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Posts from the ‘Genetic testing’ Category

Shall We Sequence Genomes At Homes? – The Future of Genomics

As a geneticist, talking with George Church or the President of the Personalized Medicine Coalition was a fascinating experience while writing my recently published book, The Guide to the Future of Medicine. This is still one of the most promising fields of medicine but without getting it closer to the general public, genomics will never play a pivotal role in practicing medicine.

Let’s start from the beginning. From the years of 2005, 2006 and 2007, patients have been able to order genetic tests online with 23andme, Navigenics or Pathway Genomics. In 2013, 23andme received a letter from FDA about ceasing marketing of the screening service. Since then, the market has been transforming into something new that could also meet the regulations of the FDA. At least, hopefully.

My Gentle Labs package.

My Gentle Labs package.

I’ve had 3 genomic tests with Navigenics, Pathway Genomics and My Gentle Labs with 3 different results and experience. I thought the direct-to-consumer (DTC) market is just not ready for prime time. I also analyzed my own raw data with Promethease and got to very interesting conclusions about the future of my life. I loved the possibility to get insights about my genome as well, not just measuring my vital signs. Here is my overall experience with genetic testing:

Similarly to how the wearable revolution is transforming into a world of smart clothes, disease prevention and insideables (swallowed sensors), the field of DTC genomics has been changing too. Here are some reasons why.

  • While the cost of sequencing one person’s genome was about $3 billion in 2003, now it’s possible for under $1-3000 (see figure below). The $1000 genome is still not here, but the trends are clear and soon the shipping cost of the sample will be higher than actually sequencing that genome.
  • The number of sequenced genomes is skyrocketing. Illumina said that 228,000 Human Genomes would be sequenced only in 2014 and the predictions for this year are even bigger. Soon we will all have access to our own genomes.
  • It is known that fetal DNA is circulating in the mother’s blood,and it can be separated from her blood to allow analysis of the fetus’s genetic makeup. Imagine the possibilities.
  • Large US hospitals are about to begin sequencing the genomes of healthy newborn babies as part of a government-funded research program called BabySeq. Major diseases could be pointed out and precautions could be made about others far in time.
  • Oxford Nanopore developed the MinION™ portable device for molecular analyses of DNA, RNA and proteins that is driven by nanopore technology. It might be the first step towards sequencing genes at home, despite early criticisms.
  • There are more and more targeted cancer therapies available. As certain tumors have specific genetic mutations such as BRCA in breast cancer or EGFR in lung cancer, among others, they might be sensitive to targeted drugs. Sequencing a tumor’s own genome is becoming a routine step in designing the therapy for cancer patients, although the costs are exceptionally high.
Cost of genome sequencing.

Cost of genome sequencing.

As you can see, examples underscore the notion that genomics could play a very important role in everyday medicine, but numerous steps and elements are needed for that.

  1. Comprehensive and thorough regulation from organizations such as the FDA or EMA about what DTC companies can offer and actually do. Can patients order tests online or only their caregivers?
  2. Innovative companies connecting patients to medical professionals through the genomic knowledge behind cancer and other diseases.
  3. Reliable algorithms that could help use the huge amount of data genome sequencing leads to in analyzing health outcomes. A great example is how Joel Dudley at Mount Sinai Medical Center is working on implementing big data in medical decision making. IBM Watson is also analyzing genomic data to find treatments in brain cancer.
  4. With the widespread of genetic testing and the decline in the cost, it should be a common thing to analyze my genome or get a detailed analysis. Moreover, caregivers should be trained to be able to use that data in patients’ health or disease management.
  5. A better understanding of what genomics can and cannot offer by the general public. Professor Church pointed out to me that without educating people about the pros and cons of the genomic revolution, we cannot make the right steps forward.

It has become clear, seeing the trends, that the technology letting us sequence genomes at home is coming. Although it’s still hard to make good, evidence-based decisions purely based on genetic background; to get reimbursed if genetics-based personalized treatments are cost-effective on the long term (but expensive on the short term); and to interpret the huge amount of data. Cognitive computers are meant to help us with that, but I’m sure ever-improving technologies will provide all of us with our own genomes far before we could do anything with that information.

Read more about the future of genomics in my book, The Guide to the Future of Medicine.

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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.

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