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Posts from the ‘Genome’ 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:

Human Longevity Inc. Launches To Make Us Live Longer

When Google launched Calico last year to find new solutions against aging, people thought that might be the ultimate attempt. Now, here is Human Longevity Inc., which has a much more scientific background for doing the same.

Human Longevity Inc. (HLI), a genomics and cell therapy-based diagnostic and therapeutic company focused on extending the healthy, high performance human life span, was announced today by co-founders J. Craig Venter, Ph.D., Robert Hariri, M.D., Ph.D., and Peter H. Diamandis, M.D.

The company, headquartered in San Diego, California, is being capitalized with an initial $70 million in investor funding.

It will also involve the biggest genome sequencing effort in history with the aim of sequencing the genomes of 100 000 people every year! Let’s follow them closely!

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My CNN Article: 10 ways technology will save your life in the future

I was invited to write an article about 10 ways technology will save our lives in the future for CNN.com and I was happy to do so. It was featured today on the main page of CNN. I hope you will find it useful. Here is the introduction:

The medical and healthcare sectors are in the midst of rapid change, and it can be difficult to see which new technologies will have a long-lasting impact.

Ideally, the future of healthcare will balance innovative medical technologies with the human touch. Here, I’ve outlined the trends most likely to change our lives, now or in the near future.

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The Era of the $1000 USD Genome? Not Yet!

When I started my PhD in 2009, the industry of genomics was really loud about the upcoming era of the 1000 USD genome. Then I met George Church at Scifoo organized in Googleplex and he told me the same, it was coming. Meanwhile, I finished my PhD in 2012, then one more year passed and now Illumina announced they have a machine that can sequence an entire human genome for about 1000 USD.

In the past few days, the press has been loud about the era of the 1000 USD genome. Well, did we call it the smartphone era when the first developments related to future smartphones became public? No! We started calling our time the smartphone era when I could walk into a store and buy an iPhone or an Android.

The same goes for the industry of genomics. We will live in the 1000 USD era when I can walk into a lab and have my genome sequenced for less than 1000 USD in days. It’s not here yet, although it’s coming.

Moreover, I don’t think the cost of sequencing your genome will be less than 1000 USD, but totally free!

DNA cubes

The Fastest DNA Sequencer: On USB

I’ve lived through the era of the Human Genome Project, then the Personal Genome Project, after that, the race to lower the price of genome sequencing, but what if sequencing your genome would cost nothing and you shouldn’t have to send your samples to laboratories full of sequencing machines, but you could sequence your genome at home using a USB stick.

We are not far from that.

To sequence anything longer than a few hundred base pairs, scientists mince up thousands of copies of the target DNA, sequence all the fragments, and use software to painstakingly reconstruct the order of the DNA bases by matching overlap within fragments. A new approach, called nanopore sequencing, can handle long strands of DNA at once, eliminating the need for overlap analysis. As a result, nanopore sequencers could be cheaper, faster, and more compact than other DNA sequencers. They can also accurately sequence stretches with many repeating base pairs. The MinION from Oxford Nanopore Technologies connects to a USB port. Soon, anyone with $1,000 and a computer will be able to sequence DNA.

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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.

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