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Posts tagged ‘Genome’

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.

KONYVBORITO_online final s 350

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.

dna

 

 

Navigenics: What my genome tells me to do

A few months ago, Navigenics.com offered me to analyze my saliva sample and genome. I happily accepted the offer and was curious to see what they could tell me. After graduating from medical school, I will start PhD training in personalized genetics this September so I’m quite into this emerging field of medicine.

navigenics-main-page2

I sent my saliva sample back to their laboratory this January and received the results in about 3-4 weeks.

navigenics-view-my-results1

I clicked on View my results and saw what kind of risks I have for certain medical conditions such as glaucoma, heart disease, prostate cancer, Crohn’s disease or osteoarthritis (9 conditions all together).

When I check one medical condition, I see something like that:

navigenics-results1

They tell me my risk compared to the whole population.

navigenics-risk

And how that medical condition is affected by environmental and genetic factors.

navigenics-all-risk

And if I’m interested in the particular single nucleotide polymorphism they analyzed, I can check the details.

navigenics-ratio

Pros:

  • The information this service provided me with was useful and I will change some things in my lifestyle.
  • I can talk with a genetic counselor to discuss the results of my genetic variations.
  • I can print the results and share it with my doctor through an understandable report that mentions the references on which they based my risk percentages.
  • They help me what I can do in order to lower my risks for specific conditions. They also let me know things that prevent multiple conditions on the Navigenics panels.
  • Each condition is covered in details (causes, symptoms, treatments, etc.). This information is powered by Mayo Clinic.
  • I can find support groups or more information on prevention.

Cons:

  • Let’s say 3 SNPs tell me I have elevated risk for heart disease. But next year, they will discover 4 new ones that defend me from this condition. So Navigenics, just like any other similar companies, can only tell me risk percentages that might change a lot in the future.
  • For example, if based on my genomic results, I have elevated risk for heart disease, what I can do to lower this risk? Exercises, healthy lifestyle, etc. Things you can tell me without analyzing my genome. Though it’s not the fault of the service, but of the state genetics is in at the moment.
  • It’s still way too expensive compared to what I get for my money as the results cannot really be used for medical decisions  (I got a free package so I know I shouldn’t say that).
  • Well, a few genetic tests can be useful when making medical decisions, but such tests should be ordered only by medical professionals. Or if not, at least genetic counseling should be for free as patients need serious guidance when reading the results of their genomic variations. (Update: Navigenics provides free genetic counseling for all Health Compass members and 1 hour of free counseling for all Insight members. And you can order the tests through a medical professional or on your own.)
  • I think I can handle many things but it was almost impossible for me to understand which documents I have to send back to the lab with my saliva sample. A step-by-step video tutorial would be useful.

I’m thankful to the Team of Navigenics.com for showing me how their service works in action. I’m impressed and looking forward to seeing how they can make their service even better.

2009 Predictions in Personalized Genetics

Hsien-Hsien Lei shared her 2009 predictions about personalized genetics with us and that’s where I would like to leave a few comments.

1. 23andMe will begin selling their tests on drugstore shelves.

I think they would be sued soon.

2. President Barack Obama will be offered genome sequencing.

He cannot and mustn’t accept it.

3. Apple will launch iSEQ – instant DNA testing and analysis in a handheld device.

I don’t think Apple will ever enter this market.

4. The first 10 participants in the Personal Genome Project will band together to be called Fantastic Ten. Each will reveal secret superpowers that are embedded in their DNA.

That is a possibility. But if they think wisely, they will never do something like that.

5. The U.S. government passes laws to obtain DNA from all its citizens which it says will help protect the innocent and punish criminals.

It was only possible in Iceland and will never be possible in the US.

What I think about 2009 is that Navigenics will rule the market even if its service is more expensive than the kit of 23andMe.

navigenics

Further reading:

AccessDNA: Know Your Genetics

I’ve recently discovered AccessDNA on Twitter and I thought I should give it a try. On the main page, it says I should create my personalized report. Well, let’s do so.

accessdna

It asked me about the medical conditions that occurred in my family; environmental factors I have to face; tests I would be interested in, etc. And then I received the personalized genetic report; actually a list of genetic tests that might be useful for me.

accessdna-report

What can I do with that information? Yes, of course I want full genome scanning. But should this be my decision? Not the decision of my doctor? Just beacuse I reported to be of Caucasian descent, I should order genetic tests that cost several thousands of dollars?

You know what? I would love to hear the opinion of Steve Murphy here. And yours!

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