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Posts from the ‘1000$ 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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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

Personalized Genomics News: From Virtuality to the Streets

  • DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful.

“Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.”

The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three prominent DTC companies: 23andMe, Pathway Genomics and Navigenics.

  • 23andme: A detailed review of the data the blogger just received from 23andMe.

The family said they received no medical counseling here and are making their own conclusions.  One comment made is that the parents stated they will probably be using more pharmaceuticals, interesting.

A patient analyzes her own 23andMe data:

Whole-Genome Sequencing: Any Useful Data?

I met George Church at this year’s Scifoo event in San Francisco and we talked about how useful the data is that was obtained from whole genome sequencing methods. There are almost 50 people in the world right now whose genomes were sequenced like that but the number of useful genomes is very low (e.g. who made it public) . That’s one reason why the ClinSeq project is really promosing.

ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of disease, implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analyzing, and displaying sequence data.

In the initial phase of ClinSeq, we are enrolling roughly 1,000 participants; the evaluation of each includes obtaining a detailed family and medical history as well as a clinical evaluation. The participants are being consented broadly for research on many traits and for whole-genome sequencing. Initially, Sanger-based sequencing of 300-400 genes thought to be relevant to atherosclerosis is being performed, with the resulting data analyzed for rare, high-penetrance variants associated with specific clinical traits.

He also mentioned the 1000$ genome project and the unofficial estimation is that now it’s possible to sequence a person’s genome for under 5000$ and the 1000$ aim can become a reality at the end of this year.

Gene Genie #41: Carnivalome

Gene Genie is the blog carnival of clinical genetics and personalized medicine. I’ve received more than 25 submissions for this edition which is dedicated to the human genome and videos in clinical genetics.

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Many thanks to Ricardo Vidal for the logo!

The molecular level:

Daniel MacArthur at Genetic Future wrote about Genetics of gene expression in African-Americans: ominous news for personal genomics?

Alex Palazzo at The Daily Transcript analyzed 100 years of genetic research.

Greg Laden‘s submission was The Scientific, Political, Social, and Pedagogical Context for the claim that “Race does not exist.”

Larry Moran at Sandwalk talked about Genes and Straw Men

The clinical level:

Chavonne Jones at Human Genetics Disorders shared Muscular Dystrophy Gene Therapy Video:

The Daily Scan informed us about Breaking Cancer’s Gene Code.

Walter Jessen at Highlight Health focused on Potential Location of Autism Genes Identified and Gene Expression Can Predict the Survival of Lymphoma Patients.

The PHG Foundation posted about Helping physicians understand genetic risk and Epilepsy Phenome / Genome Project.

Grace Ibay at Genetics and Health published two interesting articles: Gene therapy research presents hope for sickle cell anemia and The genetic disorder that kept her from dancing.

Chavonne Jones at Human Genetics Disorders also shared a Wilson’s disease video with us:

The personalized genetic level:

The Navigenics Blog said Leading genomic researcher discusses his own test results.

Hsien-Hsien Lei at Eye on DNA unveiled Singapore Company DNA Dynasty Will (Not) Tell Your Children’s Future.

Do you know costs are plummeting for human genome sequencing?

The PredictER Blog focused on genetic privacy.

Daniel MacArthur at Genetic Future featured advice for doctors on dealing with personal genomics customers.

Read more about The Spitterati and Trickle-Down Genomics at the site of Center for Genetics and Society.

Blaine Bettinger at The Genetic Genealogist analyzed Familybuilder that announces DNA Testing.

Now: The rest of the genome (Herald Tribune).

Lygeia Ricciardi at Project HealthDesign asked “Would knowing your genes change how you act?

And don’t miss the Book of Me.

Genetic Testing for Heart Disease:

The President level:

The Genetic Privacy of Presidential Candidates (New England Journal of Medicine):

Using genetic information to disparage opponents has no place in presidential campaigns. Nonetheless, the threat of genetic McCarthyism provides us with an opportunity to engage in a public dialogue about the limitations and complexities of using genomic information for decisions about life and health — including voting for our president.

Gene Screen: Will We Vote Against a Candidate’s DNA? (Wall Street Journal):

“DNA is not an issue in this campaign, but in the next campaign it will be bigger,” says George Annas, a leading authority on bioethics and human rights at Boston University. “It’s coming.”

If you want to host an issue of Gene Genie in 2009, let me know (berci.mesko [at] gmail.com). Don’t forget to submit your articles (berci.mesko [at] gmail.com).

And also check the Gene Genie blog out!

Personalized Genetics: On the train again

I’ve got a huge backlog now, but will try to keep sharing interesting genetic articles and posts with you regularly. So here is this week’s collection:

  • One of the main issues in the blogosphere is the 1000$ genome, the aim is to let everyone access their genomic data for 1000$. We thought we could reach that goal in the next couple of years, but according to Blaine Bettinger’s post, it might be done by the end of 2009.
  • The Genomic Revolution and the Future of Medicine and Health: A nice lecture about an essential subject

Personalized Genetics: Crystal Ball?

The world of personalized medicine must be much more than a crystal ball. Here are some new articles about the steps that have to be made and some aspects that might help us :

Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)….gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service? Some would argue yes….I say no.

It’s not as bloody as you think.

Very soon, the cost for routine whole human genome sequencing will become cheaper, and some day will be offered during routine clinical testing along with the CBC, blood count and chemistry panel. Also, we will very soon have a greater understanding of gene variation and disease risk, which will hopefully allow intelligent and useful interpretation of the routine clinical sequencing of the entire human genome. As of May 2008, we are not quite there yet.

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