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Posts from the ‘genetics’ Category

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.


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.

Health 2.0 News: From Microsoft Surface to Gene Machine

The ER doctors were able to effectively treat her because she had her digital device which provided them all of her medications, conditions, allergies (she is allergic to latex). Because of this rare condition and her acute distress she was told by the doctors had she not had this device there would have been adverse events, medical errors and it would have been fatal.

Audaciously named the Personal Genome Machine (PGM), the silicon-based device is the smallest and cheapest DNA decoder ever to hit the market. It can read 10 million letters of genetic code, with a high degree of accuracy, in just two hours. Unlike existing DNA scanners the size of mainframes and servers, it fits on a tabletop and sells for only $50,000, one-tenth the price of machines already out there. For the first time every scientist, local hospital and college will be able to afford one. If the PGM takes off and regulators let him, your family doctor could buy one–and so could you, if, say, you wanted to see how fast that thing growing in your fridge is mutating.

Residency program directors from different generations had different views regarding social media information and its use in residency applicant selections. Residency program directors anticipated using social media information to aid in future decisions for resident selection and hiring.

Can you imagine managing a Facebook community of more than 1.2 million people?  You could if you were Brooke McMillan. Brooke is the online community evangelist for LIVESTRONG Foundation, and in this video she talks about how to manage this huge community of support for people with cancer.

Phylo – A Human Computing Framework for Comparative Genomics

Phylo – A Human Computing Framework for Comparative Genomics is an interactive game that lets you contribute to science. I’ve been playing with that for a while.

The Problem:

Genetic sequences are difficult to understand and so to decipher their structure, we need to compare them to detect any similar regions they may have. Similar regions may indicate important elements of our genetic code. We have several genomes to align and we call this the multiple alignment problem.

The Game:

We abstract the multiple alignment problem to a game where the goal will be to align words made by pieces of different color instead of letters representing the genetic code (A,C,G,T).

Most doctors are behind the learning curve on genetic tests

My old friend, Steve Murphy, MD shared a recent USA Today article with me in which he is also featured. A few excerpts:

“The majority of people we see have a very strong family history of X, Y or Z disease,” says Murphy, who’ll be 34 this week. He doesn’t bring up genetic testing until after taking a detailed personal and family medical history and assessing such risk factors as cholesterol and blood pressure. “I tell them there are lots of ways to dig deeper. Then I also tell them the limitations.”

On the other hand, Topol says, doctors have ordered 250,000 $100 tests for a gene called KIF6, tests that were aggressively marketed. One KIF6 variation was thought to raise heart disease risk by up to 55%, but, Topol says, a study this month in the Journal of the American College of Cardiology shot that down.



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