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Posts from the ‘Genetic testing’ Category

Gentle Sequenced All My Genes

Years ago, I had two direct-to-consumer (DTC) genomic tests. One with Navigenics and one with Pathway Genomics. Both tests gave me great insights about how this industry works and it was really exciting getting a clear picture about them as a geneticist myself. Although, when I saw the FDA-23andMe battle and the results, I was not surprised.

After these, I came across a new company, Gentle, a few weeks ago and had a chance to give a try to their genomic test. Why Gentle? Well, I had a few reasons:

  • They sequence all my genes, not just 1.9% of them as other DTC companies do.
  • They test me for 1700+ conditions (carrier status, from common to rare genetic disorders).
  • They provide revolutionary iOS apps.
  • I can download my raw data and I own it!

The package arrived, and I provided the required saliva sample. The process was quite simple.

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With a personal note:

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After a few weeks, I got access to my results and I was impressed. Here is the format they used to interpret my data:

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I could take a look at my carrier status and it turned out my genome doesn’t really carry anything serious. A color coded circle let me discover the details and for each condition or disease, I could access a more detailed description.

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The different layouts allowed me to discover the meanings behind the data in the way I preferred. Here is the chromosome view.

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Finally, the genetic counselor scheduled a talk with me about my results and she answered all my questions.

In overall, Gentle told me things about my genome that are backed by scientific evidence; they let me download the raw data and analyze it in my own way and provided me with a lot of details focusing on those carrier statuses. They do everything regulations let them do and they do that by keeping an eye on scientific quality.

Here is a video about the service:

My New Genetic Test is on the Way: Gentle Analyzes 1700+ Conditions

I’ve had two direct-to-consumer genomic tests before with Navigenics and Pathway Genomics. The topic of analyzing the genetic background to make decisions about lifestyle is really close to my heart, although as someone with a PhD in clinical genomics I know exactly what scientific limitations those companies have to face. Therefore I was glad to get a  chance to order a Gentle genetic test and see how they try to tackle these problems. Gentle will sequence all my genes and test me for 1700+ medical conditions.

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Here is a short interview with Peter Schols, CEO of Gentle Labs.

How does Gentle differ from all those direct-to-consumer genetic companies?

Gentle is different in many ways:
– We screen for over 1700 conditions, which is 5 times more than our closest competitor
– We screen more markers per condition, making our test more accurate and reliable
– We offer great mobile and web apps, check out our iPad app
– We don’t just dump results into people’s web accounts: we have genetic counseling with a medical doctor built-in

Prospective customers should have a look at this page for more info

How can companies performing sequencing compete with the next generation sequencing paradise in Beijing (Beijing Genomics Institute)?

We don’t want to compete on the sequencing itself: we outsource all lab work. Our focus is on DNA storage, DNA-analysis and on the communication of genetic test results.

The key part in a DTC genomic analysis is genetic counseling. Do your customers get access to such help in interpreting their results?

Absolutely, we have two levels of genetic counseling built-in: first of all, all test results are communicated by a medical doctor with a specialisation in medical genetics, through a teleconference. We have an exclusive agreement with Royal Doctors to provide our clients with the best medical geneticists worldwide. Alternatively, clients can choose to have the results communicated by their own doctor.

Secondly, our own Gentle geneticists are available to answer any questions our clients might have, whether it’s before taking the test or after discussing the results with the doctor. They’re are always there to help.

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I cannot wait to get my results back which I will publish here as well.

Crowdfunding in Genomics

Crowdsource and crowdfunding are everywhere these days.

Jimmy Lin, a medical student at Johns Hopkins University, and other young scientists created the Rare Genomics Institute, a non-profit that leverages falling DNA sequencing costs and rising online giving to support medical research. Great idea!

In mid-July, the institute announced that it had completed its first crowdfunded gene sequencing and discovered what it believes is the root cause afflicting 4-year-old Bronx resident Maya Nieder. The girl can’t speak, and doctors are unsure whether she can hear. They had likewise failed to determine why she has missed so many developmental milestones. Lin’s team posted Nieder’s story online, and within hours donors had given the $3,500 needed to sequence key slices of the Nieder family’s DNA. (Yale University covered the rest of the costs.) The results, RGI says, point to a flaw in a gene crucial to fetal development.

Moreover, my friend, Lucien Engelen just published the results of his genomic analysis at 23andme. He aims at crowdsourcing potentially underlying genetic consequences of his genome.

What do you think? Was it a good idea? Would you make such information public?

23andMe Now Offers Sequencing for $999

Years ago, I wrote about how 23andMe analyzed someone’s genes for $999 (only a few gene variations were used for predicting disease risks). And now they offer exome sequencing for the same price.

What 23andMe is offering is to make people’s exomes available to them, and the DNA sequencer will go over their DNA 80 times (known as 80-fold coverage) to make sure that the genetic code is accurate. This is stunning because a year ago this would have cost ten times as much or more. 23andMe isn’t the first company to offer consumers exomes — that would be Knome, of Cambridge, Mass. — but still the low price is eye-popping. It’s also a lot more data than the DNA chips 23andMe has used up until now, which capture single-letter changes in genetic code scattered across the genome.

What is an exome? Your exome is the 50 million DNA bases of your genome containing the information necessary to encode all your proteins

Direct-To-Consumer Genetic Tests are Not Beneficial

While 23andMe brings down the price of consumer genetic tests and builds up relations with big pharma (doesn’t share individual data though), it seems the DTC genetic testing is neither accurate in predictions nor beneficial to individuals according to a study described on Medical News Today.

Working under the supervision of Associate Professor Cecile Janssens, together with researchers from Leiden, The Netherlands, and Boston, USA, Ms Kalf examined the risk predictions supplied by two large DTC companies, deCODEme (Iceland) and 23andMe (USA). They simulated genotype data for 100,000 individuals based on established genotype frequencies and then used the formulas and risk data provided by the companies to obtain predicted risks for eight common multi-factorial diseases – age-related macular degeneration (AMD), atrial fibrillation, celiac disease, Crohn’s disease, heart attack, prostate cancer, and Type 1 and Type 2 diabetes (T2D).

Although the predictive ability of the DTC tests in the study was moderate for all diseases, both companies assigned an increased risk to a substantial part of the group. Yet the risk of disease in this group was often not substantially higher than the risk in the rest of the population studied. For AMD, the disease with the highest predictive ability, both companies assumed that the risk in the population was around 8%. Of all subjects designated as having an increased risk, 16% using the 23andMe risk estimations and 19% using deCODEme’s estimations would develop AMD, compared to the 4% found in the rest of the population studied.

Visiting Direct-To-Consumer Genetic Companies

When I had a free test at Navigenics and Pathway Genomics, I had a chance to visit the Navigenics HQ as well in San Francisco. Now Daniel MacArthur visited the 23andMe and Complete Genomics HQs.

I was graciously received by Shirley Wu, who gave me the grand tour, and various members of the 23andMe science team (especially Nick Eriksson and Tom Do) then uncomplainingly put up with my questions for what must have seemed like hours. The visit reinforced my overall impression of the company: this is a group of very smart people working with an increasingly impressive customer data-set on some seriously interesting problems. Their recently announced discovery of two novel genetic regions associated with Parkinson’s disease (due for publication in the near future) is a taste of what’s to come.

Psychological Effects of Personal Genetic Testing

Direct-to-consumer genetic testing is becoming more and more apparent even though its clinical validity and utility are pretty questionable regarding medical decisions. Eric Topol and his team now studied over 2000 patients who had genomic tests (Navigenics) and reported if there was any changes in symptoms of anxiety, intake of dietary fat, and exercise behavior. The results are not surprising therefore they raise the question whether these tests can be used for anything at all. The study was published in NEJM.

From a cohort of 3639 enrolled subjects, 2037 completed follow-up. Primary analyses showed no significant differences between baseline and follow-up in anxiety symptoms (P=0.80), dietary fat intake (P=0.89), or exercise behavior (P=0.61). Secondary analyses revealed that test-related distress was positively correlated with the average estimated lifetime risk among all the assessed conditions (β=0.117, P<0.001). However, 90.3% of subjects who completed follow-up had scores indicating no test-related distress. There was no significant increase in the rate of use of screening tests associated with genomewide profiling, most of which are not considered appropriate for screening asymptomatic persons in any case.

In a selected sample of subjects who completed follow-up after undergoing consumer genomewide testing, such testing did not result in any measurable short-term changes in psychological health, diet or exercise behavior, or use of screening tests. Potential effects of this type of genetic testing on the population at large are not known.

(Hat tip: Medgadget)

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