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

Monday, June 8, 2009

Journey to my Genes second most voted

Twenty science blog posts have been selected for the semi-finals of the 3QD 2009 Prize in Science.

As you can see here, My Genes and Me: Journey to My Genes, was the second blog post most voted by the public.

To all those who voted for it, my sincerest thanks.

On June 11, seven finalists will be announced – among which scientist Steven Pinker will then have to choose three winners by June 21.

Wish me luck!

Friday, June 5, 2009

Those never-ending lists

I’ve been trying for days (I should rather say nights) to find my father’s and his family’s names in the Hamburg ship lines passenger lists that sailed for Buenos Aires in the year 1925 (in this picture of the Nansen passport which allowed them to leave Poland, he’s the baby, on his mother’s lap, with his older brother on one side and an aunt on the other). The only clue I have for their emigration date is that my father was around six months old at the time – so they must have left at the end of that year.

The website has all that stuff in a database – or rather, almost all of it, since for the period I’m looking at, they only have scanned images of the ledgers containing those records. They’ve been digitized with the best possible quality – which sometimes means no quality at all. Imagine thin, ancient pages, frequently glued together and full of ink blots. Some you can easily read, others are a mix of words written in both directions (the ink having passed through the paper or from one page to next), and they are basically unreadable. This last week-end, I browsed through a thousand or so pages, hand-written or typed, large, small, sometimes wrinkled (you can judge for yourself from the images below!). I haven’t found anything yet, but I’m planning to keep on reading. I’ve become somewhat knowledgeable at detecting potentially relevant data in this sea of paperwork.

Tuesday, June 2, 2009

Overturning the Mosaic Law through genetics

The rabbinical law of Israel, or Mosaic Law, considers as Jewish (even if he or she practices another religion, even if he or she doesn’t have a clue) anyone whose mother was Jewish, and who in turn had a Jewish mother, and so on and so forth, straight back to Adam and Eve (or rather, just Eve).

David Goldstein, from Duke University (whom I already mentioned), specializes in the analysis of mitochondrial DNA – that little bit of our genetic heritage that comes down to us exclusively from our mothers, and to them from their own mothers, etc. – that is, by direct matrilineal descent. And ironically, through genetic studies, Goldstein is questioning the traditional matrilineal view of Judaism.

Genetics revealed that there are currently a few scores of haplogroups (genetic lines) of mitochondrial DNA in the world, each one derived from a “founding mother” who lived thousands of years ago (and each one of these mothers being, in turn, a daughter of the “Mother of all Mothers”, the so-called mitochondrial Eve, who lived in Africa some 200 thousand years ago).

Through a genetic analysis of mitochondrial DNA, Goldstein discovered, in 2002, that the mitochondrial DNA of Jewish people appears to be derived from that of local populations living in Europe thousands of years ago – and not from any hypothetical Jewish “ancestral mothers.”

I can illustrate this with my own example: I’m Jewish, and the analysis of my genes shows that I belong to mitochondrial haplogroup H7, a subgroup of haplogroup H, itself the most common haplogroup of people of European ancestry living today, be they Jewish or not.

Meanwhile, the situation is completely different when one considers the Y chromosome, which is inherited exclusively by men, and exclusively from their fathers (women don’t have a Y chromosome, as this is the defining chromosome for males).

Well, in 2000, Michael Hammer, at the University of Arizona, showed that the Y chromosome of Jewish men seems to have come down from a very small number of middle-eastern “founding fathers”, different from those of other populations.

Golsdtein’s theory actually explains the double genetic state of affairs configured by the unspecific characterisctics of mitochondrial DNA and the very specific ones of the Y chromosome.

His theory, as an article in The New York Times explained a few months back, is that European Jewish communities were in fact founded by Jewish men who migrated to Europe from the Middle-East and then married local women. These women weren’t Jewish to begin with: they converted to Judaism as they got married.

The Mosaic Law has thus been overturned by the laws of genetics.

However, in 2006, a team led by Doron Behar, of Rambam Medical Center in Haifa, Israel, discovered – once again, through the genetic study of mitochondrial DNA – 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. For those Jews, maybe the Mosaic Law still makes some sense.

Anyway, the bottom line is that part of the fist Jews who migrated to the European continent moved from the Middle-East to Europe with their whole family, while others travelled alone and founded a family in loco. Which, far from being unusual, is after all very much your garden-variety immigrant story.

Image: Study for The Great Jewish Bride (credit: Endless Forms Most Beautiful/Flickr)

Monday, June 1, 2009

I've been nominated, now you can vote for me!

It is with great pleasure that I can announce that my post , Journey to my genes, has been nominated for the 3 Quarks Daily 2009 Science Prize. Thanks to all those who made this possible!

Now it’s time to vote, which you can do here. Just select My Genes and Me: Journey to My Genes from the list and then click Vote at the bottom of the list.

Final results will be announced on the website on June 8th. The winners, on June 21st.