Oh cousin, who art thou?

23andme has a thing called Relative Finder which allows us to discover, among all the people who had their DNA analyzed by them, which are our "genetic cousins" - and also gives us the estimated proximity of that family relationship. But, for obvious privacy reasons, they don't reveal those persons' identities, and we are required to send them an invitation if we wish to contact them. Once we know who they are, we can proceed to try and compare paper trails and see if we have any known ancestors in common.

That's what I did with the one person estimated by RF to be my second cousin
(which would mean we have a set of great-grandparents in common): I sent her an invitation to contact me. She replied saying she accepted contact, but still didn't tell me who she was (did she forget to do it, did she not know how to do it, did she not wish to do it? I really don't know). But I still only know about her that she is a female and that her maternal haplogroup is N1b2. And I have no way to do anything else. I wrote her back several other messages, the last one on November 8, but still no answer. It's frustrating.

Abraham's Children in the Genome Era

Beautiful results published here! For the non-specialist, everything explained here (in Newsweek)

I earned a badge

This morning, when I logged into my 23andme account, I found out that I had earned myself a Research Pioneer Badge for my contribution “to the first 23andWe research discoveries” published yesterday in PLoS Genetics, and derived from the DNA testing of thousands of people from the public at large. Namely, from the company’s clients who, like me, consented to the use for research purposes of their personal genetic data and of their answers to one or more surveys.

This is the first time, says an editorial in that same publication, that a human genome-wide association study, or GWAS, is performed based on information gathered through the Internet and stemming from such a population. The study shows, according to its authors, that this approach is not only reliable, but that it also allows the discovery of novel genetic associations.

DNA swapping at 23andme

A few days ago, 23andme sent emails to 96 potentially affected clients warning them that the lab who reads the DNA for the company had mixed-up their genetic identities and sent them some other persons’ results.

The first sign that there was something wrong was a post, published on June 2nd, in the 23andme community section, by a mother who panicked when she accessed her family’s results online: “He was not a match for any of us. I checked his haplogroups and they were different from ours. I started screaming. A month before my son was born two local hospitals had baby switches”, she wrote. 23andme responded two days later telling her they were analyzing what might have happened.

Mistakes happen. What I don’t understand is that non-affected clients like myself only today learned about this through various blogs, and not directly from 23andme. The company’s response has been overly discrete, and to date, there has been no public announcement from them. It would really help if they were more transparent!

Spit again, please!

Two days ago I received my Family Tree DNA kit (by their kind courtesy). This means I’ll have to spit again into a little tube, this time to have my mitochondrial DNA fully sequenced, and not just a few SNPs, or point variations, as I’ve already done.

This is the ultimate test you can take to learn about your origins along your direct maternal line. Not only will it pinpoint ethnic and geographical origins with unprecedented precision, but it will also allow me to see if anybody else’s mtDNA in their database (which is currently the largest one there is, according to them) matches mine.

Still according to their site , this would mean that person and I share a common “grand-mother” in the not too distant past. And if so, we will have the opportunity to get in touch with each other.

I haven’t drooled into the tube yet, but when I do and the results come in, I’ll come back to this in due detail.

Inuk and me

In The Spittoon, 23andme’s blog, we are given the opportunity to compare some of our SNPs with those of Inuk, the man from 4000 years ago in Greenland who today officially became the first ancient human to have his genome almost completely sequenced (you can read here the article I published today in my newspaper, PÚBLICO - and if you don't read Portuguese you can read the Spittoon's post). I went and compared. Cool!

Image: Inuk by Nuka Godfredsen/Nature

Cancer risks revisited

The Spitton, 23andme’s blog, mentions a paper in Nature Genetics by Gloria Petersen from Mayo Clinic and colleagues which pinpoints several locations in the genome which may me associated with higher risks of developing pancreatic cancer – maybe the most lethal of all cancers.

Randy Pausch (photo), the computer scientist at Carnegie-Mellon U., died of it a year and a half ago. (Remember his famous and moving “Last Lecture”?)

I went and tried to evaluate my own risk by following the instructions in that post, which consist in looking at my raw genetic data from 23andme at the following SNPs (or point mutations): rs9543325 (on chromosome 13), rs3790844 (on chromosome 1) and rs401681 (on chromosome 5).

The results are not clear-cut.

At rs9543325, my genetic make-up (CT) corresponds, according to the study in Nature Genetics, to 1.23 times higher odds to get one day this type of cancer than if it were the most common one (TT).

At rs3790844, I’m AG e that lower my odss (it multiplies the typical odds by 0.75);

And at rs401681, I’m CC, which means typical odds – lower in particular, than those of ao people who are CT ou TT at this location, and who might also have higher odds, according to previous studies, of contracting melanoma and colorectal cancer.

But even this last SNP, in spite of my genetic configuration apparently being the best possible one, is a two-sided coin, since having one or two C’s in this position has been associated, also in previous studies, to higher odds of getting other types of cancer: basal cell carcinoma (a type of "benign" skin cancer, I had one removed last year, thank you very much), as well as lung, bladder, prostate (which doesn’t concern me), cervical and endometrial (lining of the uterus) cancer.

Enough!

(Image: all rights reserved)

Genealogical stalker

Genealogical stalkers are people who find our name in the publicly available records accessed by the search engine of an online genealogical database, become convinced that they are distantly or closely related to us and absolutely want to know who we are and to get to know us better.

One of the participants in a mailing list I subscribe to has actually experienced the phenomenon personally. The other day, she wrote to the list that a genealogical stalker had found her name on a well-known genealogy website and had then gone to the extent of phoning her mother (looking for her phone number, I suppose). The mother's number, by the way, is unlisted, which only highlights the level of obsession involved in the stranger's act.

Creepy but predictable, don't you think?

Alzheimer’s false scare

Icelandic company deCODEme, currently in financial straits, decided to offer clients of rival American company 23andme a nice Christmas present, allowing them to upload their 23andme raw genetic data to their website, at deCODEme.com, in order to, a few hours later, and at no cost whatsoever, have them (re)analized through the deCODEme looking glass. What a fine idea, I thought – and took instantly advantage of their offer.

Two unpleasant things then happened. First, my mitochondrial haplogroup (maternal line) suddenly changed radically. According to 23andme, I’m H7, but at deCODEme.com I was now K. Second, I was suddenly afforded the opportunity of knowing (but only apparently, as I have since learned) my lifelong-risk of getting Alzheimer’s Disease.

Concerning the first remarkable consequence of the deCODEme invite, almost immediately I received an email informing me that there had been a mistake in the interpretation of the mitochondrial data and apologizing for the inconvenience. I should wait a few days and everything would return to normal. By the way, I looked it up again this morning, and currently my mitochondrial haplogroup is back to H (simply H, which means it’s less informative than 23andme’s H7).

Concerning the second instance, I put off looking at my Alzheimer risk for days; I confess that I was afraid to see the results (you have to opt-in to access them). But this morning I learned that my inaction had probably been the best option – and for unexpected reasons: it turns out that, based on the 23andme results, deCODEme is unable to calculate that risk.

Only that didn’t keep some of those who had the audacity to opt-in to get really scary – and false – results! (see here). In short, the estimation of the risk is based on the detection of certain alterations in a gene called APOE, but 23andme doesn’t read the whole set needed to calculate it, which in this case makes the data useless – and sometimes exaggerated.

Currently, the opt-in option for Alzheimer’s has disappeared from my list of opt-in health conditions at deCODEme.com. But up till now, the company hasn’t offered any explanation for this, nor has it apologized for possibly scaring some people to death. I find this completely irresponsible.

Concerning myself, I learned something, though: I feel truly relieved not to have these results at hand for the time being, and I think that when the hour of truth comes, I may not have the courage to know it (the truth) with respect to certain particularly devastating diseases. I recently read a novel, Still Alice, by American neuroscientist-turned-writer Lisa Genova, about a case of early-onset Alzheimer’s. I manage to endure reality up to that point (I think the book is great), but if I get closer to it, I fear I might burn my wings...

Image: Drawing of neurons by Santiago Ramón y Cajal, 1899