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Posts from the ‘Genetic testing’ Category

23andMe swapped samples!

What we were all afraid of finally happened. 23andMe admitted that it swapped some samples in the lab. Even if these things happen in labs, it should really not happen in such a sensitive area. We, bloggers and geneticians, have been writing about how hard it is for patients to analyze and interprete their direct-to-consumer genetic results properly and how hard it is for this market to remain attractive despite all the criticisms. And now they swap samples. Daniel MacArthur at Genetic Future has a nice review about all the related articles and news.

For example, a mother posted her recent story on the 23andMe community:

Still upset I checked family inheritance and noticed my daughter shared with me, and then I checked my son’s. He was not a match for any of us. I checked his haplogroup’s and they were different from ours. I started screaming. A month before my son was born two local hospitals had baby switches. I panicked and I checked over and over. My kid’s were sitting at the computer because we all wanted to see the results. My son laughed but he looked upset. I called my sister in tears.

Here is the full 23andMe announcement:

We recently determined that a number of new 23andMe customer samples were incorrectly processed by our contracted lab. We want to clarify what happened with the sample errors, how it happened and what we’re doing to prevent it from happening again. Providing each and every one of our customers with accurate data is 23andMe’s number one priority, and we fully realize the gravity of this incident.

Up to 96 customers may have received and viewed data that was not their own. Upon learning of the mix-ups, we immediately identified all customers potentially affected, notified them of the problem and removed the data from their accounts. The lab is now concurrently conducting an investigation and re-processing the samples of the affected customers and their accurate results will be posted early next week. We expect the investigation will be complete over the next several days and we will provide further details when we have them.

We are currently putting additional procedures in place that will add an extra layer of safeguards to help assure that similar incidents do not occur in the future. We are deliberating on a process that would include removing manual steps at the lab, completely automating the sample analyses, and implementing further checks of the data before it gets loaded into customer accounts. Please be assured that our testing laboratory’s processes comply with strict professional, regulatory, and corporate quality assurance standards for ensuring that all laboratory test results are accurate. The laboratory will adopt corrective action as warranted based on the findings of the investigation.

The science behind 23andMe’s personal genetics service remains proven and sound. We recognize that this is a very serious issue and your trust is of the utmost importance. We hope that this helps clarify what has happened and what we are doing to prevent these problems in the future. Please contact me at khomenko@23andme.com if you have any further questions. We appreciate your comments and feedback.

I cannot wait to hear what you have to say, Steve!

DIYgenomics on Smartphones

In personal or direct-to-consumer genomics, what we need is reliable, scientifically correct smartphone applications. Here is DIY Genomics, and Android app, which performs a side-by-side comparison of consumer genomic services such as deCODEme, Navigenics and 23andme by loci and variants for 20 conditions. It also does the same for drug responses and health risks.

What can you do?

Select 1 of 20 top conditions covered by consumer genomic services

Side-by-side locus, gene and SNP comparison of deCODEme, Navigenics and 23andme

Selecting any SNP row, comparison of underlying studies cited by company

Click-through to PubMed study listing

Actually it provides the user with reliable pieces of information that might help interprete the data.

Personal Genomics Comes to US Drugstores

I’ve been writing about personal genomics for years. The standard concept of it is that you can order such genetic tests online, send your saliva or buccal swab to the lab where they analyze your DNA, then you can check online what kind of diseases you have elevated or lowered risk for. That’s how Navigenics, 23andMe or Pathway Genomics works. Now Pathway had a major announcement:

San Diego based startup Pathway Genomics announced today that it will begin selling its DNA collection kits at Walgreens drugstores beginning in mid-May, for about $20 to $30. Unlike a pregnancy test, users won’t be able to get results immediately. They will have to send in their saliva sample and then go to Pathway’s website to select the particular test they want. Users choose from drug response ($79), which assesses how well an individual can metabolize certain drugs, predicting the best dosage for that person or whether they will be susceptible to certain side effects; pre-pregnancy planning ($179), which determines whether parents carry mutations for serious genetic diseases; health conditions ($179), which assesses risk for a number of conditions, including diabetes, Alzheimer’s, prostate cancer and more; or a combination of all three ($249). The kits won’t be sold in New York because the state’s laws require medical professionals to be involved in this type of testing.

As you may know, I’m not totally against direct-to-consumer genetic testing, but I really would like to see doctors and genetic counselors in this process. I think selling such kits through drugstores can only happen in the US right now.

Well the Genomics Law Report blog has an extended and very detailed review about this important topic. An excerpt:

What has changed is their visibility. It is just possible that one of the safest strategies for avoiding regulation – out-of-sight, out-of-mind – played a significant role in the regulation (or lack thereof) of DTC genetic testing. Tests once predominantly available only to early adopters capable of seeking them out online will now begin to appear on the shelves of thousands of neighborhood drugstores nationwide. To a greater degree than ever before, genetic testing will soon be available to mainstream America (and subject to the impulse buy). And that, for better or for worse, may be all that it takes to convince some regulators that the time for action is finally at hand.

Personalized Genomics: Genetic Testing Registry and Next-Gen Sequencing

I know I have not been updating you about the improvements of personalized genomics lately, but here are the most interesting and important news focusing on this emerging field of medicine.

  • When DNA means do not ask (TIME): Quite a negative (but partly valid) article from Camilla Long about genetic testing and DTC companies.

If Long wishes to stay ignorant of her own genetic risks – just as she has managed to remain ignorant of the entire field of genetics, even while writing an op-ed piece about it – that should be her choice. But her criticism of others who choose to pursue a greater understanding of their own genetic risk is entirely, horrendously misplaced.

Pathway Genomics: Let’s see my genes

As I’m doing PhD in clinical genomics and I’m really interested in the connection between internet and medicine, so I was very happy when Pathway Genomics, one of the newest direct-to-consumer genetic companies, offered me a free genetic test. After an interview I did with them, I sent my saliva sample back and 3-4 weeks later, I received an e-mail that my results were ready. This is just an entry about my experience and the things I found interesting. As I got a free test from Navigenics a year ago, I plan to compare these services in a future entry.

The reason why I was very interested in the service of Pathway Genomics is what they analyze:

1) Sampling: It was quite an easy process with only a few papers to fill (though it’s always hard to solve FedEX issues from Europe) and clear instructions. A video about a patient showing the whole process in 1-2 minutes including salive collection and filling papers would be useful.

2) Preparations: I liked that I had to fill a questionnaire focusing on my lifestyle and patient history (Your Environment and Lifestyle, The Shape You’re In and You and Your Family). As family history is the best genetic test out there, it’s important to use that data while analyzing genetic results. Though, I couldn’t calculate my BMI (couldn’t use kg and centimeter) and the Family history app has never been working for me.

3) Results: I still think that predicting risk of diseases based on a few SNPs cannot be accurate enough and we cannot base a medical decision on that. But drug responses and carrier status are totally different. For example, now I know I’m not a carrier for any of the disease they analyze, and I’m a slow metabolizer of caffeine (I never drink coffee as it has quite a negative effect on my work maybe due to this slow rate of metabolization).

4) Health conditions: Based on your genetic profile, it creates different groups for conditions such as Immediate Action, Take action, Be proactive, Learn More and Live a healthy lifestyle. It’s also shown whether the risk is based on validated or preliminary study results. It seems to me it creates a score for diseases based on SNPs and elevates the score by the number of questionnaire answers that proved to be risk factors. That’s where a genetic counselor is very important. For example, just because I’m 25 years old and Caucasian, I’m in the risk group for ulcerative colitis. I would love to see the combined risk (genetic + lifestyle) and would love to download the raw data in order to analyze it again with Prometheus and SNPedia.

Also I’m not sure whether an SNP with 1.07 odds ratio can really elevate my risk for anything.

Anyway,  it’s easy to navigate among the results and I like that there is no percentage of risk which makes it easier to understand for laypeople. I plan to contact one of their genetic counselors next week.

5) Ancestry: I’m in the same maternal haplogroup as Benjamin Franklin or Marie Antoinette (see migration map below on which we can adjust the migration pattern with the timline). The descriptions are detailed and full of references information. I particularly liked the numerous Pubmed links. My paternal haplogroups is quite interesting and is the same as Thomas Jefferson’s.

My friend, Blaine Bettinger also commented on this test.

6) To sum it up: I liked the service mostly because of the carrier status and drug responses features. It helped me analyze the results, find more information in peer-reviewed journals and maybe make lifestyle decisions.

Pros:

  • The 100% Moneyback Guarantee is still fantastic.
  • It analyzes not only disease risks but carrier status and drug responses.
  • No percentage of health risks, but a clear score system.

Cons:

  • Charging for the genetic counseling is not a good idea ($40 for a call up to twenty minutes, or a full hour for $99). It costs almost as much as the service itself. (Update: It turns out it was an old page and genetic counseling actually is for free)
  • The blog and Twitter account are not too active. There is no significant social media activity which would be crucial.
  • Obviously USA-focused
  • Raw data is not available for download.

In the next entry, I will compare my experiences with Navigenics and Pathway Genomics.

23andMe: Medical Advice?

ThinkGene reported that Myriad and 23andMe perform the same breast cancer genetic test on the BRCA gene. The problem is 23andMe cannot provide medical advice. The conclusion is interesting and it would be great to hear what 23andMe has to say about this.

The objections to this claim are that this same test is already defined for use as “health ascertainment or disease purposes” and that the use of this test is already included in standard medical practices in the United States. One implementation of this test for use as “health ascertainment or disease purposes” includes the Myriad “Multisite 3 BRACAnalysis” test.

Thus, either the 23andMe “BRCA Cancer Mutations (Selected)” test is medicine, or the the Myriad “Multisite 3 BRACAnalysis” test is not medicine.

And the second part of the results:

Pathway Genomics: I spit again

Last year, I got an offer from Navigenics to analyze my salive sample and of course, I gladly accepted it and shared the results with you. I also visited Navigenics HQ in Redwood City. Now, after an interview with Pathway Genomics, I got a chance to send my saliva sample to Pathway Genomics as well. I’m very interested to see the ancestry, carrier status and drug responses.

Here are some pictures I took:

I plan to share my experiences and also compare the results and the sampling processes which is going to be quite exciting. I will keep you posted.

Smartphone as a Personal Genome Assistant

A few months ago, I wrote about a press release:

Using the Google Phone’s built-in bar code reader, Dr. Pellionisz demonstrated how personal genome computing can detect genome-friendly and genome-supportive products from foods to cosmetics to building materials and beyond.

You upload data from personal health record system such as Microsoft Healthvault or Google Health; genomic data from 23andMe or Navigenics to your smartphone and then by using the bar code reader, you can find products that are probably good for you based on your genomic and health profiles. Though the system has several limitations (e.g. how useful genomic data is right now regarding medical decisions), it sounds quite interesting.

Here is the process on video:

Esther Dyson on Personalized Medicine

Esther Dyson is a catalysist of start-ups in the IT field, and also a director of 23andMe, the popular direct-to-consumer genetic testing company. She was now interviewed about personalized medicine.

Pathway Genomics: Interview

Some months ago, I wrote about the importance of customer service in the life of direct-to-consumer genomic companies. After the post, Pathway Genomics contacted me and said they were excited to speak more openly about their service. They also want to educate the community on genetic testing services and what these test results will and will not tell you. Here is the interview they have recently given to me.

  • Pathway Genomics is one of the newest competitors in the DTC genomics market. How do you aim to make a difference?

Quality. Pathway has a wholly owned federal CLIA and California State licensed laboratory. This onsite lab removes any “middle-man” issues. DNA samples are collected in Pathway’s custom-designed DNA collection kits and shipped directly to Pathway’s laboratory in San Diego, California. Genetic testing services, across five different technology platforms (including gene sequencing) are carried out by staff geneticists. Genetic health, lifestyle, and family history data and ancestry data are interpreted using unique algorithms developed by Pathway. Genetic test results are reviewed by medical staff and genetic counselors for accuracy and then reported via our online secure web site. When appropriate, our genetic counselors will contact customers to present and review their data. At any time, customers can contact Pathway’s Genetic Counselors for help understanding their genetic information.

Content. Pathway offers genetic testing services for both health and ancestry. As part of Pathway’s genetic health testing service, customers can learn about their propensity to develop disease, sensitivities to prescription drugs, or carrier status for mutations causing monogenic disorders. In the case of drug responses, Pathway is the market leader and reports on nearly a dozen different drug responses and adverse reactions. This includes clopidogrel (Plavix), statins, oral contraceptives, and certain cancer fighting treatments. This is important information because not all drugs are effective for all people and in some cases can cause adverse reactions.

Price. Genetic tests ordered through traditional medical outlets may be cost prohibitive for consumers. Pathway offers genetic health and ancestry testing services that are easy and affordable, with tests starting at $99. And for less than $350, consumers can access both health (drug response, carrier status, health conditions) and genetic ancestry tests.

  • How many Single Nucleotide Polymorphisms do you test and how many of them do you really use for the analysis?

As of today, Pathway reports on 71 health conditions, including tests for health diseases (24), drug responses and adverse reactions (10), and carrier status (37). Pathway shares this number because this is the information we believe helps consumers choose a genetic testing service right for them. Concerning the number of SNPs tested, we do not disclose this information, as we believe this to be competitive in nature and not informative to the consumer until otherwise validated by research.

  • You analyze drug responses, among other features. How accurate are these tests? I mean if you tell me I have a variance in my CYP2C9 gene, should I ask my GP to change the level of Coumadin I’ve been prescribed to?

Pathway has taken great effort to validate the accuracy and specificity of all the markers we report. Our standards exceed those required for federal CLIA certification. Therefore, you can be assured that the genotypes you receive from Pathway are highly accurate. That said, if Pathway told you that you had a genetic variation in your CYP2C9 gene that increased your sensitivity to Coumadin (Warfarin), we believe it’s important to share this information with your physician and discuss a personalized treatment plan based on this genetic data.

  • I don’t totally understand the concept behind the 100% money back guarantee. If I think my results don’t represent my real genetic background properly (e.g. because my family history predicts something different), I can get my money back?

Ultimately, we want each of our customers to feel confident about the information they receive about their genetic health or ancestry tests. While some people may not “like” what they learn about their genetic information, we want to do our best in serving our customers. Therefore, if for any reason a customer is not happy with their genetic testing service we will offer them 100% money back.

  • Please tell us about your plans for the near future? How do you plan to improve the service?

It’s important to continue to educate consumers, physicians, and the genetics community at large about the benefits associated with genetic testing services-specifically, what genetic testing can and can’t tell you. As the research community continues to make discoveries linking genetic variations to complex diseases, drug responses, etc., we will translate this information into an easy to understand format for our customers, thus helping to make personalized medicine a reality.

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