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Posts from the ‘genetics’ Category

Would You Volunteer for Google’s Moonshot Medical Study?

The new moonshot project from Google is to create a Google Maps of the human body including molecular and genomic information as well. The Personal Genome Project (PGP) had a similar mission years ago, but this one seems to be even bigger.

The 175 healthy people will go through an exam that includes the collection of body fluids like blood and saliva, after which Google X researchers will review what they have learnt and engage researchers at Duke University and Stanford University for a much larger study.

The eventual aim is for Baseline to act as a reference for the chemistry of a well-run, healthy body, and in turn, identify anomalies far earlier. The hope is that the medicine industry moves more towards prevention rather than treatment in response to illnesses.

A major difference is the institution or company standing behind both projects. The PGP was initiated by Harvard University’s Professor George M. Church, while this new project is launched by Google. I have to note though that Google plans to make the results available for “qualified researchers in health”; data collected will be anonymous and not be shared with insurance companies.

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But Dan Munro at Re/code immediately shared his concerns about participating in such a study due to legal risks and the level of trust related to Google.

I’m sure Google wants my genetic data — preferably for free of, course — and will say anything in order to get it. Does that mean that it has earned my trust to use that data as part of an ambiguous, long-term experiment? Not with my genetic data. At least not yet. Thanks for the offer, but no thanks.

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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Disruptive Technologies in Medicine: Preparing Medical Students For The Future!

I’m very excited to announce that this semester we launch a new course, “Disruptive Technologies in Medicine” with Professor Maria Judit Molnar MD, PhD, DSc, the scientific Vice Rector of Semmelweis University. Our plan is to prepare medical students for those future technologies they will face by the time they start actually practicing medicine. I want to persuade them that the relation between the human touch and technologies is AND instead of OR.

Here are the topics we will cover with experts.

  • How Exponential and Disruptive Technologies Shape The Future of Medicine
  • Personalized Medicine – Genomic Health
  • Point of Care Diagnostics
  • The Future of Medical Imaging
  • Social Media in Medicine
  • Harnessing Big Data in Healthcare
  • Biotechnology and Gene Therapy
  • Mobile Health and Telemedicine
  • Regenerative Medicine, Optogenetics and 3D Printing
  • Medical Robotics, Bionics, Virtual Reality, and Future of Medical Technologies

We are going to teach them offline and online at the same time with plenty of assignments and interesting projects such as collaboration with the students of the course of Kim Solez at University of Alberta.

Feel free to follow all the developments and announcements of the course on Facebook. All the seats are already taken by international students. This is going to be an amazing semester!

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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.

The Guide to the Future of Medicine: Download the White Paper with Infographic

Being a medical futurist means I work on bringing disruptive technologies to medicine & healthcare; assisting medical professionals and students in using these in an efficient and secure way; and educating e-patients about how to become equal partners with their caregivers.

Based on what we see in other industries, this is going to be an exploding series of changes and while redesigning healthcare takes a lot of time and efforts, the best we can do is to prepare all stakeholders for what is coming next. That was the reason behind creating The Guide to the Future of Medicine white paper which you can download for free.

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Please use the Twitter hashtag #MedicalFuture for giving feedback.

In the white paper, there is an infographic featuring the main trends that shape the future of medicine visualized from 3 perspectives:

  1. Which stage of the delivery of healthcare and the practice of medicine is affected by that (Prevent & Prepare; Data Input & Diagnostics; Therapy & Follow-up; and Outcomes & Consequences);
  2. Whether it affects patients or healthcare professionals;
  3. The practicability of it (already available – green boxes; in progress – orange boxes; and still needs time – red boxes)

Click here to see the infographic in the original size.

Guide to the Future of Medicine Infographic

I hope you will find the guide useful in your work or in preparing your company and colleagues for the future of medicine.

Here is my PhD thesis

Two weeks ago, my childhood dream became true and I finished PhD therefore becoming a medical geneticist. If you are interested in the pharmacogenomic implications of autoimmune conditions, here is my PhD thesis in PDF format.

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Visiting Direct-To-Consumer Genetic Companies

When I had a free test at Navigenics and Pathway Genomics, I had a chance to visit the Navigenics HQ as well in San Francisco. Now Daniel MacArthur visited the 23andMe and Complete Genomics HQs.

I was graciously received by Shirley Wu, who gave me the grand tour, and various members of the 23andMe science team (especially Nick Eriksson and Tom Do) then uncomplainingly put up with my questions for what must have seemed like hours. The visit reinforced my overall impression of the company: this is a group of very smart people working with an increasingly impressive customer data-set on some seriously interesting problems. Their recently announced discovery of two novel genetic regions associated with Parkinson’s disease (due for publication in the near future) is a taste of what’s to come.

Opening your genome to the public

Ramūnas Janavičius, a clinical geneticist (MD) and blogger at Cancer Genetics, just made his genomic data open to the public. The Personal Genome project did the same with 10 volunteers. An excerpt from the entry of Ramunas:

Today is a good day. I can not imagine a better day than personal birthday (and forthcoming DNA Day) to share my personal genome scan information, which you can find in this blog HERE* [GenomeScan_RJv2].
This is quite low density profile generated through 23andMe v.2 genotyping on Illumina Hap550+ array while a year ago.

He shared his genomic data under Creative Commons 3.0 license. Though it would be better to see his genomic raw data, but the Excel file with the SNP variants is also very interesting.

The first commenter pointed out that he doesn’t have curly hair as indicated by a variant, but he has a strange variant:

rs17602729, a SNP located in the AMPD1 gene and also known as ‘C34T’, has at times been called the “most prevalent genetic disease mutation”, at least in Caucasians. [PMID 11331279] Perhaps up to 10% of Caucasians and African-American carry one C34T allele (i.e. carry one rs17602729(A) allele) – and actually, most of them are unaware of any medically related issues since they don’t typically have any particular symptoms that would warrant a trip to the doctor.

Feel free to discover the data and let him know if you find anything interesting.

Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases

It’s a pleasure to share the great news that we just published our review in Trends in Molecular Medicine under the title, Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases. We looked at the literature and wrote about whether peripheral blood can be used for the diagnosis of autoimmune diseases or the prediction of the effectiveness of therapies. We also came up with a decision tree and a set of proposed guides in order to facilitate inter-disciplinary collaborations.

The paper is not publicly available, but if you are interested, I’d be happy to send it to you via e-mail.

Gene expression profiling in clinical genomics has yet to deliver robust and reliable approaches for developing diagnostics and contributing to personalized medicine. Owing to technological developments and the recent accumulation of expression profiles, it is a timely and relevant question whether peripheral blood gene expression profiling can be used routinely in clinical decision making. Here, we review the available gene expression profiling data of peripheral blood in autoimmune and chronic inflammatory diseases and suggest that peripheral blood mononuclear cells are suitable for descriptive and comparative gene expression analyses. A gene-disease interaction network in chronic inflammatory diseases, a general protocol for future studies and a decision tree for researchers are presented to facilitate standardization and adoption of this approach.

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