Original URL: http://www.theregister.co.uk/2013/04/19/dna_test/

It's official! Register hack is an alcohol-flushed cave dweller

Budget DNA test reveals our man's genome secrets

By Lester Haines

Posted in SPB, 19th April 2013 15:04 GMT

It's official: this Reg hack is 2.7 per cent Neanderthal, belongs to the J1c3b haplogroup, is at increased risk of coronary heart disease and Restless Legs Syndrome, has wet ear wax, and slightly decreased odds of suffering male pattern baldness.

That's according to the enlightening results of a personal genome test by 23andMe, which for a budget $99 plus P&P, tells me that while I have a higher than average risk of developing Parkinson's Disease and psoriasis, I'm less likely to be afflicted with Type 2 Diabetes and Alzheimer's Disease.

A couple of months back, I ordered the test online and duly received a "spit pack" - basically a plastic tube for a saliva sample and a prepaid courier's envelope to whisk my sample back to 23andMe's lab for the once-over.

The company has been knocking out cheap tests since securing $50m in venture funding in 2012, in a bid to increase its sample base to one million individuals.

23andMe's mission statement says it wants to be "the world's trusted source of personal genetic information", with the aim of creating "a common, standardized resource that has the potential to accelerate drug discovery and bring personalized medicine to the public".

For customers, there's the prospect of taking "a bold, informed step toward self-knowledge" and participating in research "that could improve understanding of how genetics influences our lives".

So, determined to take a bold step towards self-knowledge, I submitted my DNA for analysis. The test involves pinpointing 1,000,000 single nucleotide polymorphisms (SNPs), using a "BeadChip", provided by Illumina. 23andMe explains that "although the process relies heavily on massive computer power, the chip itself is not a microprocessor but a miniaturized genetics lab".

It adds: "The BeadChip is a small glass slide with millions of tiny beads on its surface. Attached to each bead are probes - bits of DNA complementary to sites in your genome where SNPs of interest are located. Your DNA will stick to the probe that matches whichever SNP you happen to have."

While I twiddled my thumbs waiting for the BeadChip to work its magic, I did suffer some doubts about just how much self-knowledge I actually wanted. 23andMe notes: "Learning that your genotype is associated with an increased risk of a particular condition can be difficult, especially if you have seen a friend or family member struggle with a similar issue.

"One of the potential benefits of having more information is that by working with your physician you may better manage your health. But as a matter of personal choice, some people prefer not to know."

He's in his element - hydrogen!

Lester Haines preparing SPB flight hardware

When the results arrived, though, my natural curiosity overcame any misgivings. Diving straight into "Health Risks", I found I was at 58.8 per cent risk of coronary heart disease, compared to an average of 46.8 per cent, since the former percentage of "men of European ethnicity who share Lester Haines's genotype will develop coronary heart disease between the ages of 45 and 79".

23andMe rates its confidence in this result as high, based on "established research" of "at least two studies [which] examined more than 750 people with the trait or condition and/or the associations are widely accepted in the scientific community".

In the case of alopecia areata - to which I'm slightly more susceptible - the result rates slightly less confidence, based as it is on "preliminary research" where "750 people with the condition were studied, but the findings still need to be confirmed by the scientific community in an independent study of similar size".

Moving down the confidence scale, I find I have "substantially increased odds" of suffering hypertriglyceridemia, but that's based on preliminary research in which "fewer than 750 people were studied" and "multiple large studies are needed to confirm these findings".

Having dodged that bullet, pending further research at least, I dipped into "Inherited Conditions", where I found my parents had rather unkindly gifted me hemochromatosis (HFE-related).

Or rather, I've got "one mutation in the HFE gene linked to hemochromatosis". The results conclude: "A person with one of these mutations is not typically prone to higher levels of iron in the body, but can pass the mutation to offspring."

What mum and dad didn't pass down was Cystic Fibrosis, since I don't have any known mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. 23and Me notes: "Cystic fibrosis is inherited in a recessive manner, meaning that only a child who receives two mutated copies of the CFTR gene (one from each parent) will get the disease."

Give me the bad news, doc, but perhaps not quite all the bad news

At this point I was beginning to explore darker waters. Some results are "locked", in the sense that you have to opt in to view them. This was the case regarding TTR-related familial amyloid polyneuropathy, a rare disease which "can affect the nervous system, heart, eyes, and other organs".

Before clicking the button, I was informed: "More than 90 mutations in the TTR gene have been linked to familial amyloid polyneuropathy. This report covers two mutations called Val30Met and Thr60Ala.

"The Val30Met mutation causes most cases of the disease in people with Portuguese, Swedish or Japanese ancestry. The Thr60Ala mutation is found primarily in people with Irish ancestry. These two mutations account for the majority of the disease in people with Asian and European ancestry."

Having decided to take the plunge, I was mercifully informed I don't have "any of the TTR mutations linked with familial amyloid polyneuropathy reported by 23andMe".

This locked report approach is sound for those who "prefer not to know", although I can't really imagine anyone having opted to be tested in the first place not clicking the button, for better or worse.

On a lighter note, I was unsurprised to learn I don't suffer from alcohol flush reaction, which for sufferers means booze "has such an unpleasant, noxious effect that they tend to avoid it altogether". As my liver can attest, I have two working copies of the ALDH2 gene, that "encodes a protein called aldehyde dehydrogenase". This is an enzyme "responsible for the second step of ethanol processing: the conversion of the highly toxic acetaldehyde to the harmless acetic acid (vinegar)".

Regarding the aforementioned ear wax, it is indeed enlightening to discover that you're either wet or dry, according to a Mendelian trait, as determined by the ABCC11 gene.

23andMe elaborates: "This gene encodes a protein known to transport fat-like compounds out of cells, including various types of drugs. The C version of the SNP makes a version of the protein that is a much more efficient pump than the one encoded by the T version. The protein may thus be directly involved in secreting some of the oily substances that make earwax wet."

It concludes: "It is not known whether there would be any evolutionary advantage to having wet versus dry earwax."

Of course, I'd like to believe that there's a direct genetic link between wet ear wax and evolutionary success, and indeed intelligence, athletic prowess and sexual attractiveness, but while I await confirmation of that, I'll have to make do with having a direct genetic link to the Arabian Peninsula.

My maternal lineage puts me in the J1c3b subdivision of haplogroup J1. 23andMe explains: "Haplogroup J originated about 45,000 years ago on the Arabian Peninsula not long after modern humans expanded out of Africa and onto the Eurasian continent. About 7,000 years ago the expansion of farming carried daughter lineages of J, including J1, into Europe. Today the haplogroup extends as far west as Britain and as far east as Central Asia."

On dad's side of the family, meanwhile, I'm part of R1b1b2a1a1 - a subgroup of R1b1b, the "most common haplogroup in western Europe, with distinct branches in specific regions".

Fascinating stuff, although level-headed boffins have warned about reading too much into such revelations, and that in the end, everyone is distantly related to everyone else.

Likewise, the fact I'm 2.7 per cent Neanderthal isn't particularly significant. All modern humans contain between one and four per cent Neanderthal DNA, and we'll leave it to readers to decide whether those packing higher than average amount of caveman can be identified by troglodytic tendencies.

I've still got more results from my test to trawl through, while I ponder what future use they might serve. One appealing possibility is that although the info is "for research and educational purposes only, and is not for diagnostic use", I could download all of the raw SNP data, slap it on in my doctor's desk and say: "There you go, work it out from that while me and my ALDH2 genes go for a few pints." ®

Bootnote

No doubt readers have concerns about the possible implications of wide-scale DNA testing. 23andMe acknowledges that "the availability of personal genetic information raises important issues at the nexus of ethics, law, and public policy". We'll examine these issues in a follow-up article.