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Posts Tagged ‘Genetic testing’

I mean, how many people are really needed to run a sufficiently powered genome-wide association study?  Are there enough people on the planet?  Heather J. Cordell’s review, Detecting gene-gene interactions that underlie human diseases, seems optimistic, but, at this point, it seems a valid question … at least if you want to detect gene-gene interactions.

“The historical lack of success in genetic studies of complex disease can largely be attributed, not to ignored biological interactions, but rather to under-powered studies that surveyed only a fraction of genetic variation …”

thanks for the pic heckyeahart

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A LOT of genetic data is out there … and more coming all the time … easy to get excited about, but hard to make sense of.  Here’s an epic story of just one SNP.

One of the best research teams in the business performed a genomewide association study (GWAS) of neuroticism in 1,227 US Caucasion participants and found associations (P values of 10−5 to 10−6) with several markers – including rs7151262 in the MAMDC1 gene.  Later they replicated the finding in a German sample of 1,880 (P values in the same directions 0.006–0.025).

Very exciting to ponder the ways in which this SNP might relate to the development of brain systems that process emotional information!

More recently, they attempted another replication of the MAMDC1 gene for association with neuroticism in 2,722 US Caucasion participants.  This time they report, “the current analysis failed to detect a significant association signal“.

Some 5,829 people were involved in the research and the data suggest that rs7151262 may or may not contribute to one’s neurotic tendencies.  If you knew your rs7151262 genotype would it change the way you think about yourself?

I don’t know … the confusion over the (+) vs. (-) association data would make me … well, neurotic.

thanks for the photo jinxmesomethingcrazy.

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“Listen Eric, you should think about how useful your newfangled Personal Genome is going to be.  There are a lot of reasons why all this information doesn’t tell you much”

“For example, have you thought about epigenetic effects that might be environmentally induced and can be transmitted across multiple subsequent generations?  Genotypes of individuals in previous generations might even be a better predictor of phenotype than an individual’s own genotype.”

“I know that Copy-Number Polymorphic (CNP) duplications are highly variable among individual and are considered inaccessible by most existing genotyping and sequencing technologies, but I’m still getting my genome sequenced anyway.”

“Can you please help Eric understand that rare variants and large variants (deletions, duplications and inversions) are individually rare, but collectively common in the human population might account for much more of heritability than common variation.  Nothing is known about these rare variants!”

“Yeah, Eric doesn’t realize that a very large number of closely linked genes can exhibit context-dependent and non-additive effects.”

“Gene by environment innnterraaaaactiiooon … coooool.”

–real science here.

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I probably deserve a punch in the head (see video). I will try harder to emphasize that this blog is NOT about “genes cause this” and “genes cause that”, but rather about the way we can use our genetic information as a tool – just one of many – to explore our relationships with each other, our past, other species and the environment. Still, you are welcome to punch me in the head (see video) if you like.

 

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Great commentary by neuroscientist Dorothy Bishop on the limits of personal genomics …

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View of Capitol Hill from the U.S. Supreme Court
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Pointer to Daniel MacArthur’s (Genomes Unzipped) post on the recent political grandstanding in consumer genetics.

This blog is more genomes, brains, social entrepreneurship and health 2.0 – than politics.   Hopefully the political phase will soon pass and some sensible regulations will preserve the right of consumers to access their genomes, while protecting consumers from scammers.

The one thing I hope does not happen is that the regulatory agencies (they work for us right?) “punt” on the issue and turn the whole consumer genetics ball of wax over to medical doctors and the medical insurance complex.  Like many, I am inspired by open-source, open-access, crowd-sourcing, bioinformatic and other open, web-based tools that allow consumers to by-pass the so-called “experts” in news media, finance, health and so many other industries that are being transformed by information technology.   The economic benefits for consumers are well documented, and so,  a country like the U.S. – economically sinking in a healthcare affordability crisis – might benefit (in the longer run) if it nurtured industries that helped consumers freely and openly ascertain their risks for illness without having to go through the economic choke point of an establishment of medical “experts”.

See health 2.0,  Regina Herzlinger’s “Who Killed Health Care?“,  Michael E. Porter and Elizabeth Olmsted Teisberg’s “Redefining Health Care: Creating Value-Based Competition on Results“,  Andy Kessler’s “The End of Medicine: How Silicon Valley (and Naked Mice) Will Reboot Your Doctor”  and Nobel Prize-winning economist Kenneth Arrow’s classic 1963 essay “Uncertainty and the Welfare Economics of Medical Care”  for some more on this.

Update:  The comment stream on Daniel MacArthur’s (Genomes Unzipped) post are chilling.  Many of the responders seem to have experience in the direct-to-consumer genetics business, and they don’t sound as optimistic as my (naive) self.  Part of one comment:

Seriously, you don’t understand. The DTC testing industry is ALREADY DEAD. In the Wall Street Journal, Shuren declared DTC subject to PMA approval, which costs tens of million of dollars! People are quitting the companies by the droves. 23andMe’s former director of regulatory affairs left for NextBio. VCs have refused to re-up. There will be no Series X+1 financing for an industry with no growth potential.

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The structure of part of a DNA double helix
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just a pointer to: Genetic Future’s pointer to the recent article, “Family become first to have DNA sequenced for non-medical reasons“.    The father suggests, “it will be ethically improper if you don’t have your children sequenced“.

Early days.

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