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a bio blog about genetics, genomics, and biotechnology
Posts Tagged ‘Industry’
Previous: Andrew’s 23andMe kit
The Good
 The best feature of 23andMe is their trial account, for which you must apply at 23andMe.com. Everything you can see with your trial account, I can see with my personal account. There are no secret features for members.
23andMe’s excellent trial user account is a manifestation of their excellent user interface design. The graphics are subdued and functional; obviously 23andMe web designers have been making websites long enough not to be impressed with the latest web bling. Instead, what they have created is a clean, easy to navigate, easy to use site out of a tangled mess of complex data and information.
Congratulations to the 23andMe web team; you deserve it. Given that a trial account is free to the public, you have created the single most public-accessible repository of genetic information in the world. My single complaint is that some traits unpredictably use an Odds Calculator and others use a “What It Means” table.
The Lame
I don’t have any family or friends on the system, so both the “family & friends” and the “my ancestors” sections were useless to me. OK, so I’m white and European. I knew that already.
The Disappointing
Of all the 70 possible traits described by the 23andMe test, no trait reported anything useful except perhaps a moderate (almost 30%) risk of rheumatoid arthritis.
Even more disappointing is that despite claims in the press of joining some elite genetic social club, I have yet to be invited to any parties… or even receive an email written in a festive tone. Come on, 23andMe, that’s not cool. Think Gene gets more traffic than you do, so maybe we can be friends after all?
I bought a 23andMe kit in March. Here’s what the kit looks like:
Comes in a Fedex box….
Oh, a box in a box!
Opening the 23andMe kit box is a disclaimer strip that I must tear to get into the contents. Is this a legally-enforceable statement of consent? I thought that this was clever.
Close-up of the consent-strip.
Kit contents. Not included are the mailing instructions and FedEx packing slip. The four-page disclaimer is the same as the one on 23andMe’s website.
- Oragene spit collector
- 23andMe Information card
- disclaimer document
- pre-paid return envelope
- plastic sample bag
A close-up of the Oragene collector
The text of the Information card.
 
I filled the spit collector and returned the kit. Unfortunately, I happened to send my kit during the 23andMe CLIA-certified lab change, so my results took over a month to process.
 If you have a 23andMe account, my user name is andrewyates. Send me an invite! (under account => My Profiles) I promise to only use your genetic information for tweaking clones, raising your health insurance premiums, and raising venture capital.
Yes, bask in the all encompassing Power of WE!
Anne Wojcicki:
“We’re at the beginning of a revolution that combines genetics and the Internet. Wikipedia, YouTube and MySpace have all changed the world by empowering individuals to share information. We believe this same phenomenon can revolutionize healthcare.”
The press reads this and thinks that 23andMe (and by proxy, deCODEme) is “yet another social network.” It’s not. It could help collect more genomic samples for research, which would benefit everyone, but so far, that’s a stretch considering that phenotypes are self-reported. (update: report on 23andWe coming soon)
Mark Hopkins of social networking news site Mashable:
One of the ideas floated to them from the press, one that was warmly received by both Linda and Anne, was a social network available at 23andMe where social connections were made for you by DNA genotype similarity. It was described by the press member asking the question as “the ultimate in social networking,” a sentiment that seemed to be echoed in tone by Linda and Anne.
I can’t imagine the usefulness or entertainment value in such a system, but then I’m not much of a geneticist (perhaps someone out there with a bit more of a background in it can explain the inside joke I seem to be missing).
Is “the ultimate social network” some kind of tongue-in-cheek joke? Can middle-aged wives of billionaires be snarky about the Silicon Valley press echo chamber when Rupert Murdoch entertains your questions about your stinky piss internet quiz? If you were one degree away from valley’s most connected company, and the success of your startup was independent of sucking everyone who could write a check, would silicon-valley-buzz like “the ultimate in social networking” be a big in-house joke?
I’m just saying, if I was a bored 30-something billionaire…
MY SNPedia REPORT
Services like 23andMe and deCODEme test for hundreds of thousands of SNPs (genetic datapoints). Yet, these services only attempt to interpret less than 100 traits in their web reports. [1]
Fortunately, these services allow you to download the raw data from your test to be interpreted elsewhere.
For example, recently Mike Cariaso “creatively profiled” Lilly Mendel (23andMe’s female demo user) using the public SNPedia database and Promethease software to win the 23andMe Win Your Genome Contest.
These tools are not yet user friendly, and they certainly exist beyond the general consumer. However, I purchased a 23andMe test a couple months ago, and as a power user, I wanted ALL the data. Yes, I know that the research is new, the interpretations can be highly speculative, and 23andMe is making a laudable effort to make the best research accessible. But hey, I spent $1000; I want to know everything. Further, while these services do not report many high-penetrance genes like BRCA (breast cancer) for legal reasons [2], some of that information is in the raw test data “for your own interpretation.”
If 23andMe is the Apple I of genomics, this is the box of parts for garage assembly. Enjoy!
How To Use SNPedia for 23andMe and deCODEme
1) Get Data
Download your test results. If you do not have a 23andMe or deCODEme account, you may download a sample dataset from 23andMe’s trial users. (deCODEme’s trial user does not yet support data download)
Download Lilly Mendel’s raw data from ThinkGene
23andMe:
- Login (either as your account or as a Mendel trial user)
- Go to “Browse Raw Data” in the left menu
- Click “download raw data” link at the top right of the “browse raw data” page
- Enter password, secret question, select profile, and click “Download Data”
- The download will be about a 2MB zipped text file.
Here is what raw 23andMe data looks like from my genome:
# rsid chromosome position genotype
rs3094315 1 742429 AA
rs12562034 1 758311 GG
rs3934834 1 995669 CC
rs9442372 1 1008567 AA
rs3737728 1 1011278 AG
rs11260588 1 1011521 GG
rs6687776 1 1020428 CC
rs9651273 1 1021403 AG
rs4970405 1 1038818 AA
rs12726255 1 1039813 AA
rs11807848 1 1051029 CT
rs9442373 1 1052501 CC
...
and so on for over 570,000 lines.
Raw deCODEme data looks like this:
Name,Variation,Chromosome,Position,Strand,YourCode
rs2278544,A/G,2,136262580,+,AG
rs4954633,C/T,2,136263105,+,CC
rs3213890,A/G,2,136268658,+,AG
rs1807356,A/G,2,136271954,-,AA
rs2015532,A/C,2,136271995,-,AC
rs2322659,C/T,2,136272129,+,CT
rs3769013,A/G,2,136272652,-,AG
rs2304371,C/T,2,136278027,-,CT
rs2304370,C/T,2,136278205,-,CT
rs3739022,C/T,2,136278942,-,CC
rs12988076,A/C,2,136286318,+,AC
rs6719488,G/T,2,136291669,+,GT
...
and so on for over 1,000,000 lines.
2) Get Software
Download Promethease (windows only, version 0.1.14) from SNPepida. Also, see Promethease’s homepage.
3) Run Software
Launch Promethease and select your data file. Select your race. Begin Analysis. Note that Promethease automatically detects which service generated your SNP data.
WARNING: generating a report with Promethease may take hours. If there is demand (and time), I’ll write / help write better Open SNP software. Please contact me if this interests you.
4) View Report
MY REPORT: Andrew Yates’s SNPedia report via Promethease [3]
Promethease outputs a final report of about SNP 1300 entries as an HTML file to your desktop. It’s not pretty or easy to read —let alone understand as actionable medical information. But this is the best that Open SNP software has to offer today.
See Interpreting Promethease / SNPedia Results for help understanding your Promethease report.
5) Report Reflection
While my SNPedia report contained more information about my SNPs, I didn’t learn anything worth knowing that 23andMe (or deCODEme) didn’t already tell me. Further, running and understanding my “open SNP” report, while interesting, took hours. While much potential exists for community efforts to understand our genome, SNPedia is not yet ready for the majority of genetics enthusiasts, let alone the general public.
Notes
[1] 23andMe and deCODEme officially report less than one hundred traits, plus ancestry. 23andMe tests for about 500,000 SNPs; deCODE tests for about 1,000,000. However, the useful information in both tests is about the same (for now).
[2] The industry line is that users shouldn’t know about some high-penetrance genes for reasons including “it’s for your own good” and “high penetrance genes are not common enough,” but the real reason is that these genes are defended by walls of patents, expensive licenses, and litigious companies. See “Low penetrance genes v high penetrance genes”
[3] At first, I was leery about posting my genome online, but then I realized: hey, if I’m ever discriminated against (and I can easily check my server logs to see who has viewed my genome report), maybe I’ll get to participate in a landmark judicial case!
 Cupertino, CA, April 28, 2008 - NextBio today announced the next step in making Open Biology a reality: a free version of the NextBio life science search engine has been made available to the general public. Using NextBio, any researcher or clinician can search the world’s public life sciences data and literature - over 10,000 experiments, 16 million articles, and literally billions of data points. Moreover, users can import their own experimental data into the NextBio search engine, share it with the community, and collaborate with others as never before.
“The NextBio life science search engine presents a powerful and intuitive solution available for researchers and clinicians who wish to truly unlock the value of large-scale studies in the public domain,” stated Leroy Hood, M.D., Ph.D., President of the Institute for Systems Biology. “NextBio is an entirely new and better way of doing scientific research.”
“With the public launch of the free version of our life science search engine, our goal is to make NextBio an invaluable resource for every researcher and clinician in the world,” said Saeid Akhtari, NextBio’s co-founder and Chief Executive Officer. “While we continue to grow our enterprise accounts with the world’s leading R&D companies and organizations who demand added data integration services, security and support, the free version of our product is the culmination of years of development and our vision of open collaboration in science.”
“The public launch of NextBio’s free search and collaboration tools is at the center of our vision of Open Biology,” stated Ilya Kupershmidt, co-founder and VP of Product Management at NextBio. “NextBio’s search engine provides a unique opportunity for the research community to collaborate through information sharing and to perform an important part of their biological work in silico. Our users can glean new insights into gene function, disease progression and compound effects, as well as into their own studies using the world’s quality public experiments done to date.”
With NextBio, researchers and clinicians can:
- Search in real-time over 1,200,000,000 scientific data points, tens of thousands of study results and millions of scientific articles
- Find topics of interest quickly with an intelligent semantic auto-complete search feature
- Make correlations across six species, enabling effortless exploration of animal models relative to human studies
- Search NextBio to validate or generate novel hypotheses prior to investing in new experiments
- Understand their own study results by correlating them with the world’s collective experimental data
- Create their own user profiles to more easily collaborate with scientists around the world
Videos explaining the NextBio life science search engine and how it works, as well as a demonstration of a search, are available for viewing at http://www.nextbio.com/b/corp/demo.nb.
NextBio Featured at Bio-IT World Conference
The NextBio life science search engine will be highlighted this week at the Bio-IT World Conference in Boston. In a presentation on Tuesday April 29 at 2:30 pm Eastern Time, Ilya Kupershmidt, NextBio co-founder and Vice President of Product Management, will describe the conceptual framework behind NextBio and present applications investigating diverse biological questions. More information on the conference can be found at http://www.nextbio.com/b/corp/events.nb.
Source: NextBio
 Knome is the Cambridge, Mass personal genomics company which will whole-sequence consumer genomes for $350,000 USD (223,000 EUR). By comparison, competing personal genomic companies like deCODEme, 23andme, and Navigenics only test for a tiny fraction of known SNPs (single nucleotide polymorphisms) for between $1000 and $2500. The difference is like buying a complete dictionary of the human language and buying every thousandth letter of that dictionary.
What does $350,000 buy?
According to the informational email sent by Knome, the service begins with a personal visit by a physician to collect a blood sample and a 50% deposit to begin sequencing. A further 30% is due on sequence completion and the remaining 20% due on delivery of your personal genome sequence report and analysis. The service then includes up to 20 hours of private consultation with Knome-board certified genetic counselors to review your results and analysis.
Knome also invites customers to share their anonymous sequences with the genomic research community, though this personal scientific contribution (unlike competing services like 23andme) is optional.
In all, the amount of actionable medical information purchased by both Knome’s complete sequence and competing SNP chip services like deCODEme are comparable, though Knome costs more and provides more raw data. Clearly, at even $1000 (and especially at $350,000), the today’s personal genomics industry is more about seizing the early-sequencing market rather than providing a widely-available, invaluable medical service. However, I actively encourage anyone with $350,000 to spend to buy Knome’s service as this revenue will directly fund the personal genomic market, eventually bringing prices down to the general consumer, and science up to what’s medically invaluable.
 April 08, 2008 — Today, Silicon Valley startup Navigenics officially joins competitors deCODEme and 23andMe by launching its own personal genome scanning service.
Navigenics emphasizes the clinical aspects of genome scanning including genetic counseling and medical implications. While Navigenics uses the same technique as deCODEme and 23andMe, a chip which tests for one million SNPs (Single Nucleotide Polymorphisms, or “single-letter mutations”), Navigenics claims to better interpret the results. Disease risks are calculated by “life time risk” rather than average risk, and 24/7 genetic counseling is provided. Navigenics’ price reflects their interpretation confidence: $2500 for a one year membership and $250 per year thereafter as compared to $1000 one time for deCODEme and 23andMe.
One benefit of Navigenics that its competitors do not offer: Navigenics freezes your DNA sample to be retested as genomics testing advances, perhaps two to three times per year according to Mari Baker, Navigenic’s CEO. deCODEme and 23andme offer more raw information, but do not pledge to retest. Another benefit is an online primer for physicians which a Navigenics user’s health care provider could reference to help interpret test results.
Navigenics has positioned itself as less of a novelty test for genomics enthusiasts and more as an ongoing investment in personal medicine. With lead investors including Kleiner Perkins, MDV, and Sequoia Capital, Navigenics is a strong new competitor in the previously non-existent personal genomics industry.
 April 07, 2008 — New York Times correspondent Amy Harmon won her second Pulitzer prize for her series “The DNA Age.” “The DNA Age” addressed current controversial topics in ongoing DNA testing including its potential to improve preventive medicine and concerns about privacy and a “genetic elite.” Other finalists were The Boston Globe’s Beth Daley on how global warming affects New England and the staff of The Oregonian in Portland on modern microprocessor innovation.
That “The DNA Age” won is a statement about the increasing importance of nascent genomics advances and the growing awareness of genomic’s potential impact on society. Read the complete series at: The DNA Age at the New York Times
Full story at Editor & Publisher.
Photo: “Amy Harmon,” Lars Klove, The New York Times
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The best feature of 23andMe is their trial account, for which you must apply at 23andMe.com. Everything you can see with your trial account, I can see with my personal account. There are no secret features for members.
Think Gene at Technorati
