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Posts from the ‘Personalized medicine’ Category

Personalized Genomics: DTC Companies are in Huge Trouble

Today’s US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry was a vicious affair. Representatives from testing companies 23andMe, Navigenics and Pathway faced a barrage of questions about the accuracy and utility of their tests, made all the worse by the fact that many of the Committee’s members seemed unable to distinguish between the more responsible companies in the field and the scammers and bottom-feeders.

Therefore, while advertising beef, the genetics community only seems to be delivering tofu. The complexity of genetic diseases has been far greater than anticipated, and the public’s interest in learning about genetic predispositions is unexpectedly low. So, will genetics ever impact primary care? It already has and will continue to do so, but it is likely to continue in an evolutionary rather than revolutionary manner. Primary health care providers who keep current by reading the medical literature and attending professional meetings will not be left in the dust. And, in time, the benefits of genetic technology will benefit our patients.

Personalized Genomics News: From Virtuality to the Streets

  • DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful.

“Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.”

The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three prominent DTC companies: 23andMe, Pathway Genomics and Navigenics.

  • 23andme: A detailed review of the data the blogger just received from 23andMe.

The family said they received no medical counseling here and are making their own conclusions.  One comment made is that the parents stated they will probably be using more pharmaceuticals, interesting.

A patient analyzes her own 23andMe 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.

Really Personalized Medicine

Stephen Quake had his genome sequenced a year ago and since then he and 30 collegues have been working on the medical aspects of this huge amount of data. They try to make connections between genetic background and medical decisions. The results they found were published in The Lancet.

Analysis of 2·6 million single nucleotide polymorphisms and 752 copy number variations showed increased genetic risk for myocardial infarction, type 2 diabetes, and some cancers. We discovered rare variants in three genes that are clinically associated with sudden cardiac death—TMEM43, DSP, and MYBPC3. A variant in LPA was consistent with a family history of coronary artery disease. The patient had a heterozygous null mutation in CYP2C19 suggesting probable clopidogrel resistance, several variants associated with a positive response to lipid-lowering therapy, and variants in CYP4F2 and VKORC1 that suggest he might have a low initial dosing requirement for warfarin. Many variants of uncertain importance were reported.

Medical News Today also covered this important step in revealing the power of personal genomics.

Quake told the media that: “We’re at the dawn of a new age in genomics.”

“Information like this will enable doctors to deliver personalized health care like never before,” he added, explaining for example, that it will help fine tune care so that patients at higher risk get closer, more relevant surveillance and patients at lower risk are spared unnecessary tests.

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.

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.

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