Skip to content

Posts from the ‘1000$ Genome’ Category

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.

gene_genie_logo_400.jpg

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.

X-Prizes for Health and Medicine?

Have you ever heard about the Ansari X Prize that resulted in constructing the world’s first privately developed spacecraft?

Source

Have you ever heard about the Archon X-Prize for Genomics? It will lead us to a new generation of genome sequencing methods.

What about an X Prize for Health and Medicine? Students at the Massachusetts Institute of Technology came up with some interesting ideas.

Of the specific proposals, one team suggested a prize for a major milestone in dealing with the problem of TB, which remains endemic in 22 nations and costs 1.7 million lives every year. Effective treatments exist, but the testing is relatively expensive and often misses active cases. So they proposed a $10 million prize for a new cheap, fast and accurate diagnostic system that could reach most of the 50 percent of cases that now go undiagnosed. Winning the prize would require not just laboratory demonstrations but field tests on 1,000 patients to show that it really works under difficult conditions.

The second proposal was for a simple, portable system that could be used by community health workers to carry out initial diagnostic evaluations for the 10 most widespread fatal, transmissible diseases. Such screening could lead to prescriptions of drugs or treatment for some conditions or referral to a doctor or nurse for conditions that require skilled care or more difficult diagnosis.

What do you think? An X Prize for Health and Medicine would be a good idea? Which medical specialty would be your choice?

Personalized Genetics: Towards the 100$ Genome

Please don’t forget to contribute to the database of real clinical examples I’m currently working on. Anyway,  I should create something like an RSS feed for all the interesting news and announcement I usually find in the field of individualized medicine.  But now I’m going to try to share some of them with you:

What makes the sequencing of Watson’s genome different from that of Venter’s? It’s the technology. Watson’s genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn’t a $1000 genome, but it’s a step in that direction.

The current study involves a much larger sample number of 120,000, which will allow researchers to gain a better understanding of 25 diseases through examining single nucleotide polymorphisms (SNPs) and a comprehensive number of copy number variants (CNVs).

The rapidly falling cost and time needed to map your DNA

2003
$437,000,000
13 years to map

2007
$10,000,000
4 years

2008
$100,000
4 weeks

2012
$100*
2 days

What you have to know about personalized genetics

Genes load the gun. Lifestyle pulls the trigger.

By Dr. Elliot Joslin

I’ve written at least a hundred times about personalized medicine so it’s the perfect time to come up with a short description of what individualized medicine is about. In this new world of medicine, you get a treatment that is not only based on the epidemiological data of your population, but your own genetic background. But let’s start with a more appropriate definition:

Personalized medicine is use of information and data from a patient’s genotype, level of gene expression and/or other clinical information to stratify disease, select a medication, provide a therapy, or initiate a preventative measure that is particularly suited to that patient at the time of administration. Personalized medicine makes it possible to give: “the appropriate drug, at the appropriate dose, to the appropriate patient, at the appropriate time”. The benefits of this approach are in its accuracy, efficacy, safety and speed.

All right, here is an even shorter one.

…turning genetic variations associated with population-level risks of disease into medically advice useful for a single person sitting in an exam room.

We can also watch it on video:

Who are the key players?

23andMe: Single Nucleotide Polymorphism and genealogy analysis for 1000$. Check out my review or the demo account I created.

23andme2.jpg

Knome: Whole-genome sequencing for 350,000$. Check out my review.

knome-logo.jpg

Navigenics: Will launch the service in days. My review is here.
navigenics.jpg

Helix Health: A New York company founded by our gene sherpa, Steve Murphy, who answered my questions some months ago. Helix Health focuses on the family history of the patient and their genetic background as well. Genetic counselors discuss the disease-specific risks with the patients.

helix-health.jpg

DecodeMe: It analyzes over one million variants in our genomes; calculates genetic risk for 23 diseases and finds our ancestors for $985.

decodeme.jpg

Who and what do stand behind the whole concept?

Archon X PRIZE for Genomics: The $10 million X PRIZE for Genomics prize purse will be awarded to the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.

The aim is the 1000$ genome.

Craig Venter’s genome that was published in September, 2007.

venter.jpg

Who and what should you follow to know everything about personalized medicine?

Personalized Genetics: The User Aspect

As personalized genetics is still rising, users start to write more and more posts about these genetic services. And this user aspect should and will play a major role in the future of genomic medicine.

Do not trust any genetic testing company that does not make it clear what genetic variants they are analyzing. Never let anyone take your DNA unless they are clear about what they plan to do with it, what information they will give you from the analysis, and what they’ll do with the DNA after all the testing is complete. You are the consumer. You have the right to choose and the right to say no.

  • Steve Murphy asks an interesting questions. So what if we have a 1000 USD genome? What would we have? I guess only one thing would change: we would have our genomes on a USB drive. That’s all. The medical aspect couldn’t change in such a short period of time. We still need years of research to be able to use properly that amount of genomic data.

While writing your answer in the comment section, listen to a presentation about Decision Making in the Genomic Era:

Follow

Get every new post delivered to your Inbox.

Join 39,576 other followers

%d bloggers like this: