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Posts tagged ‘genomics’

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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Identifying Genetic Disorders From Family Photos

Although the area of genomics has not been developing at an exponential rate that experts expected when the Human Genome Project was announced to be completed, more and more ways of potential use of genomic data in medicine have showed how it might transform our lives. A few months ago, it was published that so-called “genetic mugshots” can  be recreated from DNA. By only using a person’s DNA, a face can be generated which sounds like pure science fiction.

Now researchers at Oxford University have developed a computer program that can diagnose rare genetic disorders in children simply by analyzing family photos.

One day we might be able to sequence the genomes of newborns immediately after birth (or even before) to tell parents what major conditions the child might have to deal with in the future. As an additional feature, children without genomic sequences made available could get an instant diagnosis only by looking into the camera of a computer using this algorithm.

An excerpt about how it works:

The program works by recognising certain characteristic facial structures that can be present with certain conditions, including Down’s syndrome, Teacher Collins, Progeria, Fragile X and Angelman syndrome. It combines computer vision and machine learning to scan pictures for similarities to a database of pictures of people with known conditions, and then returns matches ranked by likelihood.

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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 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!

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20 Potential Technological Advances in the Future of Medicine: Part II.

As I mentioned in the first part of this series, the job of a medical futurist is to give a good summary of the ongoing projects and detect the ones with the biggest potential to be used in everyday medical practices and to determine the future of medicine. Here is the second part of the list of 20 technological advances:

11) Switching from long and extremely expensive clinical trials to tiny microchips which can be used as models of human organs or whole physiological systems provides clear advantages. Drugs or components could be tested on these without limitations which would make clinical trials faster and even more accurate (in each case the conditions and circumstances would be the same). The picture below shows a microchip with living cells that models how a lung works. Obviously, we need more complicated microchips that can mimic the whole human body, but this ultimate solution will arrive soon.

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12) Medical students will study anatomy on virtual dissection tables and not on human cadavers. What we studied in small textbooks will be transformed into virtual 3D solutions and models using augmented reality. We can observe, change and create anatomical models as fast as we want, as well as analyze structures in every detail. Examples include Anatomage, ImageVis3D and 4DAnatomy.

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13) Optogenetics will provide new solutions in therapies. A recent study published in Science reported that scientists were able to create false memories in the hippocampus of mice. This is the first time fear memory was generated via artificial means. By time, we will understand the placebo effect clearly; and just imagine the outcomes we can reach when false memories of taking drugs can be generated in humans as well. The idea is a bit futuristic, but the basics of the method are almost available now.

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14) With the growing number of elderly patients, introducing robot assistants to care homes and hospitals is inevitable. It could be a fair solution from moving patients to performing basic procedures. The robot in the picture below is the prototype made by a company based in California that aims at combining robotics and image-analysis technology so then it can find a good vein in your arm and also draw your blood. In the next step, it will also perform analysis on the blood from detecting biomarkers to obtaining genetic data.

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15) Now we wear a FitBit and other devices that measure easily quantifiable data, but the future belongs to digestible and wearable sensors that can work like a thin e-skin. These sensors will measure all important health parameters and vital signs from temperature, and blood biomarkers to neurological symptoms 24 hours a day transmitting data to the cloud and sending alerts to medical systems when a stroke is happening real time. It will call the ambulance itself and sends all the related data immediately.

e-skin

16) It is not just about checking and monitoring vital signs but intervention is also the key to a better health. Imagine tooth-embedded sensors that can recognize jaw movements, coughing, speaking and even smoking so it records when you eat too much or smoke no matter what the doctor told you. Again, it’s going to be extremely hard not to keep the doctor’s pieces of advice. Imagine the same wireless technology used in organs providing real-time data.

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17) If wearing thin e-skins or having embedded sensors is not a viable option for us, then let’s make an old dream come true. The concept of the tricorder from Star Trek has been there for decades and we still don’t have it. The Qualcomm Tricorder X Prize challenge will hopefully lead to the development of a device that can diagnose any diseases and give individuals more choices in their own health. The competition is hard as devices such as Scanadu are also being developed. What matters is patients will control their own health.

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18) I’ve always been a fan of IBM Watson and seen its potentials as huge opportunities in medicine. Watson will assist physicians in everyday medical decision-making, although it will not substitute humans at all.  While a physician can follow a few papers, maybe a few dozens of papers with digital solutions, Watson can process over 200 million pages in 3 seconds, therefore with the increasing amount of scientific data, it would be a wise decision using this in the practice of medicine.

IBMWatson

19) Since the completion of the Human Genome Project, we have been envisioning the era of personalized medicine in which everyone gets customized therapy with customized dosages. The truth is that there are only about 30 cases when personal genomics can be applied with evidence in the background according to the Personalized Medicine Coalition. As we move along this path, we will have more and more opportunities for using DNA analysis at the patient’s bedside which should be a must have before actually prescribing drugs.

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20) I thought I would put the simplest and most predictable medical advance to the bottom of this list. In the near future, whether it is the right and reliable medical information, dynamic resources or medical records; everything will simply be available to everyone which might not sound that interesting, but this would purely be the most important development in the history of medicine.

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It would be great if you could share your insights about other technological advances in the comment section after the post. I hope you enjoyed these two journeys into the future of medicine.

Navigenics Interview: Annual Insight

In my post about the predictions for 2009 in genomics, I said Navigenics would rule the market even if its service was more expensive than the kit of 23andMe. Now I had a chance to do an interview about the scientific background of the service and I have already sent my saliva sample back to their lab so the results should arrive soon.

Now, they came up with a totally new website, a new product and a lower price (read the press release). I’m always saying such genetic tests should be ordered by physicians. Well, here is an excerpt from the press release:

Accessible through Navigenics’ website, the secure portal empowers physicians with a suite of tools including a single access point to all of their participating patients’ genomic information, along with learning tools and case studies for integrating genomic information into their clinical practice.

I believe that was a crucial step to make.

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1. There are more and more companies offering direct-to-consumer DNA testing. How does Navigenics try to make a difference?

  • Navigenics focuses exclusively on providing genetic information for health conditions – all of which can be delayed, prevented or diagnosed early.
  • We offer two DNA testing experiences that provide different levels of premium analysis and service to best meet your needs. With both, you’ll get relevant health information and the support to help you share your results with your doctor effectively.
  • We are the only personalized genetic testing company that provides the support of board-certified genetic
  • ounselors, to help you understand your results and take action.
  • We use only government-certified laboratories.
  • Our results are based on science of the highest possible caliber. We only report on genetic markers that have met stringent criteria developed by our team of Ph.D. geneticists.
  • Privacy is our priority. Your results are kept private and secure, so the only person who has access to your results is you.
  • Navigenics is committed to research and we serve as a leader and collaborator to advance the science of genetics. We collaborate with some of the best medical institutions in the world.

2. So far, the terms of service of Navigenics have stated the results shouldn’t be used for healthcare decisions. Will it change in the near future?

Our Terms and Conditions indicate that our services are not intended to substitute for professional medical advice, diagnosis or treatment, and we have always encouraged customers to work with their physician before taking any steps after receiving their Navigenics results. As our service offerings evolve and more physicians incorporate our services into their practice, we will consider whether that necessitates any changes or clarifications to our Terms and Conditions of service .

3. The new Annual Insight provides a genetic check up for 9 common medical conditions. Personalized genetic services usually analyze more than 20 conditions. What is the reason behind the decision to analyze only 9?

The Navigenics Annual Insight service offers a highly focused snapshot of your genetic predisposition to nine select health conditions. We use a customized test for each marker in order to gather 100% of the genetic information needed to give you a highly targeted analysis of your risk information for those health conditions . By focusing on 10 common conditions, you get a targeted look at some of the most common causes of disease and disability in the U.S. today.

4. What is the genetic background of the analysis? Do you use SNP chips to determine personal risks?

I have attached a detailed white paper that addresses this – please review and let me know if you have further questions. (Access to the pdf file: Applying Preventive Genomic Medicine in Clinical Practice)

5. How accurate do you think SNP analysis is nowadays? Of course, as science is moving forward, it can change, but do you think patients understand the scientific background? Can they make health decisions based on SNP studies?

Again, we encourage our customers to work with their physician before making any changes in their healthcare strategy after they receive their Navigenics results.

6. Are you open to use the tools of telemedicine or patients will have to meet genetic counselors in person? How do you ensure security?

Currently our genetic counseling sessions are conducted by phone. We have found this to be an effective and convenient means of providing professional support to those who engage in our testing services.

Navigenics adheres to rigid security standards throughout the genetic testing process. All of our Genetic Counselors are board-certified professionals who adhere to a code of ethics that includes maintaining the highest levels of privacy and confidentiality.

Navigenics is committed to protecting your privacy. You own your genetic data, and it is our responsibility to safeguard your genetic information. Using the most advanced data protection systems available, we:

  • Anonymize all member profiles to assure data security
  • Capture the minimum account information necessary for transactions.
  • Encrypt all your personal genomic data
  • Generate your genetic risk assessment reports on demand so they exist only as you view them
  • Maintain multiple layers of physical and electronic security measures.
  • Constantly monitor all relevant processes to ensure your genetic test results are not compromised
  • Have our operational, infrastructure and applications procedures independently audited.
  • Have a sophisticated customer identification process and authenticate all transactions.

Thank you for the answers!

What I especially liked on the new portal is the Genetic testing: Myths and truths section.

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What do you think? Could Navigenics make the important steps regarding lower prices and more serious physician involvement?

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