Monday, November 23, 2009

Worries

When new scientific research is released, 23andme updates our genetic info with so-called “clinical reports”. The latest one of these didn’t please me at all.

The reason is I was told that my genetic risk of having something called atrial fibrillation (AF) is higher than average (20.5 percent instead of 15.9 percent in the general population). The estimated hereditary component of AF is around 60 per cent, which means that genes weigh more than environmental factors.

AF in itself is no big deal, but being a type of cardiac arrhythmia – and especially when combined with certain other risk factors (like hypertension or diabetes) – it increases the risk of having a stroke. And that I certainly find worrisome.

AF symptoms: palpitations (racing heart, which I experience not unfrequently); lack of energy (who doesn’t?). All this to say that although it doesn’t mean I have AF, it makes me wonder.

One way to reduce the risk of stroke is treatment with drugs that dilute the blood, preventing potentially dangerous clotting when the arryhtmia hits. One of those drugs is warfarin – and the biggest problem with this drug is determining the right dosage for each person. Too much of it can lead to internal bleeding, to little won't serve its purpose.

Precisely where warfarin is concerned, 23andme also provided me, some time ago, a piece of relevant information about the most likely reaction I should have to it if I ever had to take it. Once again, my genes say that I am apparently more sensitive than average to this drug – which means that I might have to take smaller quantities of it to be on the safe side.

For the first time since I had my genes tested at 23andme, I feel the need to talk about this to my doctor when I next see him. Is this the empowerment they’re always "selling" us as being THE big promise of personal genomics? For the time being, I feel mostly a little unnerved.

Monday, November 9, 2009

Good news


I received the following message, posted on Family Tree DNA website, through one of the mailing lists I subscribed:

"An academic research team, including our chief mtDNA scientist Dr. Doron Behar, is collecting mtDNA haplogroup H full sequence results for a population study. The study will update the haplogroup H tree and provide information on the distribution of subclades. Every sample used will help the research team to develop and resolve the H haplogroup tree. Your mtDNA full sequence results qualify for possible inclusion in this study."

Which means that Israeli scientist Doron Behar and his team are going to start analysing the details of the mitochondrial haplogroup (matrilineal descent) that goes by the letter H, to which I belong (my sub-haplogroup, or subclade, is H7, as I have already mentioned here). Finally!

I heard about Behar’s work for the first time in 2006 (he was then at Rambam Medical Center in Haifa), when he and his colleagues published an amazing paper in the American Journal of Human Genetics. As I already wrote in a previous post, through the genetic study of mitochondrial DNA, they discovered that nearly half of Ashkenazi Jews (“German” Jews) in the world today are descended from just four “founding mothers”, most likely Hebrew women from the Middle-East, who lived in Northern Europe, in what is now Germany, one to two thousand years ago.

Apparently, Behar, who as the message says is chief mitochondrial DNA scientist at Family Tree DNA (www.familytreedna.com), has now decided he has enough data to go on, from clients there, to undertake the same kind of study on haplogroup H. And he is inviting participation.

I think this is a fantastic example of how scientists can put to good use individual genetic data (without disclosing anybody’s identity) to further our understanding of the migration routes of human populations through the ages.

The message, though, is only visible to those who have had their mitochondrial DNA fully sequenced at FTDNA - and who belong to mitochondrial haplogroup H.

Since I tested with 23andme (which does not offer full sequentiation of mitochondrial DNA), I won’t be able to participate personally. But I’m really curious about what the results will reveal about my own past.

Image: Mitochondrial haplogroup H tree - Fonte: familytreedna.com

Monday, July 20, 2009

Paternal Haplogroup: I

My brother ended up doing the Y-chromosome genetic test to determine our direct patrilinear descent (and I thank him dearly for that). The answer that came back a few days ago from GenoMed, the Lisbon-based company which carried out the test, was: haplogroup I (defined by a single mutation called M170).

The GenoMed site explains:

The first populations belonging to group I originated in Southern Europe, immediately before the last Ice Age. Their ancestors arrived in Europe through a migration route starting in the Middle East and ending in the present-day region of the Balkans. (…) During the Ice Age (20 to 12 thousand years ago), these populations remained confined to climatic refuges predominantly situated on the shores of the Dead Sea and in the Balkans. Later, when climatic conditions improved, (…) they started reclaiming the land and spreading their offspring all over Europe.

Then:

Today, group I represents nearly one fifth of the European genetic pool. (…) Group I lineages predominate in Scandinavia and in the Balkans. The highest frequencies (nearly 40%) are detected in the populations of Herzegovina, Croatia, Bosnia, Sardinia and Scandinavia.

And finally:

The genetic group I is not usually associated to Jewish ancestrality.

This last sentence reminded me of a memorable scene in the Woody Allen classic Annie Hall. In it, the main character, Alvy Singer, makes the following remark during a flashback to his childhood: “My grammy never gave gifts. She was too busy getting raped by Cossacks.”

I apologize to all those who might be shocked by the very bad taste of this joke, by its political incorrectness, etc., etc.. But the truth is that the idea Allen was playing with in that sentence undoubtedly corresponds to the tragic reality experienced by many Jewish families during the blood-shedding pogroms that took place in Ukraine and Poland during the nineteenth century and the beginning of the twentieth (and forced so many Jews to emigrate to the Americas).

As far as I know, luckily nothing of the sort happened to any of my grand-mothers, great-grandmothers and great-great-grandmothers – but before that, I can’t guarantee it didn’t.

My family’s genes might thus be telling a story of persecution and violence.

Image: DNA Root Tester

Friday, June 26, 2009

Should we fully share our genetic data?


I subscribed to a genetics mailing list and through it, I was asked on several occasions by other participants to send my raw genetic data for this or that chromosome (that is, the sequence of letters that resulted from my genetic testing).

A lot of people are interested in this kind of information, since certain comparisons between individuals can only be carried out using ad hoc software. There are many amateur geneticists out there – and some of them have developed little computer programs, more or less easy to use, to extract information from the raw DNA data – and which are of particular interest for the search of common ancestors when the people involved didn’t have their genes read by the same company.

I must confess that I have ignored these invitations/requests. I confess that the idea that my genome, even a mere part of it (or to be precise, of the 500 thousand letters of my DNA that were read by 23andme when I got tested) could be circulating in cyberspace, without my knowing exactly where, gives me the creeps.

A few days ago, however, I attached all of my raw data (to which I have access) to an email in order to participate in a scientific project that I find very interesting. But when, just for an moment, I thought I had sent it to the wrong email address (in fact, to the public mailing list I just mentioned), I became really nervous. Luckily, it was only a false alarm…

A few months ago, in an article in the New York Times, well-known scientist Steven Pinker asked himself what could be the consequences of publishing one’s genome (and in his case, his whole genome, since he is participating in a full-sequencing project).

His answer boiled down to this: if an insurance company ou any other entity wanted to to read secrets from our genes to infer our individual characteristics, the effort would be doomed from the start. Genes offer essentially statistical information, which apply to groups of people. And, apart from a few exceptions, their contribution to every disease and physical or psychological trait is almost inextricable.

Many of the dystopian fears raised by personal genomics”, Pinker wrote, “are simply out of touch with the complex and probabilistic nature of genes. Forget about the hyperparents who want to implant math genes in their unborn children, the “Gattaca” corporations that scan people’s DNA to assign them to castes, the employers or suitors who hack into your genome to find out what kind of worker or spouse you’d make. Let them try; they’d be wasting their time.

This is true in most cases. But what about those serious genetic diseases that depend on only one gene – and owing to which and insurance company, for example, could rapidly determine our individual propensity and deny us an insurance policy – or a potential employer refuse to give us a job? Even in that tiny bit of DNA contained in our mitochondria, which is used to determine our matrilineal ancestry, there are some disease genes – some of which haven’t yet been identified.

When I had my DNA tested and wrote about it, I knew I could be unveiling things that could one day “be used against me” in a worst-case scenario. After all, the exploitation of genetic data by third parties is virtually devoid of regulation. But I decided to take that risk because my curiosity was greater than my fear of the hypothetical risks involved – and because I thought it was important to write on the subject.

As to the scientific project I said I’m involved in – which is being done by scientists at Harvard I know that they will use it, together with that of many other people, to search for clues to the ancestrality of a community of people as a whole (I’ll say more about it one of these days). But they will not reveal any of my individual traits or results to anyone other than myself. To ensure this was clear on both sides, I had to sign several consent forms where they, on their side, specify extensively what they are and aren’t allowed to do with my genetic data.

But sending out my genetic “letter soup” in more informal terms is altogether a different matter: we know information can spread like a virus in the Internet and end up in the wrong hands. I’m utterly sure that the people who are asking me to send them parts of my raw data are well-intentioned – there’s absolutely no question in my mind about it. But I feel that accepting to do it means that I will cease to have control over that data. And for the time being, in spite of the remoteness of the risks this entails (in this I agree with Pinker), is a step I’m not ready for just yet.

Photo credit: Dollar Bin/Flickr

Monday, June 15, 2009

An interesting little sofware

EURO-DNA-CALC is a piece of software that allows anyone who’s been gene-tested by 23andme or its rival company, deCODEme in Iceland, to calculate the mix of Northwestern European, Southeastern European and Ashkenazi Jew any person of European descent carries in his or her genes.

I didn’t immediately understand how this worked. To download the program, you have to go to its inventor’s Dienekes Pontikos’ Anthropology Blog – more precisely here.

Calculations are based on data from a study by Alkes Price, of Harvard U. and colleages, published in 2008 in PLoS Genetics under the title: Discerning the ancestry of European Americans in genetic association studies.

In that study, the authors define Northwestern Europeans as people who originally came from Sweden, the UK or Poland, Southeastern Europeans as coming from Greece, Italy or (stretching the Compass Rose a bit) Spain, and Ashkenazi Jew as coming from the general region of modern-day Germany.

When you read the software’s README.txt file, you learn that you need to fetch another software, which is the one which will actually do the statistics and calculate the estimated contributions of each of those three ancestral populations to your genome. That’s the part that took me some time to figure out… But I eventually did; it’s all there, you just need to read it carefully.

Then you download your raw data file from one of the above mentioned company sites (both offer that functionality), and apply the software to the data exactly as specified in the instructions.

In my case, it came up with this pie chart:

And this caption:
> EuroDNACalc("23andme")
[1] "NORTHWEST EURO: Maximum Likelihood Estimate=17% Interval=[0, 34]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=0% Interval=[0, 36]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=83% Interval=[61, 100]"

I have no idea of the scientific validity of such a result – and I don’t even think it’s much use either, but there it is.

Thursday, June 11, 2009

And the seven finalists are...

seven other blogs.

I wasn’t selected for the final of the 3QD Science Prize 2009, despite my post being the second most voted by the public.

Many thanks to all those who voted for me!

Tuesday, June 9, 2009

Books from a lost world

A few days ago, I ordered two books which mention the town of Derazhnia, in Ukraine, where my paternal grand-mother, Mania Rosenblatt, was born in 1895.

The Nazis slaughtered the whole Jewish population in that town – around 4,000 people. Today, a few typical Jewish houses from that lost word are all that remains – together with a sort of stone pyramid that marks the site, in the nearby woods, of the massacre and of the mass grave where women, men and children were thrown, one on top of the other, after they were shot, some of them still breathing.

One of those books, The Road from Letichev - The history and culture of a forgotten Jewish community in Eastern Europe, by David A. Chapin and Ben Weinstock, is a detailed account, in two volumes, almost individual family by individual family, of the Jewish inhabitants of that area.

I also ordered a book of short stories by Yiddish author Sholem Aleichem (in English, Tevye's Daughters: Collected Stories of Sholom Aleichem) one of which, under the title “The German” that takes place in Derazhnia (which had a very important train station)

Last but not least, but on a different subject, Maurice Rosenblatt and the Fall of Joseph McCarthy, a book by journalist Shelby Scates from the Seattle Post Intelligencer. One of these day I will explain here what Maurice Rosenblatt – a famous lobbyist who was a central character in the fall of mccarthyism in America – and I have in common.

Photo credit: Alexandra Laignel-Lavastine