCODEme survives, it will follow the examples of others, so I propose no special effort to make them a negative example. It’s more important to focus the already diluted messages of the personalized medicine community than it is to be “fair.” However, I propose to hold deCODEme to the same standards as Navigenics if the challenge arises.

Coriell Personalized Medicine Collaborative (PMC)

Coriell is a non-profit medical research institution providing the same SNP testing technology, but as a responsible, accountable medical research collaboration to determine its clinical application. Coriell provides its SNP tests at no cost to participants, and they only offer testing in a medical setting, not directly to consumers through the mail. Further, Coriell fully claims that their genomic tests are to be used by physicians to produce actionable medical advice (NOT as “information only”). Finally, unlike other SNP test competitors, Coriell has always operated with CLIA certification, has always operated under the supervision of an Informed Cohort Oversight Board (ICOB), and has obtained a Certificate of Confidentially which authorizes Coriell “to withhold the names and other identifying characteristics of individuals who participate in the CPMC… protecting against the compelled disclosure of any personally identifiable information in any Federal, State, or local civil, criminal, administrative, legislative or other proceedings.” No other similar service offers this protection.

In short, Coriell is what personalized medicine should be that 23andMe and Navigenics are not. However, Coriell needs our help, because rather than depending on glamorous marketing, elite press relations, celebrity parties, and top venture capital connections, Coriell trusts that the public will recognize and appreciate its medical responsibility and non-commercial modesty. Sadly, this is not how the world works —unless you, the medical community, make it so.

Steve and I have some ideas how we can help as a community, and we’ll make announcements soon when we can present something concrete.

Conclusion

There is no reason why valuable medical advice can’t be theoretically generated by computers. However, the unclear accountability of such computationally generated medical advice is alarming, and a precedent of responsibility, transparency, and accountability must be set now. Initiatives like “evidence-based medicine” are evidence that medicine has been evolving from scholarship to informatics these past two decades. Changes will happen quickly. All we ask is your continued attention and support because ethical medicine is so vital, but it won’t happen without enthusiastic community guidance. The free and open software running the world’s Internet was started by one programmer posting to a mailing list. The same can happen in medicine. Let’s work to make something great!

-Andrew Yates
Helix Health Network

23andme-tos-highlights-1navigenics-tos-11coriell-0privacy-11


Why the “Database Sale Story” is Silly

It’s not a sale if your left hand pays your right.

Left… 23andMe: Right! Google (the world’s most successful mass computation company… and the most profitable)

Left… deCODEme: Right! deCODE (a genomics research company)

Left… Navigenics: uhhhhhh…. You don’t sell your test at a 250% mark-up from your competitors if your plan is to build the biggest genomic database first. However, you might lie about how the real market is “for the database” later when nobody buys your product… and hope that nobody remembers that the “customer” for that database is already supposed to be fronting the losses of your business.

I’ve heard chatter that some people are upset because 23andMe is likely getting special pricing from Illumina and that they are selling their tests ludicrously below cost.

23andMe isn’t operating by the meritocratic rules of business of profitability because of their private connections?

Gosh gee golly! That just ain’t how alls I remember learning the American Dream back at the ol’ high school like.

Well, don’t worry. Good ol’ Midwestern morals always win in the end, and attempts to nuke the market by artificially lowering the price are never rewarded.

I promise.

Scientists use Iceland’s genealogical database to pinpoint the heritage of a deadly disease

A collaboration of scientists from Iceland and the United States has used Iceland’s genealogical database (by deCODE genetics) to trace the ancestors of patients suffering from hereditary cystatin C amyloid angiopathy (HCCAA). Analysis shows that the deadly mutation in the cystatin C gene, L68Q, derives from a common ancestor born roughly 18 generations ago, around 1550AD. Details are published June 20th in the open-access journal PLoS Genetics.

This dominantly inherited disease, which is due to a mutation in cystatin C (L68Q), strikes young adults with healthy blood pressure. The disease results in death from repeated brain haemorrhages, on average by the age of 30. The origin of the mutation causing HCCAA was previously unknown, but using DNA haplotype analysis the scientists have shed light on the history of this autosomal dominant disease that has high penetrance in contemporary Icelanders.

The scientists found that 200 years ago, obligate carriers of the mutation lived a normal life span compared to the control population (their spouses). In carriers born around 1820, however, a trend of shortening life span began, resulting in an average life span of only 30 years in people born around 1900. This 30-year lifespan has stayed constant since then in both men and women.

At the same time, a matrilinear effect appeared whereby those who inherited the mutation from the mother died earlier. For carriers born after 1900, the difference is a loss of 9.4 years for those who inherited the mutation from their mothers rather than their fathers. Based on this information, the authors propose that the traditional diet of the nation (which in the past consisted largely of whey-preserved offal as well as meat, dried fish, and butter) “protected” the mutation carriers for almost 300 years until the Icelandic diet changed early in the early 19th century, exemplified by drastic increases in imported carbohydrates and salt.

This finding has implications for studies of Alzheimer’s disease as cerebral amyloid angiopathy (CAA) is almost universally found in Alzheimer’s patients and normal cystatin C protein is one of the proteins found in amyloid in brains of Alzheimer’s patients. Studies are underway to try to elucidate the risk factors with the hope of providing a preventive stategy for cystatin L68Q carriers.

Source: Public Library of Science

Palsdottir A, Helgason A, Palsson S, Bjornsson HT, Bragason BT, et al. (2008) A Drastic Reduction in the Life Span of Cystatin C L68Q Carriers Due to Life-Style Changes during the Last Two Centuries. PLoS Genet 4(6): e1000099. doi:10.1371/journal.pgen.1000099

Josh says:

This is amazing. It almost makes me wish that the United States and other countries had a database like Iceland does, except I don’t really trust the US government. Regardless, as the costs for sequencing decrease, we should start to see more discoveries like this.

Fun: Icelandic DNA Runic Reading

Last week, I visited deCODE Genetics in Reykjavík, Iceland. To culturally prepare (procrastinate work), I hit my trusty Wikipedia to research all about Iceland.

Obviously, the first thing one needs to know when visiting Iceland is the ancient Viking runic system.

So, for a bit of Icelandic-cultural bio-blog genomics flare:

DNA Binary Rune Name Translation Unicode
AA 0000 (00) fe rune fe wealth 0×16A0
AG 0001 (01) ur rune ur rain 0×16A2
AC 0010 (02) thurs rune thurs giant
(as in Thursday)
0×16A6
AT 0011 (03) aesir rune as aesir 0×16AC
GA 0100 (04) reidh rune reidh journey 0×16B1
GG 0101 (05) kaun rune kaun ulcer 0×16B4
GC 0110 (06) hagall rune hagall hail 0×16BC
GT 0111 (07) naud rune naud need 0×16BE
CA 1000 (08) iss rune iss ice 0×16C1
CG 1001 (09) ar rune ar boon 0×16C5
CC 1010 (10) sol rune sol sun 0×16C8
CT 1011 (11) tyr rune tyr Tyr
(as in Tuesday)
0×16CF
TA 1100 (12) bjarken rune bjarken birch 0×16D2
TG 1101 (13) madhr rune madhr man 0×16D8
TC 1110 (14) logr rune logr waterfall 0×16DA
TT 1111 (15) yr rune yr yew 0×16E6

These runes and translations are from the Icelandic interpretation of the Younger Furthark runic system. (see runic font help below if rune characters appear as “?”) (runic letter pronunciation guide)

Two 2-bit (4 bases) bases together make a 4-bit number (16 runes). Nucleotide base numbering is based on this representation:

Base Purine[0]
Pyrimidine[1]
ID Base Number
adenine (A) 0 0 00 = 0
guanine (G) 0 1 01 = 1
cytosine (C) 1 0 10 = 2
thymine (T) 1 1 11 = 3
uracil (U) 1 -1 -11 = -3 OR
100 = -3

This representation is convenient because the Base Number both identifies the base as a Purine or Pyrimidine and can be inverted to get the base’s matching Base Number. (how are bases usually represented in bioinformatic software?)

~A = ~(00) = 11 = T or U
~G = ~(01) = 01 = C
~C = ~(10) = 10 = G
~T = ~(11) = 00 = A
~U = -(~(11)) = -00 = 00 = A

Font Support

To display Unicode Younger Futhark rune characters, you need a Unicode font supporting the Unicode runic range (pdf). I use Junicode (download font). To enter characters, the easiest way to enter non-standard Unicode characters on any system is to copy-and-paste from a text table (Wikipedia’s Unicode table of runic characters in plain-text).

FAQ

Q: Why not codons, the standard grouping of three nucleotides?

A: Because that would be 64 (4^3) symbols, and that’s too many to remember. However, if you don’t mind 64 new symbols, the Cirth runic language from “Lord of the Rings” has 64 runes (60 letters + 4 punctuation marks) —and it’s in LaTeX! (However, Cirth is not official unicode… yet) Using the same base-numbering scheme, one could make a DNA codon Runic map, too.

Q: Why Younger Furthark and not other Runic systems?

A: Because Younger Furthark just so happens to have exactly 16 characters.

Q: I have been to / am from Iceland and I have never needed to know this.

A: That’s not a question.

Q: Have you considered selling “Genetic Tests” by which you take an arbitrary DNA sequence, “translate” it into runes, and make it into some kind of trendy “runic fortune?” Considering that “alternative medicine” is some bazillion dollar industry and people already buy runic shit because it’s “cool” and “spiritual,” you’d probably make a killing… probably more than (technically) scientifically-legitimate genetic testing services.

A: What? What kind of asshole do you think I am? (It’s almost like I wrote my own FAQ questions or something.)

#RuneTable { border: none; margin: 1.6em auto; width: 90%; } #RuneTable tr { padding-bottom: 4px; border-bottom: 1px dotted #ccc; } #RuneTable th, #RuneTable td { vertical-align: top; text-align: left; margin-bottom: 0.6em; border-bottom: 1px dotted #ccc; } #RuneTable th {</p> <p>} td.RuneTable-binary, td.RuneTable-num, td.RuneTable-unicode { text-align: right !important; } #RuneTable td, #RuneTable th { padding: 2px 13px 2px 0px !important; } #BaseTable { border: none; margin: 1.6em auto; width: 70%; } #InverseTable { border: none; margin: 1.6em auto; width: 70%; } #BaseTable td, #BaseTable th, #InverseTable td, #InverseTable th { padding: 2px 13px 2px 0px !important; }