The ‘redhead’ gene

I remember in high school learning about Punnet squares; people with brown hair had the dominant hair color gene and red hair was recessive. It turns out that it isn’t nearly as simple as having a red hair gene or a brown hair gene. Nor is there a blue eye gene — seems like my teachers were wrong about a lot of things.

So why am I bothering to write about hair color? We all know what our hair color is (or what it was before that box of Clairol ;-).  For me, it was not a mystery that I carry the genetic variant for red hair since my dad is a redhead. Now that my son is in college and sporting the beard that every college guy seems to grow, you can see that he carries the variant: his hair is brown but his beard, especially in the sunlight, is surprisingly red. Apparently, the Irish call this a ‘gingerbeard’.

This is important because the genetic variant that causes red shades of hair impacts other aspects of our health as well.  Carrying the variant can cause an increased risk of melanoma as well as possibly impact the way you respond to certain analgesics.

Impatient people:  jump ahead and check your 23andMe genes for the redhead variant.

Hair color genetics:
There are two types of pigments for hair color: eumelanin and pheomelanin.  Eumelanin comes in either black or brown, with varying amounts responsible for ranges of hair color from blond (low eumelanin) to black (high eumelanin). Pheomelanin contributes red and orange coloring. Most people have both eumelanin and pheomelanin, and the varying amounts of each protein contribute to the wide range of hair colors that people naturally have.

The MC1R (melanocortin-1 receptor) gene controls how much melanin vs pheomelanin is produced in the skin and hair.  Genetic variants of MC1R produce different amounts of pheomelanin, with increase pheomelanin causing the skin to be more photosensitive along with red hair. The variant forms of MC1R are also thought to not activate DNA repair as well as the more common MC1R form.  This leads to higher rates of mutations in the DNA of skin cells, possibly leading to skin cancer. [ref]  The link to melanoma is well established for the common MC1R variants that cause red hair, but what people may not realize is that just carrying one copy of the variant doubles the risk of melanoma.[ref]

The MC1R gene is also linked to freckles and more moles on the skin.[ref] Additionally, one MC1R variant (rs1805008) has also been tied to an increased risk of Parkinson’s disease.[ref]

MC1R isn’t just a human-specific gene; it causes pigmentation variation in animals from chickens to goats to carp.  It is also thought to be involved in the browning reaction of cut apples being exposed to air.

Going beyond just the ‘red hair’ gene actually gets really complicated and predicting hair color from genetic data can be tricky.  Here is a great article on 124 genes that influence hair color.


Genetic variants of the MC1R gene:
Note that people who are compound heterozygous (e.g. having CT for rs1805008 and CT for rs1805007) can also have red hair.

Check your 23andMe results for rs1805008 (v4, v5):

  • TT: red hair possible; increased risk of melanoma, pos. increased risk of Parkinson’s[ref][ref][ref]
  • CT: increased risk of melanoma
  • CC: normal

Check your 23andMe results for rs1805007 (v4, v5):

  • TT: red hair is likely; increased risk of melanoma,[ref] increased response to kappa-opioid analgesics in women [ref];
  • CT: higher risk of melanoma;
  • CC: normal

Check your 23andMe results for rs1805006 (v4, v5):

  • AA: red hair is likely; increased risk of melanoma[ref]
  • AC: higher risk of melanoma;
  • CC: normal

Check your 23andMe results for i3002507 (v4, v5):

  • CC: red hair possible, increased risk of melanoma
  • CG: higher risk of melanoma
  • GG: normal

Check your 23andMe results for rs2228479 (v4, v5):

  • AA: red or blond hair possible, increased Alzheimer’s risk [ref][ref] perhaps not increasing the risk of melanoma[ref]
  • AG: normal
  • GG: normal

Lifehacks:

If you carry one of the risk variants listed above for melanoma, common sense dictates that you should watch your sun exposure and avoid getting sunburned. While you need a certain amount of sun for vitamin D production, knowing when to cover up or put on sunscreen is important.

So what should you look for in a sunscreen if you are going to use one? The Environmental Working Group has a whole guide to sunscreens and includes research on which ingredients are concerning. High on the list of possibly hazardous ingredients are oxybenzone and octinoxate, both of which penetrate through the skin and have hormone-like activity in the body.

Here are a few sunscreens that are ranked as having better ingredients on EWG: garden goddess sunscreen, Blue Lizard Australian Sunscreen, and Badger Broadspectrum Sunscreen.

 

Oxytocin Levels: Genetics of the Love Hormone

Oxytocin is a hormone produced in the hypothalamus region of the brain.  Often called the “love hormone”, it is involved in parents bonding with their baby, recognition of other’s emotions, and overall social involvement.

Oxytocin is produced at a high level during childbirth, relaxing the cervix and causing contractions. Interestingly, it also crosses the placenta and acts on the neurotransmitters of the baby, preparing him or her for birth. It is also involved in breastfeeding and milk let down.

Outside of the physiological roles in childbirth, oxytocin acts as in the brain as a neuropeptide and influences social activity and group bonding.

Oxytocin is synthesized in a series of steps, starting with the OXT gene, which creates the inactive precursor needed for the hormone. The final activation is catalyzed by the PAM enzyme, which needs vitamin C as a co-factor.

In general, genetic variants that decrease oxytocin production have been found in psychological studies to decrease a person’s social sensitivity and empathy.  Before all of you with high oxytocin levels start thinking “oh no, poor thing”, there are some positive outcomes from not being as emotional. Genetic variants linked to lower empathy and less socially sensitive were found to be more resilient in the face of childhood maltreatment.[study][study]

A mother’s oxytocin levels also play a role in a baby’s response to early life stress, both before and after the baby is born. Yes, you can blame your mom if your brain isn’t wired the same way as others. [study]

Culture plays a role in how the oxytocin gene variants are interpreted.  For example, one study found that while Americans with a genetic variant were likely to seek out emotional support, Koreans were not.


Genetic variants in the OXT gene:
There are a couple of common genetic variants that influence a person’s level of oxytocin.

Check your 23andMe results for rs53576 (v.4 and v.5):

GG: More oxytocin, empathetic, optimistic, seeks and gives emotional support [study][study]
AG: Not as empathetic, not generally as social with groups
AA: Not as empathetic, not generally as social with groups [study]

Check your 23andMe results for rs1042778 (v.4 only)

GG: More oxytocin, more socially empathetic, less inhibited, possibly more creative[study]
GT: Less empathetic, more socially inhibited [study], possibly more creative
TT: Less emotional and social[study], higher levels of antisocial behavior in men[study]

 


Lifehacks

Looking to change your oxytocin levels? Here are several ways that research shows to alter your levels.

Petting a dog increases both the human and dog oxytocin levels.[study]  Another study showed that a dog gazing at you could increase oxytocin levels.  Gives new meaning to “puppy-dog eyes”.

Your gut microbiome can affect your oxytocin levels. Mouse studies show that maternal microbiome and diet play a role in their oxytocin levels and effects their offspring.[study] A study also showed the effects of antibiotics decreasing oxytocin levels. Lactobacillus reuteri was shown to increase oxytocin and speed wound healing.

Hormonal contraceptives in women influence oxytocin levels and partner preferences. Here is an interesting study on it.

Vitamin C.  If you are less apt to be social, perhaps some vitamin C before going to a group function might help to increase oxytocin.[study][study] Or increase your sex life.[study]

Creativity has been linked to oxytocin levels. A double-blind, placebo-controlled study found that intranasal oxytocin “reduced analytical reasoning, and increased holistic processing, divergent thinking and creative performance.”

Loving-kindness meditation may increase your oxytocin levels.[study]

Listening to music may increase oxytocin levels.[study]

Not a recommendation here…  MDMA (Ecstasy) increases oxytocin levels.[study]

More to read:

I’ll leave you with puppies gazing at you….

Ancestry.com vs 23andMe: Comparing the raw data files

I recently picked up an AncestryDNA kit out of curiosity to find out how well the data matched up to the 23andMe test that I did a few years ago.  Quick answer: It matched up better than I expected.

First, a couple of caveats:  
I’m not a genealogy expert and was not comparing the two tests as far as accuracy of determining my ancestry.  I’m also not a statistician, so the mathematical comparisons of the raw data files are just the basics.

Taking the test:
Both companies are fairly similar in the simplicity of getting the testing done.  You order the kit — either through the company websites or through Amazon.com — and it comes in the mail.  The box contains a vial to spit into, instructions on how to register the kit, and a small pre-paid shipping box to mail the vial back to the company.

Both 23andMe and Ancestry.com advertise that it takes 4 – 6 weeks to get the test results back after they receive your vial of spit.  It was faster than advertised (about 2 weeks for AncestryDNA) when I did the tests, but I think the times can vary depending on how busy the lab is when you send in your test.

The privacy policies:
Privacy policies: 23andMe.com Privacy Policy, AncestryDNA Privacy Policy  Read the terms of service and the full privacy policy.  Make sure you understand and are ok with them before you order your kit.

Once you have taken the test, you also have the option of answering research survey questions on 23andMe and on Ancestry.com.  Be sure that you understand that you are giving your survey information to the companies to use for their own purposes.

Downloading the raw data:
Both companies allow you to download and keep your raw data file.  I highly recommend that you do so as soon as you get the results.  The information is yours, and you should keep it safe.
Here are directions on how to download the raw data:
Download your genetic data from 23andMe.com
Download your genetic data from AncestryDNA

Both companies also have a clearly stated way to delete your data from their records if you choose to close your account with them. Here are the directions:  Deleting your 23andMe account; for AncestryDNA, there is a button to delete data right under the download link on your settings page.

Searching your raw data online:
23andMe.com has a convenient interface for searching through your raw data on their website.  It is in their Tools section, under Raw Data.   You can search by rs id number or by gene name.  AncestryDNA does not seem to have this option.

Using your raw data file:
The raw data file for both companies comes as a zipped text file.  Both files include the rs id #, chromosome, position, and your genotype.  AncestryDNA’s data is formatted a little bit differently in that the genotype is given separately as “allele 1” and “allele 2”, where 23andMe combines the information into a “genotype” column.

You can simply open up the text file on your computer and do a “Find” to search for a rs id number.  Everyone should have the ability to open a text file on their computer, no matter the operating system.

A better option (in my opinion) is to import the text file into Excel.  To do so, open a new Excel Workbook and click on the Data tab.  There should be an icon there labeled “Text” that will let you import a text file.  Both the 23andMe and AncestryDNA files are tab delimited.  Simply accept all of the default setting in Excel for the text import.

Importing it into Excel then gives you the option of using a second worksheet to make notes on what you learn from your genetic data.

23andMe raw data imported into Excel.

Comparing the raw data files:
I decided to compare my 23andMe (v. 4) data file with the AncestryDNA file.  23andMe gives data for over 600,000 nucleotide base pairs, and AncestryDNA’s raw data covers over 650,00 base pairs.  Comparing the two files, there were over 303,000 rs ids in common between the two.  (This isn’t a completely accurate comparison since 23andMe reports some of the chromosome positions in a proprietary i-number format instead of as a rs id, but it is close enough for my purposes.)

Of the ~303,000 rs id’s in common, for my data, there were just over 1,000 for which the genotypes did not match.  This comes out to 0.3% that did not match — or, alternatively, 99.7% that did match.

Which test is more accurate?
Knowing that for my data the two data files matched for 99.7% of the data actually doesn’t tell me anything as far as which one is ‘correct’ for the ~1,000 genotypes that differed.  Neither company guarantees that their testing is accurate, and both companies are very up-front about it with disclaimers stating that it isn’t being offered as a medical test.

I was actually expecting the mismatch percentage to be higher between the two tests.  While I’m not an expert on error rates in genetic sequencing, several studies that I had read lead me to expect that there would be more variation in the tests.

Final thoughts:
Everyone who is doing either AncestryDNA testing or 23andMe testing needs to read the privacy policies and also understand that the data shouldn’t be used as the only basis for making major medical decisions.  I’m fine with a little uncertainty in looking at my genetic data for something like deciding that I should eat more foods that are high in choline or add in more leafy greens for folate.  Any major health decisions should always be double checked with a test ordered through a lab certified for that test.

Enjoy this comparison and planning on buying a test kit?  I would appreciate you using my referrer link, which will cost you nothing but help me keep on blogging.

Biohacks – Experiments and Optimizations Based on My Genetics

After three years of digging into genetics and learning all that I can about my genes, I wanted to get a little personal and share a few things that have worked for me.

I would also love to hear back from all of you.  Leave a comment below or comment on the Facebook page if you have learned something from your genes and what impact it has had on your diet or lifestyle.

n=1 experiments:  the best lab rat is me

Methylation cycle:
I started off my genetic ‘lifehacking’ the same way that many people do: “Oh, no! I have an MTHFR polymorphism that affects so many things”.  So, of course, I read a few things by people with the word doctor next to their names and then ran out and bought some methylfolate and some hydroxycobalamin (B12).  Methylfolate, at a 400 mcg dose, was the first vitamin or supplement that ever had an effect on me: it gave me an almost immediate headache! I was fascinated by the idea that a vitamin could do something- even something bad – that quickly.

Backing off the methylfolate for a while and then re-introducing it slowly at less than 100 mcg/day got me around the headaches and gave me a new appreciation for ‘just a vitamin’.  A 400 mcg capsule is tiny and taking it apart to sprinkle out a quarter of it a day seemed like it would be impossible to affect me, but it did.

So what did adding methyl folate and hydroxocobalamin do?  It was subtle, but I found that I was no longer as foggy headed, no longer searching for words, and had more energy in the afternoons.  I was in my early forties, and I no longer had that horrible feeling that I was ‘getting old’!

What have I learned since then?  Having read a lot more from other researchers and medical doctors, I’ve come to realize that for me, creatine, glycine, and choline are bigger players in my mental fluidity and energy levels, rather than methylfolate.  I do still take 400 mcg of methylfolate periodically, but I tend to do that just when I haven’t been eating a lot of folate-rich foods.   (Want to learn more about the role of creatine and glycine in the methylation cycle?  Chris Masterjohn has an excellent podcast on the methylation system, with a transcript available if you would rather read than listen. )

Quick recap and links:
MTHFR and other methylation cycle genetic variants.
Low doses of methylfolate and hydroxocobalamin were a good start.
Optimized with increasing glycine, creatine, and choline consumption.

 

Histamine intolerance:
In looking into my methylation cycle genes, I came across some research on the genes that produce the DAO enzyme that breaks down histamine in the intestines.  Realizing that I had a couple of variants there that caused a decreased production of the DAO enzyme, I started looking into the implications of what that meant, which lead me to information on histamine intolerance.

Lightbulbs went off!  My permanently stuffy nose, constant throat clearing, migraines, heartburn, and periodic itchy hives all suddenly made sense.  I had had allergy testing about ten years earlier because I had noticed that allergy medicine reduced the frequency of hives for me.  But the doctor told me that I was only mildly allergic to a couple of types of tree pollen and that allergy medicine couldn’t be helping my migraines.  Turns out that I shouldn’t always listen to the doctor without questioning…   A low histamine diet gave me immediate results.  I could breathe through my nose, got rid of the post-nasal drip, migraines were gone, and nothing itched.  I haven’t needed to stay on a low histamine diet long term, but I do still stay away from eating a lot of high histamine foods in one meal.

While my genetic predisposition to produce less DAO was playing a role in my histamine issues, I knew that it wasn’t the root cause.  Those polymorphisms in the gene that produces DAO are fairly common and everyone with them doesn’t have histamine intolerance.  I think for me, the problem was based in my gut microbiome.  I had been doing all the ‘healthy stuff’: drinking kombucha, taking probiotics, fermenting my own sauerkraut, and making homemade yogurt.  Cutting out all the ferments helped my histamine problems.  Getting my microbiome tested and finding out that I had no bifidobacteria lead me to find a probiotic that was not full of histamine producing strains.  Adding gelatin to my morning coffee increased my glycine intake, probably helping my gut lining. Eating dinner earlier, sleeping better — everything probably plays a part.

Quick recap and links:
Histamine related genes.
Low histamine diet, microbiome testing, the right probiotics, good sleep, glycine, etc.

 

Sleeping:
I’ve always thought of myself as an ‘ok’ sleeper.  I usually could fall asleep easily and wake up at a decent time.  Yes, I had the occasional (and sometimes more frequent) bouts of being wide awake from 3 am – 5 am, but I didn’t think that sleep was something that I needed to focus on.

After reading a few studies on low levels of light impacting sleep quality, I took the plunge (ok – it ended up costing less than $100) and bought some light blocking curtains for my bedroom.  It really did make a difference in how well I slept.  Fast-forward a year…  I did more and more reading on the effects of blue-light at night, realized the research was solid and pretty definitive, and finally spent ten bucks on a pair of blue-blocking safety glasses.  I wear them every evening now for a couple of hours before going to bed.  It took a couple of weeks to notice a difference, but it hit me one day that I was sleeping like a log and jumping out of bed in the morning, wide-eyed, bushy-tailed and all the other cliches.

I’ve been wearing the dorky looking glasses now for about six weeks.  Yep, my husband and kids still laugh when I put them on.  But I feel really good each morning, and I haven’t seen 3 am in six weeks.  I have noticed that I am sleeping about a half hour less than I used to sleep.

Quick recap and links:
Melatonin is pivotal in setting circadian clock genes. Wearing blue-blocking glasses in the evening makes you look dorky, but it is worth it for great sleep and increased morning alertness.

 

Diet:
I had tried the ketogenic diet years ago (the Adkins diet) and felt truly awful on it.  With all the great studies coming out about intermittent fasting, I couldn’t figure out why it didn’t make me feel great to skip breakfast.  Figuring out that I carry a mutation for short-chain acyl-CoA dehydrogenase deficiency made sense of all of it.  I have a somewhat impaired ability to burn fat for energy, so a ketogenic diet or fasting makes me feel icky. While I think the science coming out about intermittent fasting is extremely interesting, it is good to know why eating breakfast works for me.  I have shifted dinner to be a little earlier, giving me a 12-13 hour fast overnight.

Quick recap and links:
SCADD and MCADD are two inborn errors of metabolism that may make it more difficult to rely on burning fatty acids for energy.  Eat some carbs and don’t fast for too long.

 

Vitamin A:
After looking into my genes that convert beta-carotene to vitamin A, I realized that I wasn’t coming anywhere near the RDA for vitamin A and probably never had.  So I got a vitamin A supplement that was truly vitamin A and not beta-carotene, and I took it off and on for several months.  No mental boost, no feeling great, nothing.  Except, one day I noticed the back of my arms were smooth.  I had had little bumps on my arms – keratosis pilaris – since I was a kid, and now they were completely gone.  It hit me then that if vitamin A helps acne, that it may also help keratosis pilaris.  A little research showed that was true, and I had probably been slightly deficient in vitamin A my whole life.  Since Vitamin A is a fat soluble vitamin, I didn’t want to go overboard on supplementing with it.  So I’ve taken a few months off of supplementing it several times over the past couple of years, and after a month or two of no vitamin A pills, my keratosis pilaris starts coming back.   (Yes, I know that eating liver could be a better option than vitamin A pills, but I really hate liver.)

Quick recap and links:
Vitamin A conversion genes.  Adding in vitamin K took away keratosis pilaris.
Supplement of Vitamin A (retinyl palmitate).  Don’t go overboard on Vitamin A supplements since they can build up.

 

Choline:
I mentioned above that choline plays a role in the methylation cycle.  Earlier this spring, I came across some interesting research on how people’s need for choline varied quite a bit, depending on their genetics.  I wrote a blog post on it, noted that I was in the camp of needing more choline, and made more of an effort to eat eggs several times a week for breakfast.  Recently, I read back through my own article on choline and it finally hit me that even if I ate a couple of eggs every day (and I wasn’t that consistent), it wasn’t going to get me to the level of choline that I needed.  So I finally took my own advice :-) Supplementing with a little bit of choline bitartrate gives me a nice mental boost and extra energy.  Too much, and it gives me a headache, reminiscent of the headaches that methylfolate initially gave me. This time I’m taking it slow and not going overboard with it, and I’ve got some Alpha-GPC choline ordered to see if it is a better fit for me. (Yes, I know that liver is a great source of choline as well, but…)

Quick recap and links:
Choline genetic variants.
If you don’t get enough via diet, choline bitartrate or alpha-GPC may be worth a try.

 

We are all different:
Yes, I get the irony of writing a long blog post all about myself and concluding that ‘we are all different’.  But truly, the biggest thing that I’ve learned from all my reading on genetics is that we really are all different.

What works for me may not work for you, even if you have some of the same genetic variants that I do.  Learn to listen to your own body and not what an article tells you to do.

General, population-wide nutritional advice may work for the majority of people, but on an individual level, it often misses the mark.   Read, learn, and figure out what works for you.

Intriguing Genes: Do you taste what I taste?

Ever wonder why some people don’t like Brussel sprouts or strong, dark coffee?  I love a good, dark roast, cup of coffee, and Brussel sprouts and cabbage taste great.  It turns out that I can’t taste the bitter compound in them, but the majority of people can. On the other hand, I have yet to find a brand of stevia that I like because of the awful aftertaste. It turns out that I am genetically more sensitive to the bitter taste of steviol.

If you are old enough, you probably remember the Life cereal commercials with Mikey, where the ultimate, picky taste test is whether “Mikey likes it!”  So why is it an advantage to have differences in our taste receptors?  Having part of the population able to taste a bitter toxin and warn of the danger is vital, while also having others who scarf down Brussels sprouts lets the community as a whole know that a bitter, but healthy, food is good to eat.

Taste buds on the tongue. By OpenStax – Wikimedia Commons.

Here’s a science-y example: One of the substances that some people can detect, at extremely low concentrations, is aristolochic acid, a toxin found in certain plant seeds.  In Eastern Europe, the plant tends to grow as a weed in fields, contaminating crops and causing kidney disease in those who ate the toxin. There is a 50-fold difference in people’s ability to taste aristolochic acid, although researchers are still trying to untangle the effects of taste ability vs the effect of the sensitivity of the gastrointestinal receptors on the disease-causing aspects of the toxin.

We all know that we taste food in our mouth, but it turns out that these same receptors are also found in the gastrointestinal tract, in the airways, and in the urinary tract. New studies are coming out all the time on the various functions that these ‘taste’ receptors perform in the body.[study][study]

Genes involved: 
TheTAS2R gene family, containing 43 different genes, is responsible for various bitter taste receptors, while the TAS1R family (just two genes) is responsible for sweet and umami tastes.  Salty and sour taste receptors are still being sorted out, and it turns out we also have taste receptors for fat.

Bitter taste receptors:
TAS2R38 gene:
Linked to the taste of bitter in broccoli, Brussels sprouts, cabbage, watercress, chard, ethanol, and PROP. [ref][study]  Interestingly, this taste receptor is also being studied as a target for type 2 diabetes medicines and is involved in triggering the production of bile acids.

Check your 23andMe results for rs713598 (v.4 and v.5):
GG: Can taste bitter in broccoli, etc.
CG: Probably can taste bitter
CC: Probably unable to taste some bitter flavors
Check your 23andMe results for rs10246939 (v.4 and v.5):
CC: Can taste bitter in broccoli, etc.
CT: Probably can taste bitter
TT: Probably unable to taste some bitter flavors

 

TAS2R16 gene:
Associated with the taste of beta-glycorpyranoside [clinvar], which is in ethanol, bearberry, bacteria in spoilt or fermented foods, and willow bark (salicin).  [study]  There have been studies looking into the link between TAS2R16 gene variants and colon cancer, pursuing the idea that either a variation in vegetable intake would affect cancer risk or a variation in the amount of natural salicin compounds eaten would affect colon cancer risk (aspirin being preventative in colon cancer for some). The studies done so far though haven’t been able to make that connection. [study]

Check your 23andMe results for rs846672 (v.4 and v.5):
CC: Can taste bitter in ethanol, fermented foods, etc
AC: Probably can taste bitter
AA: Probably unable to taste some bitter flavors
Check your 23andMe results for rs846664 (v.5 only):
AA: Can taste bitter in ethanol, fermented foods, etc
AC: Probably can taste bitter
CC: less able to taste some bitter flavors
Check your 23andMe results for rs978739 (v.4 and v.5 only):
TT: Can taste bitter in ethanol, fermented foods, etc
CT: Probably can taste bitter
CC: less able to taste some bitter flavors

 

TAS2R19 gene:
Linked to the taste of quinine,  the bitter taste of grapefruit and tonic water. [study]

Check your 23andMe results for rs10772420 (v.5 only):
AA: Can taste bitter in quinine
AG: Probably can taste bitter in quinine
GG: Less able to taste bitter in quinine


TAS2R14 gene
:
Stevia taste receptor — as well as absinthe, aristolochic acid, fishberries, and Hoodia Gordonii.[study] [ref]  There is a polymorphism (rs2234001, covered by AncestryDNA but not 23andMe) that causes some people to detect stevia as bitter, some as only sweet, and some as sweet with a bitter aftertaste.  You don’t really need a genetic test for this one, though, since you can just taste some stevia and know whether you think it is sweet or bitter or both.

Of those who can taste bitter, some have a much strong perception of the bitter taste based on the rs3741843 variant. [study]

Check your 23andMe results for rs3741843 (v.4 only):
TT: Lower sensitivitity to bitter taste from stevia.
CT: Stevia tastes more bitter (if able to taste the bitter)
CC: Stevia tastes more bitter (if able to taste the bitter)

Sweet and Umami Taste Receptors:

TAS1R3
Sweet taste receptor for which variations are estimated to produce about a 16% difference in variability of sweet taste perception.  This receptor also plays a role in umami taste as well, along with another gene. [ref] A study found an increase in kid’s cavities linked to those who have a decreased sensitivity to the taste of sugar, perhaps due to eating more sugar to reach the same perception as those without the variant.  Scientists are still sorting out the reason why and how the change in the taste receptor protein is also altering insulin secretion.  [study]

Check your 23andMe results for rs35744813 (v.4 only):
TT: Decreased taste sensitivity for sucrose
CT: Somewhat decreased taste sensitivity for sucrose
CC: Normal taste receptor for sucrose
Check your 23andMe results for rs307355 (v.5 only):
TT: Decreased taste sensitivity for sucrose
CT: Somewhat decreased taste
CC: Normal taste sensitivity for sucrose

 

More to read:
Here are a few more studies that are digging into the roles that our taste receptors play –outside of just the taste we perceive in our mouth.  Read through them to find out the more about the interactions of leptin, endocannabinoids, and insulin with taste receptors.  Pretty cool stuff!

Lactose Intolerance: The genetics of not producing lactase

Are you a milk drinker? Does pouring a cold glass of milk sounds good? Your genes control whether you are likely to produce lactase as an adult, and it is easy to check your 23andMe or other genetic data to see if you are likely to enjoy a big glass of milk.

Personally, I had always thought it a bit strange that my husband likes to drink a glass of milk with dinner. It just didn’t appeal to me — at all. I didn’t think ever think about lactose intolerance, though, because I still drink small amounts of milk in my coffee and on cereal. Turns out that I am one of those people who doesn’t produce lactase as an adult. I am relying on bacteria in my gut to break down lactose, so I don’t go overboard on drinking milk.

Getting into the science:
Lactose, a sugar in milk, is broken down by the enzyme lactase which our bodies produce in the small intestines. For some people, the production of the lactase enzyme stops when they become an adult, driven by a genetic variation near the LCT gene. This means that some adults are genetically predisposed to not be able to digest larger quantities of milk.

The percentage of the population with the genetic variations differs quite a bit among people with different backgrounds. Producing lactase as an adult is the most common genotype for Caucasian populations, while in Asian populations, the majority do not produce lactase as an adult. This is thought to be an adaptation by Caucasian populations in Europe who relied on dairy products as a source of protein.

For Caucasians, the main variant to look at is located in the MCM6 gene, which influences the LCT gene.  Approximately 90% of Caucasians will have AA or AG and still produce lactase to break down milk as an adult. In Asian populations, less than one percent will carry the G allele.

Bacteria in the gut also break down lactose, so even those who don’t produce lactase can often handle digesting limited amounts of milk.


Genes Involved in Lactose Production

If your genotype is GG on rs4988235, you will not produce lactase and will probably not be able to handle larger quantities of milk as an adult. From talking with other people about this, it seems that those with GG naturally limit their intake of milk.

Check your 23andMe results for rs4988235 (v.4, v.5 of 23andMe; AncestryDNA):
AA: Still produces lactase as an adult
AG: Still produces lactase as an adult (probably less than those with AA – study)
GG: No longer produces lactase as an adult

Interestingly, a Dutch study showed that while the GG genotype resulted in adults having a lower dietary calcium intake, that did not correspond to a lower bone density or more fractures.

For people of African origin, a different variant of the MCM6 gene is found in about 10-15% of the population and is associated with being able to produce lactase as an adult.

Check your 23andMe results for rs145946881 (v.4, v.5 of 23andMe; AncestryDNA):
CC: Still produces lactase as an adult [study]
AC: Still produces lactase as an adult
AA: No longer produces lactase as an adult

A very small number of people may also have a rare mutation (not covered by 23andMe or AncestryDNA) that causes the lactase gene not to function at all, even in childhood.


Lifehacks

Probiotics to the rescue?

Quite a few studies have looked at the effect of probiotics on lactose intolerance.  One study from May 2016 found that a specific strain of Lactobacillus acidophilus was significantly effective in reducing the symptoms of lactose intolerance.  There are many types of lactobacillus bacteria available as probiotics and in yogurt or other fermented foods.  It is likely that some strains will be much more effective than others in reducing lactose intolerance symptoms for an individual, and it may be worthwhile to try several different types of Lactobacillus probiotics.

If you are interested in digging deeper into the types and numbers of lactose-consuming bacteria in your gut, you could do a microbiome test from uBiome or another company.

More to read:

 

originally published 2/23/15, updated 10/17

Intriguing Genes: Differences in how we smell things

Learning about genetics has given me a new perspective on so many different subjects.  For example, seeing first-hand how much of a difference the right vitamins and minerals make in a person’s mood due to changes in their neurotransmitter balance has made me much more understanding.  Cut me off in traffic?  Instead of just assuming you are a jerk, I now wonder if you were driving aggressively due to needing a little lithium orotate along with the right type of B12.

One of the things that recently surprised me is that we don’t all smell the same odors.  I knew that some people have a loss of the sense of smell when they get older and that inability to smell could be a marker for some diseases, but I was intrigued by the idea that any two people may have as much as a 30% difference in their functional ability to detect different specific odors.[study]

So now I have to once again change my perspective. Over half the population can’t smell a compound in floral fragrance nearly as well as I can.   Instead of being irritated at that lady wearing too much floral fragrance, now I recognize that she probably thinks it is lightly pleasant — I’m the one that is different.  And now I wonder what it is that I’m not able to smell!

Humans have around 400+ different olfactory receptor proteins that are coded for by our genes.  Only a small portion of these receptors have been mapped to specific odors so far.  (I’m guessing there isn’t a lot of money in researching olfactory receptors vs. curing diseases…)

There are several different genetic variants of odor receptor genes that aren’t covered by 23andMe.  One of them, OR7D4 variant rs5020278, is linked to a persons ability to smell the sex steroid derived odorants, androstenone and androstadienone.  Researchers have studied how the ability to detect androstenone plays a role in whether a person is likely to eat pork from uncastrated male pigs.  Some people perceive the meat as smelling very unfavorable to eat, known as ‘boar taint’.[study] [study] It turns out that the same odor perception variant can also play a role in sociosexual behaviors in women.[study]

Other studies have linked odor receptor variants to increased BMI. One study found that participants who were less sensitive to smelling oleic acid were more likely to eat more nuts, seeds, and nut spreads (high in oleic acid) as well as having a higher BMI.  The study sums up: “fatty acid olfactory sensitivity is clearly linked with fatty acid taste sensitivity albeit acting through separate pathways. Hyposensitivity to fatty acid taste was associated with disinhibited eating behaviour. Furthermore, participants who were hypersensitive to oleic acid taste perception had lower BMI values than those who were hyposensitive.”

So what kind of interesting things can we learn from 23andMe data about what/how we smell odors?

OR5A1 gene:
The variant rs6591536 has been linked to the ability to smell β-ionone. Those who carry an G allele are more able to detect β-ionone, which is a floral smell found in roses, jasmine, violets, and more.  It is a compound often used by fragrance manufacturers for floral smells. [study]

Check your 23andMe results for rs6591536(v.4 and v.5):

  • AA: less able to smell floral (β-ionone)
  • AG: more able to smell floral (β-ionone)
  • GG: more able to smell floral (β-ionone)

OR10A2 gene:
Cilantro is one of those foods that people either seem to love or hate.  Turns out that an olfactory receptor gene variant may play a role in how we perceive it.  [study]

Check your 23andMe results for rs72921001(v.4 and v.5):

  • AA: less likely to think cilantro tastes like soap
  • AC: less likely to think cilantro tastes like soap
  • CC: more likely to think cilantro tastes like soap

Asparagus Pee
Asparagus pee smell….  was something that I assumed everyone smelled.  Turns out that more than half of people in a study of nearly 7000 were unable to smell asparagus pee.  A second study looked into whether it was a lack of ability to smell the odor vs. a lack of producing the odor.   The study found that 8% of participant’s urine did not have a detectable asparagus odor and also that the ability to smell the asparagus pee smell is much stronger in those who carry the A allele of rs4481887.

Check your 23andMe results for rs4481887 (v.4 and v.5):

  • AA: most likely can smell asparagus pee
  • AG: likely can smell asparagus pee
  • GG: least likely to be able to smell asparagus pee

OR7G3
Being able to smell or not smell certain odors has been linked to food preference and a risk of obesity.  For OR7G3, those carrying the C allele variant had almost a whole point higher BMI on average.

Check your 23andMe results for rs10414255 (v.4 and v.5):

  • C allele: linked to more hunger, disinhibition in eating, and higher BMI
  • TT: lower BMI (on average)

Beyond just smelling the flowers….

While this has been a rather light look at being able to smell different odors, there are more serious issues for people with anosmia (inability to smell) and I encourage you to dig deeper into the topic if you have an inability to smell.

It seems that the research into odorant receptors is just in its infancy with quite a bit of new information coming out in the past couple of years.  We actually have these odorant receptors other places than just in our nose, leading to the idea that they play other roles in the body.

“Accumulating molecular evidence indicates that the odorant and taste receptors are widely expressed throughout the body and functional beyond the oronasal cavity – with roles including nutrient sensing, autophagy, muscle regeneration, regulation of gut motility, protective airway reflexes, bronchodilation, and respiratory disease. Given this expanding array of actions, the restricted perception of these GPCRs as mere mediators of smell and taste is outdated.” [study]

HLA typing is also linked to olfactory gene variants.  A recent study looked at using smell tests as a way of determining HLA variants.

One last tidbit for your olfactory knowledge base is that some molecules are transformed in the mucus before reaching the odor receptors.  CYP1A2 genetic variants (check yours here) were found to play a role in the conversion of acetophenone (cherry, almond chicory smell) to methyl salicylate (wintergreen smell) in the nose.[study]  So the whole kit-n-kaboodle gets a little more complicated.

More to read:

 

Ear wax and body odor – it’s genetic

The ABCC11 gene determines both the type of earwax a person has and their armpit odor. A change in a single base in the code for this gene can cause the gene not to function.

Check your 23andMe results to see if you produce body odor. Or just do a sniff test…

People with a functioning ABCC11 gene have wet earwax and body odor, while those with the gene variant causing loss of function have dry earwax and little or no body odor. Loss of function of the ABCC11 gene is very common among East Asian populations (80-90% of the population!), but fairly rare in other populations (1 – 3% of Caucasians).

So what exactly does this gene do? The ABCC11 gene (ATP-binding cassette transporter sub-family C member 11) codes for a protein that is involved in transporting molecules across cellular membranes.  It is involved in the transport of lipophilic compounds, bile acids, conjugated steroids, and the substance that is in apocrine sweat and in earwax, thus causing body odor and wet earwax.

Variants of this gene are also involved in resistance to antiviral and anticancer drugs.[ref]  The wet earwax allele was also associated with a higher risk of breast cancer in Japanese women, but not in women of European descent.[ref] [ref]

Check your 23andMe results for rs17822931 (v.4 and v.5):

  • CC: wet earwax, body odor, and normal colostrum[ref] [ref]
  • CT: wet earwax, somewhat less body odor
  • TT: dry earwax, no body odor, and less colostrum

There was an interesting article in Scientific American a few years ago looking into the fact that those who genetically don’t have smelly pits often unnecessarily still wear deodorant. Other research showed that those with the ‘no body odor’ variant sometimes had other sources of body odor or social reasons for wearing deodorant.[ref]

How Well Do You Convert Beta-Carotene to Vitamin A?

How Well Do YOU ConvertBeta-Carotene to Vitamin A-Everyone knows that carrots and sweet potatoes are great sources of vitamin A, right?

Well…  it turns out it isn’t that straightforward for everyone. The beta-carotene in orange fruits and vegetables has to be converted into the form of vitamin A that our bodies can use, and genetics plays a huge role in how well we do that conversion.

Almost half of us have variants in our BCMO1 gene which cause a 30% to 70% decrease in the amount of vitamin A that we get from beta-carotene.

Background information on Vitamin A:
Vitamin A is a general term that covers several different forms of the vitamin. Animal food sources mainly provide retinyl palmitate, which is broken down in the intestines to retinol. In this form, it is stored by the body and then converted to an active form for use.

The plant forms of vitamin A are called carotenes, such as beta-carotene which is found in abundance in carrots and other orange-colored foods. Beta-carotene is broken down by an enzyme in the intestines to also form retinol. Interestingly, most carnivores are poor converters of beta-carotene, and cats cannot create any vitamin A from beta-carotene.  [source]

About 80-90% of retinoids in the body is stored in the liver and used to maintain a steady level in the blood.[study] The body then used the retinoids in a variety of ways including in stem cells, photoreceptors in the eye, epithelial cells, embryonic cells, various immune cells, red blood cells, and much more.


Genetics of Beta Carotene Conversion:
Beta-carotene is converted by the enzyme β-carotene 15,15′-monooxygenase (BCMO1 gene) into retinol. It is then used by the body in the same way as preformed vitamin A from animal products is used or stored.

There are two gene variations in the BCMO1 gene that help determine a person’s ability to convert beta-carotene into the retinol a body uses. A study in 2008 shows that the SNP’s rs12934922 and rs7501331 control a person’s conversion rate of beta-carotene into retinol. People with a T allele on both rs12934922 and rs7501331 have a 69% decreased conversion of beta-carotene to retinol.  For people with only a single T in the rs7501331 SNP, the conversion is decreased by 32%.

Check your 23andMe results for rs7501331 (v.4 and v.5):
CC: normal
CT: decreased beta-carotene conversion
TT: decreased beta-carotene conversion
Check your 23andMe results for rs12934922 (v.4 and v.5):
AA: normal
AT: decreased beta-carotene conversion
TT: decreased beta-carotene conversion

Three other variants that are found near the BCMO1 gene have also been shown in a small study to affect the rate of conversion by about 50%

  • rs11645428 – GG has lower beta-carotene conversion
  • rs6420424 – AA has lower beta-carotene conversion
  • rs6564851 – GG has lower beta-carotene conversion

Lifehacks

If you are a vegan or vegetarian, your main source of Vitamin A is probably beta-carotene. If you don’t process it into retinol very well, you may want to increase your vegetables that are high in beta-carotene or supplement with a retinol form Vitamin A.

If you are supplementing with Vitamin A, check and see if your supplement is in the form of beta-carotene or retinol palmitate. If you have a decreased ability to convert beta-carotene to retinol, you may be getting less vitamin A than you think.

A word of caution: Vitamin A is a fat-soluble vitamin that can build up in the body, so you don’t want to go overboard with it. The upper daily recommended limit of vitamin A is 3000 μg/day (3 mg/day). Most supplements list the amount of vitamin A in IU (international units). One IU is equivalent to 0.3 μg (.0003 mg) for vitamin A. So 8000 IU would equal 2.4 mg retinol.

So how much beta-carotene is in carrot juice? According to the Nutridesk website, one cup of carrot juice contains 22mg of beta-carotene. That site also claims that for an average person, 1/12th of that beta-carotene is converted into retinol thus giving 1.8 mg of retinol per cup of carrot juice. If you are a poor converter of beta-carotene, you could be getting more like 0.5mg from a cup of pure carrot juice.

Carlson’s Vitamin A on Amazon.com is a good source of the retinol form of vitamin A

Beef liver is also an excellent source of vitamin A.  A three-ounce serving of liver packs a big punch with about 15,000 IU of vitamin A.

Why is vitamin A so darn important?
A deficiency in vitamin A can cause night blindness, worsen infectious diseases, and, when severe, cause blindness. It is used by the body in a variety of different ways. In the immune system, it is involved with both the innate and adaptive immune responses.[study] Vitamin A can also help with skin problems such as some types of acne and hyperkeratosis.[study]

More to Read:

 

Updated 5/2017