DNA and Skin Color

Recent study shows association rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic* variation.  Previous studies have showed that rs1426654 SNP accounts for lighter skin in Europeans but not in East Asians.

Basically for South Asians if rs1426654 SNP is AA then light skin, if AG then medium dark and GG dark (see graph).  My rs1426654 is AG and I am medium dark. Also see this post on my DNA and heroin addiction etc.

Excerpts

We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans.


One of the key pigmentation genes in humans is SLC24A5.  That a non-synonymous variant (ref SNP ID: rs1426654) in the third exon of this gene explains 25–38% of the skin color variation between Europeans and West Africans. The ancestral (G) allele of the SNP predominates in African and East Asian populations (93–100%), whereas the derived (A) allele is almost fixed in Europe (98.7–100%)

In India here is a general trend of rs1426654-A allele frequency being higher in the Northern (0.70±0.18) and Northwestern regions (0.87±0.13), moderate in the Southern (0.55±0.22), and very low or virtually absent in Northeastern populations of the Indian subcontinent (Figure 2, Table S6). Notably, the Onge and the Great Andamanese populations of Andaman Islands also showed absence of the derived-A allele.

Loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.

More at
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912

Via
http://blogs.discovermagazine.com/gnxp/2013/11/big-sweeps-happen/#.UoHuzxC-X1U


*Genotype vs. Phenotype:
Very important concept. Even if the genes are identical (genotype) the outward expression / looks (phenotype) could be different. Example would be identical twin, who have the same genes will have differences and fingerprints will be different. Another example would be children of short parents (and also have the sort genes) could be taller because of better nutrition.

The opposite is also true in that just because outward appearance is similar (phenotype) the genes (genotype) do not have to be similar. Example: Africans and Papua New Guineans though superficially similar are about the furthest apart genetically.

My DNA 01: Heroin Addiction, Smoking etc

Got my DNA results from 23andMe, very quick in almost 3 weeks.
First off,  the 23andMe autosomal, Y-DNA, mtDNA and mitochondrial data can be downloaded here.

So until I get Zacks analysis of ancestral groups, here are a very few of the large amount of health and trait indicators I got with my DNA results analysis.  Please Note most of this type of research has been done on people with European ancestry, and applicability to South Asians is yet to be determined.

rsid       chromosome position  genotype       Trait rs1799971     6       154402490    AG       Heroin Addiction rs17822931   16        46815699    TT       Ear Wax Type rs762551     15        72828970    AA       Caffeine Metabolism rs1051730    15        76681394    AG       Smoking Behavior

Heroin Addiction: rs1799971  AG: Substantially higher odds
This study of 139 heroin addicts (primarily Swedes) and 170 non-addicts found that people with at least one G at rs1799971 have almost 2.9 times the odds of being a heroin addict. .
I was dead scared of the horse because of all the stuff I had read about teeth falling out etc. Good thing I am no longer a young adult and that I read all the warnings when i was a young adult.

• Zhang H et al. (2006) . “Association between two mu-opioid receptor gene (OPRM1) haplotype blocks and drug or alcohol dependence.” Hum Mol Genet 15(6):807-19.
• Bart G et al. (2004) . “Substantial attributable risk related to a functional mu-opioid receptor gene polymorphism in association with heroin addiction in central Sweden.” Mol Psychiatry 9(6):547-9.

Ear Wax: rs17822931  TT: Dry Ear wax
Earwax type is highly heritable. This means that this trait is controlled almost entirely by your genes-environmental factors play little or no role. Because of this, simply knowing your genotype is enough to know your earwax type.
I have dry earwax and body sweat does not smell all that much (according to others) even though I sweat profusely (overweight). The sweat does tend to smell when I eat steak over two three days (this happens only during Christmas/Year end) and when I eat Ethiopian/Indian food. I think this because of larger amounts of Fenugreek (sinhala uluhal) in Berbere and Indian curry powder.  I guess that is Environment overshadowing Genes.

• for more info see Ear Wax and Armpit Odor 

Caffeine Metabolism: rs762551  AA: Substantially higher odds
The form of the SNP rs762551 a person has determines how fast CYP1A2 metabolizes caffeine. In this study, people with the slower version of the CYP1A2 enzyme who also drank at least two to three cups of coffee per day had a significantly increased risk of a non-fatal heart attack. The study found that fast metabolizers, on the other hand, may have actually reduced their heart attack risk by drinking coffee.
I drink more than 6 cups of black coffee at work (US), specially because its free. Drink the stuff even before I go to sleep. 

• Cornelis MC et al. (2006) . “Coffee, CYP1A2 genotype, and risk of myocardial infarction.” JAMA 295(10):1135-41. 

Smoking Behavior: rs1051730  AG: More on Average if Smoker
Genes vs. Environment: Not all smokers are created equal—some light up just a few times a day, while others go through multiple packs. There are many social and environmental factors that affect whether people start smoking, but once they do, research based on Dutch Twins has shown that genetic factors play a large part in how dependent on nicotine they'll become and how much they'll smoke.
I used to smoke almost 3 packs (20 packs) as a teenager and young adult. Then stopped for about 13 years, started again and was smoking about 30 cigarettes. The only reason it was not more was cost and restrictions in ability to smoke in many locations. Stopped again and its been more than 6 years with the main motivation for stopping being cost and that I am a little too old to be bumming cigarettes.

• Lerman C., Berrettini W. Elucidating the role of genetic factors in smoking behavior and nicotine dependence. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2003;118B:48-54.

Also see
Sinhalese and Tamil DNA Admixture Analyis

Vijaya Kuveni: Paradigm for M mtDNA in South Asia