Reece Hart

A Roundup of Investigations into Direct-to-Consumer Genetic Testing

July 24th, 2010

Earlier this week, the Oversight and Investigation subcommittee of the Energy and Commerce committee of the US House of Representatives undertook an investigation of direct-to-consumer (DTC) testing. To some, this investigation was long overdue; to others, it was a witch hunt by intrusive regulators. In any case, it’s pretty clear that this event will lead to regulatory oversight that will permanently shape genetic testing. Below, I’ve provided a few links with comments and highlights.

First, a brief reminder of some of the recent travails of DTC testing. In June 2008, the California Department of Public Health sent a “Notice to Cease and Desist Performing Genetic Testing Without Licensure or Physician Order” to several DTC companies. In the summer and fall of 2009, deCode, Navigenics, and 23andme contended with financial problems and layoffs that were widely perceived as a “refudiation“ of our readiness to transform genomic data into clinically actionable information or to make this information personally intriguing. (Yes, there are examples of both; I mean that DTC does not appeal broadly for either use — yet.) Then, in October 2009, an “An agenda for personalized medicine” made the shortcomings of DTC testing very public. On May 19, the House Energy and Commerce subcommittee on Oversight and Investigations asked three prominent DTC companies to provide information. On June 8, 2010, 23andme officially responded to reports that 96 patient samples had been mixed up by LabCorp, its CLIA-certified subcontractor. Customers received test results that were not theirs, presumably leading to at least a few cases of swapped grief and relief about genetic predispositions.1 The FDA notified five companies on June 10, and another 14 on July 19, that effectively declare an intent to regulate genetic testing (see the excellent analyses by Dan Vorhaus on the first five and the the 14 more).

With this background, the House Commerce and Energy Committee meeting was a set up for a tough day for DTC testing. There are many great sources of information and commentary. I particularly like the Genomics Law Report and Genomes Unzipped blogs, which often have links to source data. Here are some critical links that cover the pro-regulation and laissez-faire viewpoints:

http://www.gao.gov/products/GAO-10-847T
The GAO, with their 2010 report on deceptive marketing practices and the audio recordings of  telephone counseling, provided damaging testimony that will make nearly everyone’s jaw drop. Think traveling salesmen with hair tonics 100 years later. If you think these were the just the small players, think again: A counselor at Navigenics was caught on tape saying “you’d be in the high risk of, you know, pretty much getting [breast cancer]“. Don’t miss the explosive audio transcripts (3 minutes) of DTC telephone counselors with undercover customers to see exactly how bad this can get. Also see the

2006 report titled Nutrigenetic Testing: Tests Purchased from Four Web Sites Mislead Consumers.

http://reason.com/blog/2010/07/23/feds-think-you-aretoo-stupid-t
http://www.genomesunzipped.org/2010/07/a-sad-day-for-personal-genomics.php
http://www.genomicslawreport.com/index.php/2010/07/22/from-gulf-oil-to-snake-oil-congress-takes-aim-at-dtc-genetic-testing/
http://spittoon.23andme.com/2010/07/23/gao-studies-science-non-scientifically/
http://www.genomeweb.com/blog/gao-sting-doesnt-bode-well-dtc-industry
http://www.councilforresponsiblegenetics.org/blog/post/Congress-Grills-DTC-Companies.aspx
  1. Clearly the bulk of the blame rests with LabCorp, but 23andme apparently had insufficient data analysis quality control (through, say, variants that would corroborate gender) to detect this themselves before results were made available to consumers. [↩]
Posted by reece, in Genome Commons, Genome Variation, Science No Comments »

Relocating a primary site directory

March 4th, 2010

UPDATE: The following *mostly* works, but I’ve had yet unresolvable problems with directory URLs not being rewritten to append the /, which causes failure. A slow investigation is in progress…

My hosting provider, HostMonster, uses cPanel to enable account administrators to configure their domains and services. By default, Hostmonster and cPanel place web data for the primary domain in ~/public_html/, with subdomains and “add-on” domains as subdirectories therein. That means that files for the primary domain are comingled with the document roots of other domains. The incongruency of that layout causes heartburn for people like me. This post tells you how to relocate those files AND have them served by the original URLs for the primary domain.

There are several reasons why you might want relocate files for the primary domain. First, there’s the compulsive disorder desire for organization that provides better containment of files related to a site, and nothing else. Good organization often leads to reduced errors and improved efficiency (not accounting for the time it takes to blog about them). A second reason is that people might access one domain’s data through the URL of a primary domain, such as http://primary.com/secondary.com/. This isn’t a concern in my case, but it might be for others. (I do use this nesting in other contexts to make dev.domain.com equivalent to domain.com/dev, but that’ll be a different story.)

My original directory structure looked something like this:

$ ls ~/public_html
400.shtml		      401.shtml			    403.shtml
404.shtml		      500.php			    500.shtml
beaconcoaching		      bruceandhanna.com		    cgi-bin
dev.genome-commons.org	      fastphp.ini		    favicon.ico
genome-commons.org	      genomeinterpretation.org	    glenparkassociation.org
home-exchange		      index.html		    nctgi
reece			      reece-ex-wp		    robots.txt
spat			      tahoe			    tmp
unison-db.org

See how the the error pages, my subdirectory, and other primary domain files are scattered among the document roots that serve domains for Beacon Coaching, a development Genome Commons site, and Unison database? Yuk.

I prefer to name directories for the domains they serve, such as ~/public_html/harts.net/. Sure, I could move the primary domain files there, but then they’d be served by URLs like http://harts.net/harts.net/reece/. [N.B. This is a bogus link that illustrates what I didn't want.] Preserve the original URLs is critical.

The solution is to move files for the primary domain into a dedicated directory and tell apache, via mod_rewrite rules in ~/public_html/.htaccess, where to look for primary domain files.

Specifically, I did this:

  1. ssh to the domain
  2. cd ~/public_html
  3. mkdir harts.net
  4. mv –target=harts.net [primary domain files]
  5. add the following stanza to ~/public_html/.htaccess:
RewriteEngine on

# rewrite requests for primary domain into harts.net/
RewriteCond %{HTTP_HOST} ^(www\.)?harts\.net
RewriteCond %{REQUEST_URI} !^/harts.net
RewriteCond %{REMOTE_HOST} !www.simplescripts.com
RewriteRule ^(.*)$ /harts.net/$1 [L]

Notice the exception for SimpleScripts — without that, simplescripts will be unable to manage domain installations. (SimpleScripts is a terrific tool that greatly facilitates installing and upgrading many common blogging, CMS, forum, wiki, commerce, and customer service tools.)

Posted by reece, in Problems of a Prop Head No Comments »

Have Monkeys, Need Climbing Wall

January 27th, 2010

blue-holdI have three kids. All of them like to climb. Margot seems unnaturally compelled to climb things — no matter how imprudent. (She broke her clavicle at age 2 after climbing up to, and falling off of, the kitchen table.) Unfortunately, our San Francisco postage stamp yard has no good places to climb. Since I spent most of my childhood in a tree, the lack of climbable structures for my kids disturbed me. So, during a recent break between jobs, I built a climbing wall in our house. The kids love it and it was a hit at our recent holiday cookie party.

Read the rest of this entry »

Posted by reece, in Projects, Round Home No Comments »

I Joined Berkeley

January 25th, 2010

Stanley Hall

As many of you know by now, I left Genentech in September to join UC Berkeley as the Chief Scientist of the Genome Commons. I’m part of QB3, the California Institute for Quantitative Biology (no I don’t understand the abbreviation either).

I’m collaborating with Steven Brenner, Jasper Rine, and Lior Pachter at Berkeley, and Robert Nussbaum and Bernie Lo at UCSF, to address the technical, scientific, clinical, and ethical opportunities associated with interpreting genomic data. It’s an exciting time and an exciting place.

To be sure, I’ll be posting a lot more about that here.

Posted by reece, in Genome Commons, Hear Ye, Hear Ye No Comments »

Hello, is this thing on?

January 23rd, 2010

How is it that someone like me, i.e. with substantial geek tendencies, goes this long without blogging? At one time, I surely thought that the young whippersnappers were wasting their time with this blogging thing. I mean, get real, who’s gonna read this crap? It turns out lots of people do.

The real surprise to me, though, was not that people write and read blogs. The surprise is the community that blogging builds around ideas and projects. I completely missed that, and it’s *the* thing.

So, I have a confession: I really do want to blog. I’ve wanted to for a while from the depths of my virtual data closet. I have a deep yearning to say something important, profound, consequential, insightful. But what?

At cathartic times like this, I turn to two people. First, there’s Curly, my erstwhile Wonder Bread Zen master and hero, who exclaimed ”I keep trying to think but nothing happens.” Exactly — too much thinking.

Then there’s Dr. Jack Pribnow, my high-school honors calculus teacher. He was the one who told me to not think too hard about a calculus proof before diving in. I was actually quite good at calculus proofs, but every once in a while one would stump me. Dr. Pribnow insightfully told me that my problem was that I wanted to see the whole thing done before I started. He was right: I hated “mistakes” so much that I didn’t start down the path.

So, this first post is for Curly and Jack (er, respectfully, Dr. Pribnow) and for their lessons that I repeat to myself often. Here’s to leaping before I look and not thinking too hard about it.

Posted by reece, in Hear Ye, Hear Ye 1 Comment »