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Posts from the ‘Genetic screening’ Category

BlogMix: the best posts of the week

Every Saturday from now, I’m going to collect all the best posts of the medical and genetic blogosphere. In this first issue, I focus on personalized genetics and web 2.0 (it’s a surprise, isn’t it?).

The Genetic Genealogist produced a fantastic series of posts about the $1000 genome:

Kudos to Blaine Bettinger!

Then don’t miss A thesaurus, wikis and text mining post at business|bytes|genes|molecules.

The goal of the project is to discover relationships and associations and eventually therapeutic mechanisms. The hope is to bring as many as 20,000 bioinformaticians and researchers into the project. From where I stand, just limiting the proposal to a relationship-oriented wiki might be too narrow.

LifeHack provides a list of the features of del.icio.us.

The community of del.icio.us allows you to find some of the best resources on the Internet without having to trudge through all of the junk.

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And two writings of Walter at HighlightHealth.com:

At last, my interview with Steven Murphy has been published at Reuters! :)

That’s why I’m proud to be a member at ScientificBlogging.com!

See you next Saturday with BlogMix…

Personalized Genetics/Genomics: Blogterview with Steven Murphy, MD

I’ve recently decided to deepen my knowledge on the field of personalized genetics/genomics as it has an exceptional future in the realm of medicine (and business). And who is the right person to answer my geek questions? Of course, Steven Murphy, MD, the blogger of the Gene Sherpa. He is the Clinical Genetics Fellow at Yale University and is also the founder of a Personalized Medicine practice.

  • We’ve heard a lot about personalized medicine, but please tell us more about personalized genetics.

Sure. There are some fundamental differences here. When I think about personalized genetics (Which is different than personalized genomics) I think about modifier genes involved in single gene disorders such as Cystic Fibrosis. A few months ago, I diagnosed a 70 year old woman with CF. She had been treated as if she had emphysema, had never smoked, and no Alpha 1 Antitrypsin deficiency. Something didn’t sit right with me. We had her get sweat tested and sequenced. Guess what? Compound heterozygote with one Delta 508 mutation. How could this happen? Modifier genes. There is a nice review of modifier genes in CF several months back in the New England Journal of Medicine. That is personalized genetics in my opinion…

Should we treat you aggresively or not? This woman clearly did ok without Creon (pancreatic enzymes), aggressve pulmonary toilet, or inhaled antibiotics. Now with the newborn screen we detect so many more patients with Cystic Fibrosis. Who should we treat? How should we treat? Personalized Genetics is like personalized medicine for those with single gene disorders. I remind you that “No gene is an Island” so we need to take it in context of the rest.

  • Personalized genetics or genomics? Is there any important difference?

Personalized Genomics is a totaly different animal. Here we deal with what everyone affectionately calls the “Personal Genome”. This is the dream of everyone gets a genome sequenced at birth, we assess risk, create prevention plans, identify idosyncratic drug reactions prior to medication therapy. The fear is obvious…”When is GATACA coming?” I think that we need to put protections in place to prevent discrimination from more than just employers and insurers. What about that University you want to get in to? In addition there are several problems with whole genome screening aside from its multimillion dollar pricetag (which is dropping quickly). That is the problem in medicine known as the incidentaloma.

Quite often when ordering a CT scan, or chest xray, or what ever radiologic test we find tumors/cysts/masses in a completely asymptomatic patient. Does this mean we identify a cancer or other life threatening thing before it can cause damage? Sometimes, but more often than not we end up spending thousands of dollars evaluating something that turns out to be nothing. Just an incidental finding in an otherwise asymptomatic patient. An article entitled The incidentalome: a threat to genomic medicine.” was published in JAMA in July of 2006. Mathemeticians modeled sequencing the whole genome. As they get up to sequencing 10.000 people they find that the fraction of the population with a false positive result skyrockets up to 60%. What does this mean? Well, we have to carefully select who we test. Or better yet we need an immense database of “Normal Variants”. At a minimum we will need 1000s of “sequence specialists” or “computer sequence analysis programs” to evaluate and decide if the “work up” is indicated or not. Personal Genomics is very complex, even more than personalized medicine.

  • What about the big companies focusing on personalized genomics/genetics?

We have key players including Illumina, 454 who has now been eaten by Roche, Affymetrix, Ventner, I could go on and on. The newest one to watch for is from the brainchild of 454 Jonathan Rothberg. He is launching a company called RainDance technologies. RainDance is already collaborating with Bayer Pharmaceuticals on high-throughput screening assays, noting the vastly superior statistics and reagent costs. What this means is a whole new means to sequence. If you add that into the nanopore sequencing mix at Harvard, then you have a robust field for development. I am sure I have missed a few, but these seem to be the key and future players to me.

As for personalized genetics, I know that the old stalwards like Genzyme, Genentech, BioMarin are all playing a role in defining the right infusion/pill for the right person with the right monogenic disease. Also you cannot forget about TGen who is building a presonalized medicine medical school in Arizona. My gosh I could just ramble about all of these things, but I will spare you all the details.

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  • As bioinformatics plays an important role in this rising field of medicine, how can web (especially web 2.0 ) help personalized genetics?

Web 2.0 and 3.0 can be best harnessed by networks of researchers sharing findings in open source forum. We need to give up the “Prize” for publication. Instead we need to nurture inter-institutional collaboration. In fact I would say we should prize how many universities were involved in every study. The web infrastructure can allow all of these things. In fact imagine coming up with a question in EST and shipping it to Mumbai for analysis during EST night-time. This is already happening in business. True, research takes more than overnight, but what if we were just talking about design. We could literally be working 24/7 to solve problems!

My dream is just that. The spirit of innovation, collaboration, and revolution all moving to solve the greatest code ever devised…DNA

I’m very thankful to Steven Murphy for the kind answers! Follow his blog for the most interesting news and explanations of personalized genetics.

News of genetics: let’s beat genetic diseases!

I’m just back from a poker tournament, and I can’t stop posting the most interesting and promising genetic news and announcements from the recent days:

A pill that can correct a wide range of faulty genes which cause crippling illnesses should be available within three years, promising a revolution in the treatment of thousands of conditions. The drug, known as PTC124, has already had encouraging results in patients with Duchenne muscular dystrophy and cystic fibrosis. The final phase of clinical trials is to begin this year, and it could be licensed as early as 2009.

I must write more about PTC124 and the possible therapeutic possibilities. A great topic.

A new automated test could enable population screening to identify carriers of the gene mutations causing fragile X syndrome (FXS), the most common inherited form of mental retardation.

Currently, there is no cure for Fragile X syndrome, so this population screening would be helpful mainly for genetic counseling.

If you’re a regular reader of this blog, then you know that I am a strong proponent of genetic testing for genealogical purposes. I believe that when used correctly genetic testing can serve as a valuable tool in the genealogist’s toolbox… the skepticism and wariness about genetic genealogy comes from the interpretation of the results.

It seems that I finally found my man… If you’d like to read great comments on the news of genetic testing, don’t miss that blog! He also made a collection of 10 genetic videos. Here is one about Mitochondrial Eve:

And at last, genetic humor… My Biotech Life presents quilts made up of nucleotides. You just have your genome sequenced and Beverly St. Clair makes your own genomic quilt. Here is an example of the patterns and a real quilt of nucleotides.

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Hepatitis Virus C gene

News of the world of medicine 2.0

After my successful urology exam, let’s take a tour into the realm of web 2.0 an medicine. First, I show you some useful sites, then we’re going to continue with blogposts and finally, a great video about genetic screening.

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  • PubMed Reader: a free web-based research program for displaying PubMed / Medline search results on an individual basis. Create your own uptodate Medline and PubMed literature search!
  • YourSciCom: Science 2.0, a completely open research project’s blog.
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