Archive for the ‘Uncategorized’ Category


We all have social networks.  Your friends and family are a network of relationships.  The neural networks in your brain that carry out computations involved in social interactions are another type of “social network”.  These two networks are obviously related – in so far as your ability to self-reference and understand your own internal thoughts and feelings predicts how well you can understand and predict the internal thoughts and feelings of others – and thus how extensive your network of friends and family is likely to be.  The structure of your brain networks may even be related to how many friends you have on facebook.

According to Lencz and colleagues, there is a genetic association between the T-allele of rs1344706 and the structure and connectivity of the neural networks that carry out self-referential processing in the brain … in the so-called “default mode network” that is associated with “stimulus independent” mental activity and with social cognition such as when you are attributing mental states to others.

Interestingly, the T-allele of this SNP – residing in the zinc finger protein 804A gene – has been previously associated with schizophrenia (SZ).

From Lencz and colleagues:

“To our knowledge, this is also the first study to identify a genetic correlate of multiple brain regional GM volumes comprising the default mode network.”

The default mode network comprises regions that show synchronized activity at ‘resting’ baseline, in the absence of specific stimulation (Raichle et al, 2001). Ongoing work has implicated this network in the development of self-referential thought (Spreng and Grady, 2010), which has been specifically implicated in the developmental psychopathology of SZ (Nelson et al, 2009).

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[link to research article on loss-of-function variants in the human genome]

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Never … except when it’s about male pattern baldness.

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Just so you know, neither of you are in charge … so please stop acting like hyper oxygen sensitive drama queens with self-absorbed Lewy body issues when it’s not even really about either of you.  I realize that you both have to work in a toxic stew of lethal reactive oxygen species to pump out limitless quantities of ATP and then die in a shallow, unmarked DNA repair enzyme complex … all so I can lay around and watch The Jerry Springer Show.  I get it.  You are under appreciated.  Listen, if you two would stop sniping at each other on Facebook, I promise I’ll eat more kale, volunteer at a soup kitchen and go to yoga 3 times a week.  Besides, AMP Kinase says that if you don’t get your shit together, he’s going to send mTORC1 over and teach both of you what being “mTORC1-dependent” is all about.

mitochondria and neural health

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Hey genome, why U make me stink at networking?

If only there was an allele that LESSENED the apprehensive and uncomfortable feelings I get when meeting new people.

As such negative feelings are the work of my amygdala, I’m wishing for some sort of LOSS-OF-FUNCTION allele that REDUCES the activity of neural circuits involved in the emotional processing of fear … but leaves other neural circuits untouched.

I just want something that takes the edge off new social experiences … yunno?

How about rs33977775 ? It contains a derived (as opposed to ancestral) T-allele that causes a Y135F change that disrupts the binding sites of the NPBWR1 receptor to its neuropeptide ligands (ie. LOSS-OF-FUNCTION).  Amazingly, this receptor has a restricted pattern of gene expression only among limbic circuits involved in emotion and reward processing (ie. EXPRESSED IN EMOTION PROCESSING CIRCUITS ONLY).

In their report, a team of authors measured the reactions of 126 university students to various social stimuli and report that individuals who carry one of these loss-of-function T-alleles (about 30% of the population) show a more positive response to social interactions.

“… the AT group perceived facial expressions more pleasantly than did the AA group, regardless of the category of facial expression. Statistical analysis … also showed that the AT group tended to feel less submissive to an angry face than did the AA group.”

So it seems that rs33977775 may dial down the amygdala response to social stimuli … just enough to ace the job interview, but not so much that you inappropriately hug your new boss. Nice!

Unfortunately, this SNP is not covered by 23andMe v3 and there is no report yet on linkage disequilibrium via 1000 genomes.  Since the frequency of the T-allele is low in African populations (1%) and about 10%-ish in other non-African populations, I guess the odds are that I’m an AA or AT.

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As the holidays approach, it’s time to confront the grim reality that is your own personal gene pool.  Forget about your SNP genotypes … as Dr. Francis Collins reminds us to, instead, record a personal family medical history.

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… but not like this.  Try openSNP.

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Our cells are full of clocks … circadian clocks … whose transcriptional and translational feedback loops at the ancient PER locus oscillate with a period of 24-ish hours … complete with diurnal peaks of vulnerability to cardiac arrest and death.

From the article:  ” … an interesting association with time of death (p = 0.015) in which rs7221412 GG individuals had a mean time of death nearly 7 hours later than rs7221412 AA/AG.”

rs7221412 is not presently covered by 23andMe, but this SNP appears to sit in a haplotype block and is flanked by rs9914077 and rs2585408 … both of which are heterozygous for me … so I guess it’s strictly “carpe diem!” (or at least 7 hours of diem) for me and my AG genotype.

If you’re interested in genomic predictions of this death clock … read more about your telomeres.

Death Clock.org Death Test

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Probably not.  The T allele at rs7294919  (“each copy of the T allele was associated with lower hippocampal volume (β=−107.8 mm3, p=2.9×10-11)” )  is very common … like 75%-ish … so, yeah, thanks for my TT genotype Mother Nature … and for yet another part of my body that is, um, small.

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Colm O’Dushlaine rocked his 23andMe profile … hard! … and then shared it with the world.

Totally. Awesome.

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Yesterday was World Diabetes Day.

I almost forgot … which may have something to do with rs6741949.

From the original article:

“… rs6741949 in a DPP4 intron on chromosome 2q24, where the G allele was associated with smaller hippocampal volume (β=−52.8 mm3, p=2.9×10-7).”

The association with DPP4 sheds light on a fascinating connection between diabetes and hippocampal (memory) function.

“Further, DPP4 is an intrinsic membrane glycoprotein and a widely expressed serine exopeptidase. It is also an adipokine over-expressed in visceral adipose tissue of obese persons and those with diabetes, conditions associated with smaller hippocampal volume. A novel class of antidiabetic medications (sitagliptin, and related incretin compounds) inhibits DPP4 to improve insulin sensitivity and glucose tolerance through increased levels of glucagon like proteins-1 and 2 (GLP-1, -2). Interestingly, endogenous incretin GLP-1 is also heavily expressed in some hippocampal neurons and has neuroprotective properties.”


note: 23andMe does not cover rs6741949, but they do cover 2 flanking SNPs that are in pretty good linkage disequilibrium with rs6741949 … so, um, I’m trying to figure out how I might impute/infer my genotype here … hmmm.

rs3788979 (bp162900889) CC D’=0.81 strand + forward
rs6741949 (bp162910223) A?G?              strand + forward
rs4664446 (bp162910403) AG D’=0.86 strand + forward

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Are you good at reading faces?  You can test yourself  (here, here, here) or just get off the interwebz and go talk to a real person.

The MET and the AKT genes encode proteins that are involved in early brain development and in the production of new synapses.  Since reading faces requires a lifetime of trial-and-error learning (ie. making new synaptic connections), these genes would likely support the development of facial recognition skills.

From the original article:  “When the individuals who were [MET/AKT rs2237717/rs1130233] C carrier and G carrier simultaneously were used as the reference group, their facial emotion perception was better than that of those with TT/AA  (p=0.015).”

I’m a MET/AKT rs2237717/rs1130233 CC/GG and, as my genome predicts,  a pretty good face reader … but am not sure if this is a good thing.  Why are you looking at me like that?

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Yes, we are all turduckens … or as the scientists formally say, the result of an ancient endosymbiosis.  And yes, if you like the individual flavors of mitochondrial genomes and/or nuclear genomes, you will enjoy the flavor of eukaryotic genomes.  And no, “Baturducken,” is not when each stage of the turducken is wrapped in bats … just bacon.

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Cheap? Yes. Fake? Not at all.  It’s another genetic study on the placebo effect and it highlights the fact that our brains are not static input-out machines that were built from scratch using a genetic blueprint.  Rather, what we expect and believe matters … a lot.

How does it work?  Nobody knows for sure, but dopamine has been implicated in synaptic mechanisms that are used to register the fulfillment or violation of expectations.  For example, if you believe that a certain something will happen … and something better happens, your brain produces a burst of dopamine.  If something worse happens, then you get a drop in dopamine.  Your expectations and beliefs influence your dopamine levels.

Apparently, some of us metabolize dopamine faster vs. slower which may be related to a weaker vs. stronger placebo response.  For example, my rs4680 GG fast dopamine metabolizing genotype says, the “medicine in my mind” is not very strong.  But, on the other hand, I do watch A LOT of Grey’s Anatomy.

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Creative destruction

Creative destruction

Photo Caption

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Who knew?  Reinius and colleagues have discovered where she’s kept it stashed away … in 85 brain-expressed genes they refer to as a conserved sexual signature … tsk tsk naughty.  Ladies, you can skip over the parts about macho men with rippling muscles and power tools … ’cause apparently, what really turns Mother Nature on is polyamine biosynthesis.

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Genetics is a lot like politics.  Mainly, a whole lotta fuss about sex & selfishness.  Take it from the Economist:

“Deciding whether or not to be part of a particular group, whom else to admit to your group, how to keep or share resources, and how much sexual freedom to afford oneself, one’s neighbors and one’s children are all, and always have been, lively matters of political debate.  But they are also matters that have an impact on the crucial Darwinian business of getting genes into the next generation.”

thanks Amanda-Edwards for the pic

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If you can’t sleep it’s because you’re awake in someone else’s dream.

That’s nice to know.  I’m currently being stalked by a DNA binding protein named  PAX6 that has an affinity for the H3K4me1 DNA element – which resides next to the polymorphic sites rs11208305 (chromosome 1p31) and rs718712 (chromosome 20p12) – who, themselves, are involved in the regulation of the expression of the ROR1 and PLCB1 genes, respectively.  Yeah, Freddy is sneaky like that.

These 2 SNPs were the most highly associated low-hanging fruits of a large genome association study of insomnia.  Interestingly, PAX6 is expressed both in the brain and in the pancreas (insomniacs often have high insulin levels at night).  The authors thus explored the notion that the expression of ROR1 and PLCB1 might be regulated by PAX6 both in the brain (where it can influence neural and circadian functions) AND in also the pancreas (where it can influence insulin secretion).


Caveat:  The authors report a minor allele frequency of 0.03353 for the “C” allele at rs11208305.  Such rare alleles can vary in frequency dramatically across populations and lead to false positive results in case-control analyses.

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Thank you for the note rs10491929

It’s 3:00am and my RORB gene called to say, “you look like shit.”

Gee thanks.  More on rs10491929 and it’s relation to circadian rhythms and mood here.

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I just want to know if your junk is functional

“Yes, I can count on one hand the number of times a geneticist has tried to pick me up with that line.”


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