Adriano Squecco of DNA-forums.org is collecting Y Chromosome information from DTC consumers and compiling an open community ancestry database: Y-DNA-FORUMS [excel spreadsheet] (my results are under “Yates” on the 23andMe v1 page)

Interestingly, he is advertising his project on the 23andMe user boards, which is how I found Adriano and his project. Since users can download their 23andMe (or deCODEme) genomic test results as a text file, any 3rd-party service in a secondary genomic market can provide interpretation and collaboration services without ever handling biological samples over the internet.

This is the future.

The sequencing of the genome itself isn’t as interesting because we know what the end is: a cheap, accurate, complete genomic sequence. We may think of genomic testing today as an obscure luxury service, but the technology will bottom out and sequencing companies will consolidate, all offering the same undifferentiated sequence, all competing on price, economy of scale, and marketing.

Instead, what is interesting, what offers an unlimited potential for differentiation, competition, and innovation —is the secondary genomic market, services which accept biological test results and produce research and interpretation. And while genomic testing is the obvious start for a secondary medical information market, why not any medical test? We already send away blood and cultures to a lab and get back data at medical facilities, why not cut out the middle and do it directly through the mail and the Web?

Que Dr. Steven Murphy freaking out about involving doctors and irresponsibility… except, now we got smart. We’re going to beat the “hackers” at their own game, right Steve?

Introducing HelixGene

PS: obviously, this is just a quick proof of execution. Give us at least more than one night to build a prototype of a radical new model of health care, ok?

Introducing: HelixGene Foundation for Better Genomic Medicine. You email us your medical questions about genomics, our licensed medical genomic doctors email answers. This announcement is our soft-launch: we are accepting and answering emails and paid subscriptions, but we are still building the service and have not officially launched. Our genomic specialist physicians include:

Steven A. R. Murphy, MD (also known as The Gene Sherpa)
Clinical Genetics Fellow, Yale School of Medicine;
Managing Partner, Helix Health, PLLC

Adam J. Messenger, MD
Pharmacogenomics Specialist, Department of Pharmacology, New York
Medical College and Graduate School of Basic Medical Sciences

Matthew B. Lubin, MD

Jennifer Ibrahim, MD

Joy Samanich, MD

Our general subscription is $14.95 per month (FREE first month alpha accounts) to post medical genomic questions to HelixGene’s public forum by email. Private emails are $145 each and will be answered by a HelixGene health professional in 48 to 72 hours.

We DO discuss the medical validity and implications of all DTC genomic tests in a medical setting including: 23andMe, deCODEme, and Navigenics.

For the press, we provide expert opinion services for journalists and sell expert review subscriptions for mass media publications including medical genomic information. To enforce accountability we feel is lacking in medical reporting in the mass media today, HelixGene publishes medical genomic report cards for publications. Pre-submitting your publications and consulting with our experts helps us help you accurately and honestly report medical genomic information to the general public. Ask our about media medical consulting plans including those for bloggers, independent journalists, and major publications. Email us for pricing.

We also host a private, invitation-only genomic specialist forum which is free. If you are qualified, ask for an invitation to our expert forum. This is a forum for doctors and scientists to discuss academic issues, particularly to discuss the merits of new genomic services, academic issues, and troubling medical genomic reporting in the popular media. Email us for an invitation.

Secondary Market Database

I’ve started a database for secondary genomic market services. Please leave a comment here to report new services or send Think Gene an email.

news.thinkgene.com needs moderators to help us edit and delete links. If you’re interested, please send a brief email to admin@thinkgene.com.

Solve this simple math question.

Statistics and disease risks are invented for this exercise!

1% of people will have Hubbub Disease by age 70. Up to 80% of people with Disease will get positive HEBOT mutation tests.  9.6% of people without Hubbub Disease will also get positive HEBOT mutation tests.  A patient had a positive HEBOT mutation test in genomic screening.  What is the probability that patient will have Hubbub Disease by age 70?

The correct answer is about 68.1%. If you got this, good job, you’re qualified, click here.

If you got a different answer or need an explanation, click here.

note: updated to be even more nonsensical to avoid confusion. Thanks, neandrothal.

Josh: For those interested, I wrote a paper for a class 2 years ago applying Bayes Theorum to medicine. It’s moderately related to the post.

I feel rationally obligated to distrust anything self-promoted as “Web 2.0″ in the same way I distrust statistics tacked with some vague quality like “40% more kick!” It’s as if those tacks are nailed right in to the body of Science itself, and I feel its pain. I feel it. Nonetheless, as I can be trusted to regularly grease the world economy $3.29 USD every late night caffeine sortie at the 7/11 across the street, there’s nothing physically impairing me from both believing that savant-like super powers wrought at the heights of all human achievement will give me more energy and help my money work for me while simultaneously loathing the idiocy that same electric blue sans-serif salespitch will sap my attention and wallet if only they could brand their goods with some impressive looking number. You know, like science and stuff. It’s as if behind the decimal point lies a secret realm where mere digits morph into runes of ancient magic, drawing the true, terrible power of tenth decimal place into a furious ball of psychogenic witchcraft burned by marketers into every web service and sugary softdrink for their duplicitous intent of short-circuiting my brain —not impairing rational thought itself, merely its ability to keep my money in my pocket and my faith to myself. It’s a near optimal function to illicit self-disgust.

Hey, I have an idea for a radical new financial instrument, it’s called: the hundredth decimal place. With marketing that tight, I may as well be selling soma to cashiers, right? It’s a brave new world out here on the interwebs, and I’ve got the confidence interval for you right anterior to my magic symbol “%.”

What was I talking about? Oh right.

Bertalan Meskó of Science Roll has officially launched Webicina, a service that sells education material and consulting to doctors about using the Internet and helps them launch a website. Regarding doctor blogs: Dr. Steven Murphy said today about his doctor blog, Gene Sherpas: “all they good things that happened to me this year have come from my blog.” Webicina is a valuable service that I endorse that will help your professional career as a medical professional —and it’s fun, too.

Here’s a funny picture of a dancing little boy wearing decimal point on his shirt. I want you think of it every time somebody uses a decimal point or any other statistic without justifying their significant digits or measurement confidence.

PS: I never want to see the expression “Web 2.0″ ever again, and God help you if I see anybody try to peddle *shutter* “Web 3.0.” To a lesser extent, that goes for that “59.5%” penetrance estimate for g2019s LRRK2 report at 23andMe, too.

You sometimes add a new dimension to blog-ramblings Andrew :-)

Here’s why you need a genetic counselor: http://tinyurl.com/4ccbo6
- and here’s why you might not need one: http://tinyurl.com/4a9ytg

Originally posted as a comment by Sciphu on Think Gene using Disqus.

Story: genetic councilors are people you pay to console you about the results of a genetic test report to make you feel better and help you make rational decisions about your health when your reasoning may be distorted by emotional distress. If that’s a service you want, buy a couple hours from a genetic councilor.

Computers can never provide human consolation, no matter how excellent and rational their reports. Doctors and scientists feel that councilor work is beneath them, nor are they typically any good at it, nor do they realistically have the capacity to do it. However, scientists tend to be much better at analyzing complex information, and medical doctors can use reports to better synthesize a general understanding of your health to recommend medical action not already prescribed by obvious standard practice.

For example, I would probably make an excellent systems biologist, but the world’s worst genetic councilor. “Beep-bop-boop, you have Huntington’s. Don’t have children.” See? A that’s perfectly rational statement, but it’s illustrative why genetic councilors are important.

But how many people in health care today can read the following expression? Or write it? Or tell me what it means not just clinically, but biologically?

re.search('(CAG){36,}',genome[4][3046205:3215485])

Steve at Gene Sherpas reports systemic medical insurance fraud in many top institutions providing genetic health care. Clinics are billing as if doctors are seeing patients, but only genetic councilors ever see the patient. “But I have a solution,” Steve exclaims. “The answer: Nurse Geneticists.” He continues, “Call your insurer. Demand to be seen by a physician or physician extender… Why should you demand this service? It will put stress on the broken system. To repair that system, we must first rebuild the foundation.”

Be careful what you wish for, Steve. Systemic abuses like this that risk high liability for meager reimbursements suggest a deeper problem than petty greed. Either the system has collectively concluded that genetic councilors are sufficient to perform the service and that they are following procedure “in spirit,” or they are desperate to keep unsustainably high margins and must resort to abuse to protect them. I suspect some of both.

The problem genetic councilors is political. Genetics used to be called “eugenics,” literally, “the science of the well born.” After World War 2 and the civil rights movement, it became taboo to socially direct population growth and the practice of human genetics was legally and institutionally castrated. Today’s “non-directive” genetic councilors are the progeny of this purposefully impotent profession.

However, scientific progressed. We discovered DNA. We learned molecular biology. We sequenced the human genome. Suddenly, the members of this small, marginalized profession were both keepers of the hereditary taboo and keepers of the code of life.

So, that’s what genetic councilors are: specialized nurses who aren’t supposed to touch you or tell you to do anything, but who have become the hands, eyes, voices, and smiles of this newest, most vital paradigm of medicine. So long as people need a warm consult and an authoritative opinion, there will be a place for you.

That’s probably the nicest thing I’ve ever said on this website.

Old medicine was dead the day you adopted “evidence-based medicine.”

There, I feel better.

What medicine? Scientific medicine. Mathematical medicine. Mechanized medicine. Terabytes of cited hyper-linked studies compiled into statistically weighted results medicine. Input symptoms and test results, output diagnosis and CPT medical billing code medicine.

Beep-bop-boop you’re dead, have a nice day. (the industry, the not patient, who of this ethnicity and phenotypic profile can expect 55.2% efficacy and 82.1% efficiency over control who received traditional care)

And no other medicinal discipline is as scientific mechanical as genetics. How mechanized? Watch, I’ll make a free clinical diagnosis machine prototype right here on my blog. Yes, not a risk report, a real diagnosis. Just input your genome sequence service account login, and my machine download your genome securely from your sequence service and practice medicine.

Your Sequence Account OpenID URL:

Your Password:

#!/usr/bin/env python
import genome
HTT = genome.autosome[4][3046205:3215485]
if genome.search('(CAG){27,35}', HTT)):
    print "mutable"
elif genome.search('(CAG){36,40}', HTT)):
    print "reduced penetrance"
elif genome.search('(CAG){41,}', HTT)):
    print "positive"
else:
    print "negative"

Would you like to subscribe to our genetic counseling service? Now, only $89.95 a month!
Don’t have a sequence? Sequence with us! Now only $999.
Enter your credit card and you gmail account and password below.

The real question is: are you dead like “mama bell” AT&T, the century-old institution that suddenly crumbled and consolidated. Or, are you dead like the newspaper, a slow and humiliating decline of consolation and standards of with only a few prestigious survivors?

So, OK, some genetic councilors will go back to school for additional nursing or physician assistant credentials, and some genetic centers may begin staffing appropriately if they can afford to despite the gross waste in health care already. But realistically, I’m supposed to believe that genetically-trained nurses are the solution? A new, more expensive kind of medical profession for which academic and institutional support will take decades to mature? When America is straining under grossly inflated health care costs during an economic depression? Meanwhile, I can hypothetically write a Python script to practice medicine and hire a perky and well-educated Indian genetic councilor to answer phones now for cheap?

Have fun breaking the system, Dr. Murphy. It needs to be broken, sure, but I’ll meet you down here at the bottom.

Oh no, my 23andMe!
By, Adoph “Nightwing” Hilter

Oh no, My 23andMe!
Please don’t make me
get an IRB.
If only everyone would forget about me
and not link my wikipedia entry
and call each other “Nazi”
in every popular book about genomics, there is me
in every talk about medical research you dislike, “you Nazi!”
because whatever minor procedural bureaucratic violation with which you disagree
is just like torturing millions of people
and here I brood in my nihilistic eternity

My Mood: Angsty
What I’m doing right now: Definitely not getting an IRB! YOUR NOT INVITED TO MY SPIT PARTYS STEVE!!!!!!1