SNPs are Us

It won’t be long before snp is added to the pantheon of approved English words in the OED. It will sit among those rarest of words, those that lack a vowel like the crafty Welsh invented—cwm (a mountain hollow), crwth (kind of violin), and cwtch (cubby hole or cuddle). We do of course insert an invisible i to make the word easier to say, but there will still be confusion for a word that began life as an abbreviation (single nucleotide polymorphism) and is the same as SNP (Scottish National Party). There is room for misunderstanding too, like the occasion when a woman asks a man if he got the results for his snps (meaning DNA) which he mishears as snips (and interprets as vasectomy). Language is wonderful, and so is modern genetics.

In the last post, I described my experience with DNA ancestry testing, and this time I’ll mention the health data that can be obtained. In 2013, the US Food and Drug Administration stalled the delivery of personalized genomic information, although that relaxed this month and 23andme have released potentially sensitive information to consumers. But we can dig much deeper after sending raw data file from our DNA chip analysis to another service.

The curious customer only has to invest $5 on top of the $100-200 already paid by uploading data to Promethease, a company that takes its name from the Greek deity that stole fire from the gods (customer beware!). Your results are delivered as a zip file a few minutes after uploading your genomics data, enough to pore over for hours. My file contains 17,844 annotated genotypes or snps which are doublets from the four-letter DNA code (A,T, G & C) for which there are about ten million variants across our 23 pairs of chromosomes in the population, most in the non-coding region (i.e. not in a gene sequence). Sometimes, a switch from, say, a G to a C in a DNA strand has a deadly or life-altering impact, but more often it is neutral or only predicts a certain kind of trait or disease with a percentage probability. I was eager for my data, and maybe the experience I describe will encourage others.

The large file received from Promethease was divided into categories, each with a list of snps in descending order of significance. Those highly associated with a trait were highlighted in red for scanning the good/ bad stuff quickly. The snps and genosets (snp combinations that have a more proven connection with traits) near the bottom of the lists were boring because the associations were so weak (just a few % + or -).

Let’s start with the GOOD category. This is how the first page appears.

Promethease

My Good News

With so much information I have to write telegraphically and hope I don’t lose the gist for readers. I was informed that I am male, white and probably of European ancestry (well, yes!). I have snps for dark eyes and blood group O (Y), a big head and higher IQ (of course), able to digest milk lactose (Y), tolerant of caffeine and my face doesn’t flush after alcohol (YY), can smell asparagus metabolites in my urine (Y), have mixed muscle types like a sprinter (eh?), won’t go completely bald (yea), have longer telomeres for long life (yipee), less endometriosis (well!), protected from headhunters’ prion disease (phew),have  lower risk of macular degeneration, diabetes, AF, obesity, various cancers (thankfully), and restless legs syndrome (mother’s problem). A lot to be thankful for until I read the next category.

Now here’s the BAD news, and an example from that first page.

Promethease

My Bad Stuff

I have snps that put me at risk of cancer, diabetes, AF, lower IQ, shorter lifespan, baldness, and macular degeneration (do they cancel the good marks above). I have a 3x risk of obesity (really!), am less empathetic (I am sorry), a later menopause (phew), and have a 4x risk of sexual dysfunction if I take SSRIs (don’t ask).

Some of the little details were telling, like the results for caffeine, asparagus and the taste of cilantro/ coriander (it doesn’t taste of soap to me), as well as my earwax and body odor which I assure you are fine! I was also correctly predicted not to have a cleft chin, hairy back, unibrow or widow’s peak, and was amazed to read that my second toe is longer than my big toe. How could they know when I don’t upload my mug and feet on my Facebook page! But occasionally a result really jarred. I am proud of the dimples they missed, and with a BMI of 21 surely I can’t be obese! Other results smudged from Good to Bad, particularly heart disease, and cancers because there are so many snps. Their magnitudes were rarely more than 3x and mostly a lot lower than 2x, not much to worry about if you take the broad picture rather than lingering on one “bad” result.

I was particularly interested in the newly released information on carrier status. It is estimated that on average we all have a copy of a recessive lethal gene. One copy is quite tolerable unless you plan to be a parent and your partner is found to have a matching mutation. 23andme provides a report on 36 genetic diseases, most of them very rare but also cystic fibrosis and Tay-Sachs. You have to go elsewhere to check status for the rather too common mutations that cause breast cancer, heart and Alzheimer diseases at early ages. Not everyone wants to know, and a positive result should lead to the door of a health professional for advice.

As health and genetics data are mined more deeply and integratively I will return to my data to see how interpretations have changed. I wrote last time that genetics is not destiny. Possessing one or even a bunch of undesirable snps is not necessarily bad news because most of the traits that worry us involve hundreds of genes. Besides, they are affected by lifestyle and environment as well as our genotype. We no longer think of nature versus nurture, but nature and nurture. In a recent Australian twin study of 18,000 traits the ratio of responsibility was close to 50:50. Tragically, however, there are single gene defects where one letter of the DNA alphabet has devastating effects, and diseases affecting nerves, eyes, and bones are more affected by genetics (bipolar disease at 70%), but mental attitudes are hardly affected at all.

Snp may be a short word with a specific meaning, but it doesn’t always make genetic sense. Nevertheless, surfing snps can fill your evening with entertainment and, unless you are a hypochondriac, is a lot less scary than checking your stocks on the Dow or FTSE Index this week.

Any Comments about your experiences with these tests?

Next Post: A Mastodon in Town

 

About Roger Gosden

I took early retirement from my post as Professor & Research Director in Reproductive Biology at Cornell Medical College in New York City to concentrate on writing about science and nature,
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