Tag: Genomics By Press Release Award

Sorry – just had to make up that little title because I had a funny conversaiton with someone where I was trying to say, concisely, that Ryan Gregory, who has a nice blog called Genomicron, had blogged about how Science Magazine had written an article where they referenced my blog about “Genomics by Press Release.”

But I was tired and it did not come out so well when I said “A science blogger wrote about science blogging and how Science wrote about my blog”. And the person just stared at me.

Anyway, all I know now is that it is a lot easier to talk about when Nature writes about “science” blogging

Ooh. Ahh. That is what we should all be saying as it has been announced that the first “female” genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman’s genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that thethere is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports “”No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.”) This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say

“If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.

I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say

Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings

And for this, Lieden University is becoming the recipient of my second “Genomics By Press Release Award.” (see my first one here, where interestingly, the discussion of sequencing a woman’s genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

Well, I have tried to hold off giving out awards here since I kind of botched my last attempt at this. But here goes.

Yesterday, researchers in South Africa announced that they had sequenced the genome of a XDR strain of the bacterium (Mycobacterium tuberculosis) that causes TB. I sniffed around this story because someone who used to work for me, James Sakwa, was mentioned in some of the stories.

The stories proclaim how quickly the researchers were able to sequence this genome with quotes like

(It) took us just over a week, using other technology it would have taken up to a year,” he told AFP.

This sounded a lot like other claims of rapid genome sequencing … and I was skeptical since just doing some shotgun sequencing, with whatever method, does not lead to a complete genome. Alas, it looks like my skepticism is valid. The AP reports

The complete genome sequencing data has not yet been shared with other scientists. Previous tuberculosis strains have already been mapped, and some experts are uncertain how quickly the research will result in new diagnostics or treatments.

So – there is apparently no paper associated with their work. And the data is not being shared. So in that spirit, I am announcing here that I have sequenced the genome of Albert Einstein Marie Curie and Al Gore Barbara McClintock this morning on my new EXCERCYCLER machine we invented here in Davis. It is a new green sequencing technology that is powered by a bicycle and the sequence data is generated by feeding pieces of DNA into the front derailer and sequence comes out of the back derailer. See hazy image below.