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Posts Tagged ‘23andMe’

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pointer to: Great Q&A on Freakonomics with 23andMe founder Anne Wojcicki. Nice overview of peoples’ concerns and interests in personal genomes.

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pointer to Jen S. McCabe’s blog on healthcare management and gracious video share of her experience with her 23andMe personal genome data.

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old class photo with grandpa, 1923
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Back in the day, when the fam would get together at my parents’ house, I would enjoy shuffling through their box of old photos.  Looking at childhood pictures of myself and relatives, it was natural to compare our adult selves to the old pictures and look for similarities – emotional expressions, gestures, etc. – that have carried on through the years and are (were) a part of who we are (became) today.  It’s always amazing what you think you can see, and if you’re like me, you may be somewhat amazed by how much of your adult self was already in full swing as a child.  The manner in which the developing brain confers such stability over time and over generations (now I see my own childhood traits in my son – yikes!) is of course a timeworn question among families and scientists alike.

That the genome would contribute to cross generational parent-child similarities in personality and temperament is fairly obvious, but not so apparent is how the genome interacts with the environment to exert an influence on psychological development.  Along this line of inquiry, a research article entitled, “Influence of RGS2 on anxiety-related temperament, personality, and brain function” by Smoller and colleagues [free access] provides an amazing perspective – from a single gene.  RGS2, eponymously named as a regulator of G-protein signaling, was first identified as a factor that regulates emotional behavior in mice [PMID] and subsequently as a risk factor for schizophrenia [PMID] as well as anxiety disorders in humans [PMID].  In the current study, the team examined the temperament of children (119 families), personality of adults (744 undergraduates) and brain activity in adults (55 participants) to ascertain whether the adult risk for anxiety conferred by RGS2 might be related to actions of the gene that occur much earlier in development – such as on the systems that regulate temperament in children.  Specifically, they focused on behavioral inhibition in children (shy, avoidant, restrained in novel situations) and introversion in adults – as these traits have been associated with increased risk for anxiety disorders.

What is so interesting to me is that RGS2 (particularly the G allele of the 3’UTR SNP rs4606) was found to be associated with both childhood temperament and adult personality.  Thus, an introverted adult who looks through an old photo album and sees themselves to have been a shy or inhibited child, may be experiencing – to a small degree – the effects of the RGS2 gene.  The team suggests, via additional brain imaging-genetic studies, that RGS2 is of particular relevance to activity in circuits containing the insular cortex and amygdala – when subjects perform an emotional face matching task.

My own 23andme record does not contain the rs4606 SNP but does contain the data for rs1819741 where a T allele was significantly associated with introversion.  Since I’m a C/T heterozygote, I guess I’ll have to look a bit harder at my old pictures to see signs of behavioral inhibition.

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Basic-helix-loop-helix structural motif of pro...
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The basic helix-loop-helix transcription factor, neurogenin-1 is known to regulate neural development and neurite outgrowth.  As such, it makes for a particularly interesting point to begin to understand mental illness and its complex developmental origins.  The recent paper by Ho et al., “Basic helix–loop–helix transcription factor NEUROG1 and schizophrenia: Effects on illness susceptibility, MRI brain morphometry and cognitive abilities ” [doi: 10.1016/l.schres.2008.08.009] makes for a very interesting read since this gene resides in the midst of the chromosome 5q31 region – which has been a risk hotspot in a number of previous linkage studies – and – two snps in NEUROG1 (the C-allele of rs2344484 and the G-allele of rs8192558) have also been associated with the disorder.

The authors report that in a sample of 392 patients and 226 control subjects, the major alleles of rs2344484 and rs8192558 were more prevalent among patients.  Furthermore, some of the participants underwent structural MR brain imaging which allowed the research team to examine where in the brain such genetic risk might arise from.  Interestingly, the team found that both patients and control subjects who carried the C-allele of rs2344484 showed somewhat smaller volumes of grey matter.  For example, in Table 3 there were 145 CC,CT individuals with an average of 662 cubic centimeters of grey matter while the 28 participants with the TT genotype showed an average volume of 682 cu.cm.  This allele was also found to be associated with poorer cognitive abilities in these C-carrier participants.

As pointed out by the research team, NEUROG1 is expressed early in the development of the human brain and is implicated in the differentiation of cortical progenitor cells and of glutamatergic excitatory cells in deep layers of the cortex.  Thus, the role of variation in a transcription factor – a gene that regulates the expression of other genes – in the risk of schizophrenia can be very early and with very broadly effects on the neocortex.

How to treat such an early deficit? Would be interesting to discuss further.  My own 23andMe profile shows a CT heterozygote which places me within the higher risk, but more common genotypic pool.  Hmmm.  What to make of that?

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Richard Westall, The Sword of Damocles, (Briti...
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Just having some fun with SNPedia’s new release of Promethase (0.1.66) which now has a superfast analysis option ($2 via a link to your Amazon.com account) as well as the usual free regular speed option.  I had some fun comparing my 23andMe profile to my wife’s using the experimental “breeding” tool and – 214 seconds later – had a glimpse of the genetic probabilities that now hang like the Sword of Damocles over my children. A few SNPpets include:
rs1726866(T;T) – unable to taste bitter 80% likely to be unable to taste bitter
rs10246939(T;T) – unable to taste bitter
rs11200638(A;A) – ~10x increased risk of wet age related macular degeneration
rs7754840(C;C) – 1.3x increased risk for type-2 diabetes
rs324650(T;T) – higher IQ The rs324650(T;T) genotype boosts intelligence
rs2802288(A;A) – longer lifespan
rs1815739(C;C) – possibly increased sprint/power performance

Although I won’t be around to vouch for the longer lifespan, I can vouch for the insensitivity to bitter taste (both kids love broccoli) and our torn up furniture must confirm the tendency to sprint muscles … as for the others, I guess we’ll see in time.  Thanks SNPedia!

(+2 points for mixing references to 2 Greek myths in 1 blog post)

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Lollipop-Nosed
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“There is a sucker born every minute”, were the words that looped through my mind on the long train ride home after losing $200 in an unfortunate encounter with a card shark over on Canal Street, many years ago.  I recall that when the card shark (actually a kindly old man) suggested to me that I would easily outwit him and $$ win $$, I have to admit that I really, sort of, well, believed him.  Hmmm, what a sucker indeed.  Come to think of it though, he didn’t even know that I was a GG homozygote at rs4570625 in the tryptophan hydroxylase-2 gene, which according to Furmark and colleagues,  is “a significant predictor of clinical placebo response“.  Lucky for him I guess.

There is actually a lot of mainstream neuroscience research on the placebo response – for good reason – it has a way of complicating & inflating the cost of clinical trials for many neuropsychiatric disorders, but also shows that “overt suggestions” and non-medication-based talk therapies can lead to outcome improvement.  In any case, whether you prefer medication or non-medication modalities of treatment, there is much to be gained from understanding the basic biology of the placebo response. A great review on the biology of the placebo response can be found here.

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nothing like hot coffee to wash down a bite of...

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I was irked to see, in today’s New York Times, a picture of a young child having his cheek swabbed so that his parents could ascertain his status at the rs1815739 C/T variant .  T-alleles at this site give rise to a premature stop codon in the alpha 3 actinin (ACTN3) gene while the C-allele encodes a full-length protein that contributes to the fast twitching of muscle fibers.  Not surprisingly, it was found [PubMed Central ID: PMC118068] that folks who have achieved status as Olympic caliber sprinters are more likely to carry the C-allele than ethnically matched controls. The company, Atlas Sports Genetics is now marketing the test, for $149 as a means to “predict a child’s natural athletic strengths”.  Holy Crap !

Its sad to think of the myriad of ways in which genetic information can be misused and misrepresented – sadder still to think of using genetic tests to deny kids the simple joy of playing with each other.  Parents may be intersted to know that among europeans and asians, the C-allele is present at about 50%, making 75% of the population either a C/C or a C/T … which, taken alone, explains very little of why a handful of individuals achieve athletic success. Parents considering paying the $149 might also wish to read a recent article by Dr. Jerome Kagan, a well-regarded developmental psychologist on recent trends in overparenting.

My 23andMe profile shows a middling C/T which is on par with my middling soccer skills.  Nevertheless, I had a great experience learning and building relationships with my pals on the soccer field, many who remain friends decades hence.

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My Promethease Unbound

Vulcan Chaining Prometheus, Rijksmuseum, Amsterdam

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Thanks so very much to the folks at SNPedia for developing and sharing the Promethease analysis tool. What a delight to delve into my 23andMe profile ! I stumbled onto the usual dreary risks for this and that, and yes, I know I’m at risk for baldness, but did come up with a few bonus IQ points and moreover an allele that protects me from cannabis dependence (will have to return to Nijmegen sooner than later I suppose).

Just a sampling from the report … what’s in YOUR genome ?

rs2165241(T;T)  >10x increased risk of exfoliation glaucoma (LOXL1)
rs2180439(T;T)  2x increased risk of baldness
rs1136287(T;T)  3.9x increased risk of wet age related macular degeneration (PEDF)
rs1426654(A;A)  probably light-skinned, European ancestry
rs601338(A;A)  resistance to Norwalk virus infection
rs324650(A;T)  somewhat higher IQ (CHRM2)
rs1815739(C;T)  mix of sprinting & endurance muscles (ACTN3)
rs16891982(C;G)  if European, 7x more likely to have black hair (SLC45A2)
rs806368(C;C)  lower risk of the development of substance dependence
rs1954787(T;T)  ~10% less likely to respond to citalopram (HTR2A)
rs17822931(C;T)  wet earwax
rs237025(A;A)  MET/MET increased diabetes susceptibility
rs6449213(T;T)  ~4x higher risk for hyperuracemia
rs1015362(C;C)  2-4x higher risk of sun sensitivity if part of risk haplotype (ASIP)
rs1800497(G;G)  A2/A2 bupropion effective (DRD2)
rs363039(A;G)  2+ IQ points (SNAP25)
rs2383207(A;G)  increased risk for heart disease
rs2987983(G;G)  increased risk for prostate cancer
rs1800955(C;C)  increased susceptibility to novelty seeking (DRD4)
rs2279744(G;G)  generally more cancer prone (MDM2)
rs10260404(C;C) rs10239794(C;C) haplotype strongly associated with ALS
rs283413(A;C)  3.2x higher risk for PD (ADH1C)
rs1024611(G;G)  increased risk of exercise induced ischemia (CCL2)
rs1328674(T;T)  higher risk for RA (HTR2A)
rs2107301(A;A)  2.47x higher risk for prostate cancer
rs1801270(A;C)  increased risk for lung cancer
rs1571801(T;T)  >1.36x risk for prostate cancer
rs1799724(C;T)  weak risk for Alzheimer’s Disease
rs733618(C;T)  1.87x risk for myasthenia gravis (CTLA4)
rs7480010(G;G)  increased susceptibility to Type II Diabetes
rs3018362(A;A)  increases susceptibility to Osteoporotic fractures
rs4870044(T;T)  increases susceptibility to Bone mineral density variations
rs806380(G;G)  protection from cannabis dependence
rs17696736(G;G)  associated with type-1 diabetes

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Day 191 - Stick it Out

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Like “Joe the Plumber” (whose real name is Samuel), CNTNAP2 (whose real name is CASPR2) has achieved a bit of fame lately.  While recently appearing almost everywhere (here, here, here) except FOX News, CNTNAP2 (not Joe the Plumber) is apparently a transcriptional target of the infamous FOXP2 “language gene” – so says Sonja C. Vernes & colleagues [doi: 10.1056/NEJMoa0802828] who precipitated DNA-protein complexes using anti-FOXP2 antibodies from a cell line transiently expressing FOXP2. The team later evaluated measures of expressive and receptive language abilities and nonsense-word repetition and found that a series of snps – most significantly rs17236239 – were associated with performance of children from a consortium of families at risk for language impairment.  This adds to several previous reports of CNTNAP2 and risk for autism, a disorder where language ability is severely impaired.

So what’s all the fuss ? How can something so insignificant (rs17236239 not Joe the Plumber) stir up so much trouble ?  Well, as reported in a previous post, the expression of CNTNAP2 in the developing superior temporal cortex may be a relevant clue since this brain region is activated by language tasks.  Also, this gene encodes a rather massive protein which (as reported by Coman et al.,) seems to participate in the establishment of myelination and “nodes” that permit rapid neural transmission and long-range coordination across neural structures in the brain. Interestingly, this gene shows evidence for recent positive selection in humans (as posted on here and here) although the newly derived G-allele at rs17236239 seems to be the allele that is causing the language difficulties.  My own 23andMe profile shows a middling A/G here which makes it slightly hard to recall and repeat “Samuel Wurzelbacher”.

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Dodged this baldness snp

Pygargue à tête blanche / Bald Eagle

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Just was skimming an article (Prodi et al., doi: 10.1038/jid.2008.60) on genetics of baldness and happened to notice that one snp mentioned is covered by 23andMe and so I, while unfortunately mostly (are there levels?) bald, felt my last few follicles stand up and cheer for my C-allele at rs1385699 in the EDA2R gene.

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U.S. Treasury Secre...

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Amidst the current economic panic, I’m feeling more shocked than usual when listening to the flip-flopping, falsehoods, fabrications, backstepping, about-facing and unabashed spin-doctoring spewing forth from the news media. If watched long enough, one may even develop empathy for Henry Paulson who carries the weight of the global economy on his shoulders. Nevertheless, what do we know about making mistakes ? Not necessarily global financial catastrophies, but little everyday mistakes. Why do some of us learn from our mistakes ? What’s going on in the brain ? Enter Michael Frank, Christopher D’Lauro and Tim Curran, in their paper entitled, “Cross-task individual differences in error processing: Neural, electrophysiological and genetic components” [Cognitive, Affective, & Behavioral Neuroscience (2007), 7 (4), 297-308]. Their paper provides some amazing insight into the workings of human error-processing.

It has been known for some time that when you make a mistakke – oops! – mistake, that there are various types of electrical current that emanate from the frontal midline (cingulate cortex) of your brain.  The so-called error related negativity (ERN) occurs more strongly when you are more focused on being correct and also seems to be more strong in people with certain personality traits (apparently not news commentators or politicians) while the error positivity (Pe) occurs more strongly when you become consciously aware that you made an error (perhaps not functioning in news commentators or politicians). Perhaps the ERN and Pe are basic neural mechanisms that facilitate an organisms adaptive ability to stop and say, “hey, wait a minute, maybe I should try something new.” The Frank et al., paper describes a relation between learning and dopamine levels, and suggests that when dopamine levels dip – as happens when our expectations are violated (“oh shit!, I bought stock in Lehman Brothers) – that this may facilitate the type of neural activity that causes us to stop and rethink things. To test whether dopamine might play a role in error processing, the team examined a common variant (rs4680) in the catechol-o-methyl transferase gene, a gene where A-carriers make a COMT enzyme that is slower to breakdown dopamine (a bulky methionine residue near the active site) than G-allele-carriers. Subjects performed a learning task where correct responses could be learned by either favoring positive feedback or avoiding negative feedback as compared to neutral stimuli. The team suspected that regardless of COMT genotype, however, there would be no COMT association with learning strategy, since COMT influences dopaminergic activity in the frontal cortex, and not in the striatum, which is the region that such reinforcement learning seems to be stored.

Interestingly, the team found that the error positivity (Pe) was higher in participants who were of the A/A genotype, but no difference in genetic groups for the error related negativity (ERN). This suggests that A/A subjects deploy more attentional focus when they realize they have made an error. Lucky folks ! My 23andMe profile shows a GG at this site, so it seems that when I make errors, I may have a normal ERN, but the subcortical dopamine that dips as a result does not (on average) result in much greater attentional focus. Oh well, I guess its the newsmedia pool for me.

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My ‘HUMAN’ brain

A reconstruction of Australopithecus afarensis

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Having a great time reading Michael Gazzaniga‘s new book, “Human – the science behind what makes us unique” and thought I’d see to what extent his conclusions might square with genetic data on population history and natural selection etc. and also evaluate my 23andMe profile to see to what extent I’m carrying the latest greatest derived alleles (more human-ish) or the older clunkier ancestral alleles.

I’ll try and keep updating this post as I work my way through the book. Here goes:

Chapter 1: Are human brains unique ?
Big Brains and Big Ideas ? (p.10) – In this section discussing how brain size may or may not relate to function and specialization of function, there are a number of genetic factors which have been linked to brain development and natural selection. Most well reported [doi: 10.1126/science.1116815] are the A44871G and C45126A variations in the ASPM gene. My 23andMe profile shows a GG and CA at these sites (rs964201 and rs3762271 respectively). Apparently, the G-allele (rs964201) and the A-allele (rs3762271) are derived, so I’m feeling very unique having scored 3/4 in this first query!

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Brazillian top model Gisele Bündchen, on Fashi...Image via Wikipedia Just thought it was strange to see the beautiful people drooling into 23andMe spit cups in today’s “Style” section of the NY Times. Strange in a good way.

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Vascular endothelial growth factor AImage via Wikipedia The mitogenic activities of the vascular endothelial growth factor protein family are well researched. A number of findings have linked this gene to learning and memory and hippocampal-dependent response to antidepressant medication. Indeed, its reasonable to expect that a mitogen such as VEGF would regulate hippocampal cell division and the accompanying benefits of new brain cells. Using high resolution structural MRI, Blumberg and team report evidence for such in their paper, “Influence of Vascular Endothelial Growth Factor Variation on Human Hippocampus Morphology“. Individuals with the CC genotype at rs833070 and rs2146323 – located in the intron of the VEGF-A gene displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively. These 2 snps lie in a haplotype block with rs833068 which was assayed in my 23andMe profile – indicating that I happen to carry the TT genotype at rs833070 giving me slightly larger, more neurogenic & resilient hippocampus – I suppose. Now, if I could just figure out a way to put it to good use !

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It has been reported that cigarettes can impart some calm and clarity from racing thoughts and mental fog. Patients with schizophrenia, who often experience cognitive disorganization, are 2-4 times more likely than the general population to smoke, and also seem to prefer stronger brands of cigarettes. This is not surprising since nicotine can raise levels of dopamine indirectly via stimulation of alpha4/beta2 high affinity nicotinic acetyl choline receptors (nAChR) expressed widely in the parietal cortex of the human brain. In an open access article entitled, “Association of attentional network function with exon 5 variations of the CHRNA4 gene“, Georg Winterer and colleagues demostrate that individuals who vary in a synonymous G/A variant (rs1044396) in the CHRNA4 gene – an snp which has previously been associated with nicotine dependence – show differential brain activity in the parietal cortex. When asked to remain alert and respond to rare visual “oddball” stimuli (visual oddball detection task), subjects with the AA genotype showed robust brain activity in the parietal cortex while subjects with the GG genotype showed very little change in activity. This finding reveals where in the brain – circuits connecting to the parietal cortex – may be especially important in mediating self-medication and even in the management of side-effects in psychiatric pharmacotherapy. Although rs1044396 is not measured in my 23andMe profile, the neighboring rs3787138 showing tight LD is measured and reveals that I am a boring, middle of the road heterozygote. As such, I do admit that I could use some mind-clearing relief from time to time – but, the yellow teeth are not quite worth it.

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Neuregulin 1Image via Wikipedia Nowadays, as many folks peer into the vast tangled thicket of their own genetic code, they, as I, assuredly wonder what it all means and how best to ascertain their health risks. One core theme that emerges from repeated forays into one’s own data is that many of us carry a scads of genetic risk for illness, but somehow, find ourselves living rather normal, healthy lives. How can this be ? A recent example of this entails a C/T snp (c) located in the 5′ flanking region of the neuregulin 1 gene which has been repeatedly associated with schizophrenia. Axel Krug and colleagues recently reported in their paper, “Genetic variation in the schizophrenia-risk gene neuregulin1 correlates with differences in frontal brain activation in a working memory task in healthy individuals” that T/C variation at this snp is associated with activation of the frontal cortex in healthy individuals. Participants were asked to keep track of a series of events and respond to a particular event that happened “2 events ago” . These so-called n-back tasks are not easy for healthy folks, and demand a lot of mental focus – a neural process that depends heavily on circuits in the frontal cortex. Generally speaking, as the task becomes harder, more activity in the frontal cortex is needed to keep up. In this case, individuals with the TT genotype seemed to perform the task while using somewhat less activity in the frontal cortex, rather than the risk-bearing CC carriers. As someone who has tried and failed to succeed at these tasks many times before, I was sure I would be a CC, but the 23andMe data show me to be a non-risk carrying TT. Hmmm … maybe my frontal cortex is just underactive.

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Angry face
Image via Wikipedia

Indeed, learning how to manage one’s response to the negative emotions of others and stay out of trouble is an important life skill. At some point, most of us learn to just avoid angry, mean or melodramatically negative people and save ourselves the strife. Roy Perlis and colleagues, in their recent paper, “Association of a Polymorphism Near CREB1 With Differential Aversion Processing in the Insula of Healthy Participants“, show how the transcriptional regulator CREB might exert an influence on this learning process. By having subjects view images of various facial expressions, the investigators found that individuals with the TT genotype at rs4675690 (C/T) showed less negative activation in the left insula, a brain region that is known to activate when subjects feel disgust, but not happiness, desire or fear. Subjects with the TT genotype have been shown to require more effort in the management of negative emotions and are at greater risk for suicide when being treated for depression. In the Perlis et al., study, TT subjects showed less of an effort (as measured in key presses) to avoid viewing emotionally distressing pictures. The known role of CREB in neural plasticity suggests that this gene may facilitate neural changes associated with memory. Unfortunately, 23andMe does not cover this SNP, so I’ll just have to hope that (during the upcoming election) my insula keeps me on the path to enlightenment.

Update: Thanks so very much Brian for the info on rs7591784. This explains a lot – I’m a GG here, which means I’m a TT at rs4675690 – and have always had difficulty handling it when folks are rude to me.

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Gene duplication illustration
Image by Colin Purrington via Flickr

A pair of Nature papers (PubMedIDs: 18668039, 18668038) find that mapping the risk of schizophrenia to the genome is more readily achieved when examining structural variation (insertions, deletions, duplications etc.). This is welcome news given the sparse success of SNP screening, although it would be reasonable to assume that SNPs can modify such structural variants (here for the most recent schizophrenia SNP association study). The pair of papers found similar sites, which is pretty amazing given that many structural variants are rare (see the 2006 survey report). The Copy Number Variation Project provides more details on this important class of variation.

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Marion Jones (L) stand...
Image by Getty Images via Daylife

Just checked for my status at UGT2B17 – locus of a 150kb deletion variant covered here in the Economist – to see whether I might have missed my chance to inject ‘roids and claim international sports glory without getting busted by the World Anti-Doping Agency. Unfortunately, the 23andMe profile provides data for the flanking genes YTHDC1 and UGT2A3 on chromosome 4, but not this specific gene. Doesn’t quite seem to validate my choice to couch-potato-dom though.Related articles by Zemanta

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inside my brain
Image by TheAlieness GiselaGiardino²³ via Flickr

Every student can recall at least one stereotypical professor who – while brilliant – kept the students amused with nervous and socially inept behavior. Let’s face it, if you’re in academia, you’re surrounded by these – uh, nerds – and, judging by the fact that you are reading (not to mention writing) this blog right now – probably one of them. So, its natural to ask whether there might be a causal connection between emotionality, on the one hand, and cognitive performance on the other. Research on the neuromodulator serotonin shows that it plays a key role in emotional states – in particular, anxiety. Might it exert effects on cognitive performance ? In their paper, “A functional variant of the tryptophan hydroxylase 2 gene impacts working memory: A genetic imaging study“, (DOI: 10.1016/j.biopsycho.2007.12.002) Reuter and colleagues use a genetic variation a G to T snp (rs4570625) in the tryptophan hydroxylase 2 gene, a rate limiting biosynthetic isoenzyme for serotonin to evaluate its effect on a cognitive task. They ask subjects (who are laying in an MRI scanner) to perform a rather difficult cognitive task called the N-back task where the participant must maintain a running memory queue of a series of sequentially presented stimuli. Previous research shows that individuals with the GG genotype show higher scores on anxiety-related personality traits and so Reuter and team ask whether these folks activate more or less of their brain when performing the N-back working memory task. It turns out that the GG group showed clusters of activity in the frontal cortex that showed less activation than the TT group. The authors suggest that the GG group can perform the task using by recruiting less of their brains – hence suggesting that perhaps there just might be a genetic factor that accounts for a possible negative correlation between efficient cognitive performance and emotionality.

My 23andMe profile shows a GG here – nerd to the hilt – what will I use the rest of my PFC for ? Something else to worry about.

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