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Posts from the ‘Personalized medicine’ Category

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.

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.

Age of Personalized Medicine: New Blog

I was glad to share the new blog of the Human Genome Organisation with you a few weeks ago. Now here is the new blog of the Age of Personalized Medicine which is a quality website dedicated to the possible implications of personalized medicine.

Welcome to The Age of Personalized Medicine Blog! Each week, our expert contributors will address the most pressing science and policy issues of the day that are shaping the future of personalized medicine.

Tomorrow, Amy Miller of the Personalized Medicine Coalition (PMC) will share her thoughts on the intersection of personalized medicine and comparative effectiveness research, and highlight the topics being discussed at the Comparative Effectiveness Research and Personalized Medicine: Policy, Science, and Business conference in Washington, D.C. We invite you to join the discussion!

Though both blogs are good initiatives, there is a clear difference between them. The difference is Dr. Hsien-Hsien Lei who is the official editor of HUGO Matters and one of the best genetic bloggers in the whole blogosphere. No matter how fantastic experts write entries for a blog if the blog itself doesn’t have an editor who is an expert in managing blogs. You can be proficient in writing articles for scientific journals or news sites, but it doesn’t mean you are a good blogger as well.

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.

Personalized Medicine Exposes a Gap in Medical Education

Do you remember the report focusing on how young physicians at Beth Israel Deaconess Medical Center test their own DNA in search of genes linked to various illnesses? I’ve now just come across a great article in PLoS Medicine about how the dawning era of personalized medicine exposes a gap in medical education.

As personal genetic information becomes an increasingly frequent component of the patient medical record, it is crucial that medical students be trained to use and interpret this information appropriately and responsibly. Here, I argue the need for medical education reform that equips physicians with the knowledge, skills, and attitudes required to practice personalized medicine.
DNA ladder
In my university credit course, “Web 2.0 in Medicine“, I cover partly this issue and describe how direct-to-consumer genetic testing works and what the advantages/disadvantages are.

Personalized Medicine in the Web 2.0 Era

A few weeks ago, Daniel Vorhaus from the Genomics Law Report asked me to provide a commentary on what I think about the future of personalized medicine regarding ethical, legal and social aspects. Now my commentary was published and here is an excerpt:

Educating medical professionals and preparing the public to be able to provide informed consent for these activities is crucial to this next phase; as is the accessibility of the enormous and growing amount of genomic data. A new generation of web services, the so-called web 2.0, seems to be playing an important role in this movement. Through such tools, people can interact with their doctors and each other easily and they can share the results of genomic tests, resulting in a self-maintained database of human genomic information. Examples include the research project of 23andMe.com or the amyotrophic lateral sclerosis research of Patientslikeme.com.

Check out the whole list of contributors.

What-ELSI-is-new-article

Personalized Genetics in the News: 3D Structure and Bar Code Reader

The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment.

Second, at a finer scale, the genome adopts an unusual organization known in mathematics as a “fractal.” The specific architecture the scientists found, called a “fractal globule,” enables the cell to pack DNA incredibly tightly – the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

The DNA Transistor is a project from IBM Research that aims to advance personalized medicine, by making it simpler (and much cheaper) to read an individual’s unique DNA sequence — the special combination of proteins that makes you unlike anyone else.

A group of doctors training at Beth Israel Deaconess Medical Center started a unique program last week to learn about genetic tests marketed to consumers, placing them in the vanguard of preparations to guide patients through the dawning Wild West age of personalized medicine.

Part of the instruction will come from having the young physicians test their own DNA in search of genes linked to various illnesses.

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