mellowtigger: (dna mouse)
I am 3.0% Neanderthal. 

Scientists have been slowly gathering testable dna samples from Neanderthal remains, but the best sample came from a 130,000-year-old toe bone.  It allowed sequencing for the entire genome, published just a month ago.  Various companies that do genetic testing are able to offer this comparison now, but my results are from 23 And Me.  Apparently interbreeding between human species happened a very long time ago, so Neanderthal genes are found in both European and Asian populations today.  Supposedly the typical European holds only about 1.7% similarity.  I'm placed in the 88th percentile among Europeans, according to 23 And Me.

I figure it's only a matter of time until somebody tries to revive the species, just as predicted in the book "Existence" (which I liked).  I'd like to meet them.  I think I'd have more in common with them than the typical Homo sapiens, besides just the eyebrows and bigger skull.  I suspect that Neanderthal psychology will have a lot more in common with modern autistics than modern neurotypicals.  I guess we'll all find out soon enough.

Slightly less dramatic, but another patron at 23 And Me might actually be a blood relative.  The website has long notified people of distant ancestry relations based on their genetic sequencing, but they added a new feature where people can build an actual family tree with names and dates.  Someone contacted me recently, and we share a suspiciously similar name in our pasts.  One of his ancestors is a "William B Walker" (born 1789) and one of mine is "Willie Burkes Walker" (born 1889).  Both family lines include tales of Tennessee before relocating to Texas.  Alone, those similarities are just coincidences, but the genetic similarity suggests that my "Willie B" might have been named after somebody's memory of a related "Willie B".  Again, time will tell.  This technology will just keep improving as the years go by.

Someday, as in the movie "Gattaca", babies will be sequenced routinely by the time of their birth.  Probably, they'll be sequenced soon after conception, so potential diseases can be addressed while the body is still in development.

Strange.  Someday, genetics might allow me to meet kin from ancestors a few centuries ago or a few hundred millenia ago.  Throw in an uplifted chimpanzee, then we'll hold a proper family reunion.
mellowtigger: (dna)
phylogenetic treeTwo of the requirements for the current definition of "life" are these: the ability to self-regulate (homoeostasis) and the ability to reproduce. It turns out that these two processes might not have to be separate.

Scientists cultivate an extremophile called Haloferax volcanii which came from the extremely salty Dead Sea.  Because it survives in that harsh environment, astrobiologists wonder if we will find its relatives in the similar environment on the surface of Mars.  A recent study into this ancient form of Earth life (called "archaea") hint that this microscopic life might be very common. It revealed that a mechanism for homeostasis can be commandeered by archaea for use in replication.  This discovery has ramifications for both astrobiology and cancer research.

Normally, a cell's daily workings result in damage to its dna, so it employs processes to repair that damage.  These micro-repair mechanisms are different from those used to produce a full copy of the dna during replication.  Archaea reveals, however, that it can induce a simultaneous bloom of micro-repairs that results in a complete copy of the original dna.

However, the Nottingham study, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Royal Society, found that the Haloferax volcanii is able to spontaneously begin a chain reaction of replication all around its chromosomes even when its replication origins have been eliminated. In addition, the scientists discovered that far from being disadvantaged by having to employ this novel survival method, the archaea without chromosomal origins grew faster.

“The amazing thing that we found wasn’t just that deleting the origins still allowed the cells to grow, but that they now actually grew almost 10 per cent faster. Everybody was thinking, ‘where’s the catch?’ But we haven’t found one” Dr Conrad Nieduszynski said. “The way cells initiates this replication process is to use a form of DNA repair that exists in all of us, but they just hijack this process for a different purpose. By using this mechanism, they kick-start replication at multiple sites around the chromosome at the same time.”
- http://www.astrobio.net/pressrelease/5805/an-archaeas-unexpected-route-to-reproduction

Interesting news.  It offers a boost to the likelihood of panspermia theory being reality.  When we venture into the universe, we may find it a much "dirtier" (and thriving) environment than we envisioned a century ago.

(p.s. I chose the title as a play on Mr. Spock's analysis in Star Trekkin' lyrics from 1987.)
mellowtigger: (dna)
On April 25th, 57 years ago, Watson and Crick published their article in Nature magazine about the structure of DNA.  To celebrate the 50th anniversary (7 years ago), the US Congress established April 25th as "DNA Day".

Since my last gattaca post, the company that did my own dna testing has further specified my maternal haplogroup.  I am now officially a member of the U5b2c segment of humanity.  Here's an image showing the geographic distribution of the encompassing U5 group.
U5b2c

About 44-55 thousand years ago, a woman was born within the R haplogroup. This woman had a mutation in her mitochondrial dna that allows us to distinguish her from other humans of the time.  Her descendants became the U haplogroup, and U5 may be the oldest sub-group in the European region.  This wikipedia chart shows how the main maternal group names are related.


Human mitochondrial DNA (mtDNA) haplogroups
  Mitochondrial Eve (L)    
L0 L1 L2 L3   L4 L5 L6
  M N  
CZ D E G Q   A S   R   I W X Y
C Z B F R0   pre-JT P  U
HV JT K
H V J T Former Clusters IWX

Semi-related, there is recent news that Homo sapiens may have interbred with other species of hominids.  And you probably thought that family trees these days were complicated because of all the trans-continental adoptions, illegitimate births, and serial marriages!
mellowtigger: (dna)
I confirmed last year via genetic testing that I am indeed Irish. (As is President Obama, for anyone who cares.) Since then, a few interesting things have happened.

First, I have received 3 notifications from the 23andme website that they have identified other people that they believe are distant relatives of mine. I have not pursued any of these leads, but I find it fascinating nevertheless.  I don't follow my lineage at 1 generation, so why pursue them 5+ generations away?

Second, people may individually choose to share genetic information with you. I have had only one Walker surname attempt to share. Again, I have not pursued any of these invitations, but I still like the idea that such interactions are possible.

Third, my subtype was further narrowed down.  I am officially a member of the R1b1b2a1a2f2 paternal haplogroup.  I share this same deeply-specific identification with [livejournal.com profile] lordalfredhenry.  According to the 23andme website:

R1b1b2 (500 years ago)Researchers have recently discovered that a large subset of men assigned to the haplogroup may be direct male descendants of an Irish king who ruled during the 4th and early 5th centuries. According to Irish history, a king named Niall of the Nine Hostages established the Ui Neill dynasty that ruled the island country for the next millennium. Northwestern Ireland is said to have been the core of Niall's kingdom; and that is exactly where men bearing the genetic signature associated with him are most common. About 17% of men in northwestern Ireland have Y-chromosomes that are exact matches to the signature, and another few percent vary from it only slightly. In New York City, a magnet for Irish immigrants during the 19th and early 20th century, 2% of men have Y-chromosomes matching the Ui Neill signature. Genetic analysis suggests that all these men share a common ancestor who lived about 1,700 years ago. Among men living in northwestern Ireland today that date is closer to 1,000 years ago. Those dates neatly bracket the era when Niall is supposed to have reigned.

So, kiss me, I'm Irish... and royalty.  ;)

oxytocin

Oct. 23rd, 2009 09:18 am
mellowtigger: (dna mouse)
MDMA (3,4 methylenedioxymethamphetamine) is known on the street as either Ecstasy or E.  The effect that it has on humans (and rats apparently) is to activate oxytocin-containing neurons and increase oxytocin levels in blood plasma.  Oxytocin is associated with the ability to read social cues and to trust other people.  An increase in oxytocin activity produces the effect that gives MDMA its colloquial names of "love drug" or "cuddle drug".  Basically, it makes people very social and friendly.  I have read elsewhere that it can be especially effective on autistics.  I emailed last month with an autistic man outside the USA who confirmed its properties.  :) 

Which brings us to today's news headline.  I mentioned 1.5 years ago that there is a good search engine in New Zealand for finding epigenetic information. Even back then, it found a few hits on autism information. Today, though, there's news about a new discovery that might be statistically relevant enough to use as a screening tool for autism risk.

Researchers identified an autistic boy with a genetic deletion of the OXTR gene.  His brother, also autistic, still had the gene but they found that it was epigenetically methylated ("turned off").  They examined a total of 119 autistics.

"In both blood samples and brain tissue, the methylation status of specific nucleotides in the oxytocin receptor gene is significantly higher in someone with autism, about 70 percent, compared to the control population, where it is about 40 percent," said co-lead author Simon G. Gregory, Ph.D., assistant professor in the Duke Department of Medicine. The work appears in BMC Medicine journal online.
- http://www.sciencedaily.com/releases/2009/10/091021212247.htm

So... epigenetics is already producing interesting and potentially useful data.  Go science!
mellowtigger: (dna)
Testing such as I had done at 23andme.com is not quite as useful as researchers (and afficionados like me) had once hoped.  They're finding that creatures are much more complex than just the programming in their dna.  Part of the problem is that genetics includes lots and lots of evolutionary baggage.  Study of the machinery that decides which parts gets used (instead of locked into "cold storage" indefinitely) is now called the science of epigenetics.  It's a second layer of inherited information.

Genetics covers the 4 main bases of dna, the chemicals that encode every protein that the body CAN produce.  Epigenetics covers additional chemical markers that are latched onto dna, "methylated" bases, that determine which of these possible proteins that a body actually WILL produce.

"One key epigenetic player is DNA methylation, which targets sites where cytosine precedes guanine in the DNA code. An enzyme called DNA methyltransferase affixes a methyl group to cytosine, creating a different but stable nucleotide called 5-methylcytosine. This modification in the promoter region of a gene results in gene silencing."
- http://www.physorg.com/news159111225.html

Quoting David Goldstein of Duke University, "With only a few exceptions, what the genomics companies are doing right now is recreational genomics... the information has little or in many cases no clinical relevance.
- http://blogs.wsj.com/health/2009/04/16/genetic-testing-provides-few-easy-answers/

So I added $400 to my Visa bill (in addition to about $1500 recently for car repairs *SIGH*) for entertainment.  I knew it was such when I did it, but I succumbed to curiosity.  That happens sometimes.  :)  I don't mind going into debt for that kind of entertainment.  I learn a lot from the process eventually.  I just need to get back onto this project, after other recent distractions are finally over.
mellowtigger: (dna)
There's not really a point to the stats that follow. I just spent way too long getting Microsoft SQL Server 2008 installed on my Vista machine, and I want something to show for it. So here is what I found out about my genotyping source file, after I finally got it into a database.

I hadn't really thought about it before, but where there's only one chromosome strand, only one code can be reported. So for the X, Y, and mitochondrial dna addresses, there will be only a single letter reported instead of the usual pair of letters, at least for males. I don't know how the female dataset is reported for the paired X chromosomes that a woman would have. So for the "DD", "II", and "DI" numbers below, they exclude the X, Y, and mitochondrial dna addresses.  A "no call" means that the chip could not produce a reliable answer at the tested location.  (edit: I'm trying to confirm at the 23andme forum that DD and II really do mean deletion and insertion.)

rows of data: 579,581

no call: 1,340 (includes X and Y chromosomes but not mitochondria)
DD deletion: 32
II insertion: 71
DI mixup: 17
mitochondrial no call: 25
mitochondrial deletion: 0
mitochondrial insertion: 1 (at i4000892, position 8286, rCRS 8285)

At first I was concerned about the mitochondrial insertion, as that would be a significant discovery.  Upon googling it, though, I find a few people who complain about this same location.  If 23andme cannot produce reliable answers for this address, it may eventually be removed from their reporting files.  Apparently this address is a known problem point, depending on your haplogroup (maternal line).

While looking up that address, I also found discussions comparing 23andme to other companies.  Some people actually pay for both and then compare result files.  One person reported a 99.6% agreement on over 500,000 SNP addresses shared by both companies.  That percentage seems low enough to be worrisome, actually.  That's still about 200 genetic calls that could be wrong.  That'd be fine if we're examining hair color, but not so fine if we're examining a drug response.
mellowtigger: (dna)
First draft, but I just want to get something "finished" enough to post, because I have other tasks to work on this week and need to try getting this one out of my head for a short while.  Summary:  I have 4 autism markers, 2 uncertain, several normal markers, and many that remain untested or unexplained.

geneaddressnormalautism riskmereference
METrs1858830GGCC x 2.27, CG x 1.67CCPubMed
ADRB2rs1042714
CCGG x 1.33 - 1.60 (or even twice that)GGPubMed
GABRB2rs2617503CC or TTCT x ?CTScienceDirect
APCrs1804197AACC x ?CCPubMed
NPAS2rs1811399?C (unspecified heterozygous risk)ACNature
EN2rs1861973?C (unspecified heterozygous risk)CTNature

For many autism markers, I have the typical dna pattern instead.  There are a lot of markers that are not tested by 23andme.  There are many studies which mention specific SNP addresses but their summaries do not indicate which base pairs were involved (and I can't afford to purchase all of those articles for their details).

Some markers were tested, but I had results not indicated in any expected combination.  For example, I have AA at rs2710102 (CNTNAP2 gene) but expected values according to the article are CC, CT, and TT for Caucasian Europeans.  Similar shenanigans occur at rs1322784 (DISC1 gene).  What these differences are supposed to mean, I have no idea.  Are they:
  1. bad gene chip results (disappointing),
  2. contamination (also disappointing),
  3. brand new mutation (exciting!), or
  4. a data mixup in how the SNP addresses are reported (confusing)?
Apparently there's some kind of left-hand versus right-hand notation involved in naming the "rs#" addresses, so it could easily be a translation problem there.   Some texts, however, were just plain confusing, like rs1861972 and rs1861973 which seem to simultaneously associate for and against autism, unless I'm misreading that somehow.  I didn't get enough sleep last night, so maybe I should try again in a few days with a fresher mind.

I still have more references to check.  There are so many autism markers!  More to say in the second draft later, I guess.

mellowtigger: (Default)
Does "8636C>A (rs1804197)" mean that the cytosine base is associated with the risk-in-question as opposed to the adenine base which is the standard form?  Argh!
http://www3.interscience.wiley.com/journal/114025178/abstract

I'm having similar problems interpreting spreadsheets of data whose column headers are abbreviations, but I don't know what the abbreviations mean.  :(
http://hmg.oxfordjournals.org/content/vol0/issue2007/images/data/ddm015/DC1/ddm015supptab1.xls

I tried loading my data file into the OpenOffice database, but it has no import function!  You have to copy-and-paste from their spreadsheet program but it limits files to 65k rows of data.  *SIGH*  I guess I won't quickly be getting statistics about deletions and no-call results.  I need a full-blown Microsoft Access program, I think, or else better familiarity with importing into other SQL databases.

*grrrrr*  Time to go to work.  Pesky "earn a living" process.
mellowtigger: (dna)
I know nothing about my family heritage other than "Irish".  Someone once mentioned: Tennessee, 1800s, Irish.  Someone else would mention Irish marrying other Irish, and later more Irish marrying into the family, and later some more Irish.  Mind you, I never once heard a name associated with any of these cases.  There was only the word Irish.  That, plus we'd always been poor and there was alcoholism in the family too.  Not that racist stereotypes are to always be believed, of course.  *big shrug*  I'm just saying that the little bit I'd heard seemed to fit with the reality of American history, where the Irish lived and worked on plantations with the slaves... in Tennessee... in the mid-1800s, I think.

Well, the haplogroup testing seems to confirm it.
http://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup
http://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup

maternal U5b2paternal R1b1c7

The maternal haplogroup U5b2 (left photo) is generally northern European, but it is also commonly found throughout Europe.  The paternal haplogroup R1b1c7 (right photo) is much more specific though.  The text at 23andme even says, "R1b1c7 reaches its peak in Ireland".

So, yes, I am Irish.
mellowtigger: (dna)
The email arrived at 11:07pm.  My genetic results are in.

Slight detour first, there was news yesterday about a new technology that may make sequencing much faster in the future.
http://www.physorg.com/news156953933.html

First glance at my "generic" results for specific conditions that they evaluate for people:

Research confidence:Condition:Their take:My take:
4 starsmultiple sclerosisI have 2 markers for increased risk. 0.52 out of 100 people of European heritage get MS.  0.71 out of 100 of them who have my genetic markers get MS.The neuropathy in my feet was considered several years ago to be a result of low B12 value, causing myelination problems. Something to investigate, perhaps, if I ever get health insurance again.
3 starsabdominal aortic aneurysm"Slightly increased" odds for me, based on 1 marker tested.There are only 36.5 cases per 100,000 people each year.  I'm not worried.
3 starsbrain aneurysm"Slightly increased" odds for me, based on 1 marker tested.Up to 5% of all people have one eventually.  I'm still not too worried.
3 starschronic lymphocytic leukemiaI have 2 of 6 markers.  One of them gives 1.5 X the odds, and the other gives 1.4 X the odds.I wouldn't dismiss the possibility someday, but it's not something I'm worried about.
2 starsdevelopmental dyslexia"Slightly higher" odds for me, based on 1 marker tested.If it hasn't been a problem by now, I don't think it will be.

I also have higher odds for gallstones, gout, and statin response.  I have decreased odds for cluster headaches, various cancers (bladder, esophageal, larynx, oral and throat, breast, and skin), Lou Gehrig's disease, and schizophrenia.  I also have decreased odds for Restless Leg Syndrome, but I know that I've had exactly those symptoms many times over the years.  It's all a matter of playing the odds, obviously, not a matter of certainty.

On various traits, I am typical in many ways.  I have average odds of living to age 100, typical caffeine metabolism, typical odds of male pattern baldness, typical progression of HIV-1 infection, typical response to antidepressants, and typical sensitivity to pain.  I have typical odds of blond hair or brown hair, and typical odds of blue-vs-green eye color.  Men in my family actually start out blond and grow darker soon after.  My eyes seem to change between their blue and green hue, plus I have yellow in there too.

I have one marker that suggests I eat more sugar per day than the average person, and I heartily disagree.  Sweets I easily ignore, but it's the high-fat foods that I get cravings for. 

I have one marker for reduced sensitivity to sweat odor.  Woe is me.  ;)   I have one marker for 0.16 inch (0.4 cm) shorter height than the average person.

I also have a genetic marker that was found in Dutch families to be associated with 3 IQ points higher in non-verbal scores.  I have 1 marker that's associated with 4-5 point increase if I'd been breastfed as a child.  I have 1 other marker associated with 6-7 point increase in IQ if I'd been breastfed.  (I think I was, but I don't know for sure.)

I'll examine specific markers next.  The initial review is not really anything very remarkable except for the Multiple Sclerosis risk.
mellowtigger: (Default)
Saturday morning, I mailed off a tube of my spit.  It will take about 8 weeks to get back my results.  When the results are posted online, I will be able to view a vast number of specific points of my DNA to see how they compare against known differences in the human genome.  I'll be using the tag "gattaca" here on LiveJournal to follow my results of this personal journey.  I suspect that I will be learning a great deal about the human genome starting about 8 weeks from now.  *laugh*

"Gattaca", for those who don't know, was a great movie about the dangers of predicting human life outcomes based on the results of genetic testing.  The name of the movie is built using the same letters as the 4 chemical parts used to build a dna molecule: guanine, adenine, thymine, cytosine.

I first learned about 23andme.com a few months ago.  (Hello, [livejournal.com profile] lordalfredhenry .)  I did not feel any overwhelming urge to run my own DNA through their system, but I confess that pure unadulterated curiosity finally got the better of me.  I added $400 to my credit card debt, and now here I am waiting for results.  I've already created my community profile there, although I think you have to have paid your money and claimed your special test kit code in order to participate.
https://www.23andme.com/user/?community_profile=92caa46f527ff773

Using their sample result data set as an example, I will get about 633,000 data points from my DNA.  These data points are called SNPs ("snips"), Single Nucleotide Polymorphisms.  These are places in the long strand of DNA code that a single difference is found.  So instead of getting my complete genetic code back, I'll be getting the "deltas", the differences.  They are using as a reference template, the published "human genome, build 36".
http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36

8 weeks until I see results.   That's 56 days.  Or 1,344 hours.  Or even 80,640 minutes.

*twiddle*

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