Get it while it’s hot! 23andMe for $99

You may have already heard the rumors floating around and they’re all true: 23andMe is having another sale — the whole thing for $99!

Edit: No discount codes are needed. There’s an instant discount of $400 off due to the Black Friday+ sale, which will go until Christmas Monday 11/29 or while supplies last. Head on over to the store, or read on for a bit more info.

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Posts in the pipeline, and in the meantime

October’s been a busy month and so I haven’t had much time to post. But busy means interesting, and so I have lots of things to write about, it just doesn’t really get done. Some of the posts I have in the pipeline — mostly just as titles with scarce notes to remind myself what they mean:

The commenting conundrum: about where and why scientists do or don’t comment on scientific articles.

Responding to “them”: about the whos, whats, wheres, whens, whys, and hows of criticism and responding (or not) to it; mostly on the web but also off.

A detailed look into PLoS’s article-level metrics data: it’s open, so why not? And the results might just surprise you.

Thoughts from Science Commons Salon: with the amount of brainpower in that room, I’m surprised it didn’t explode. In fact, I’m surprised the whole town of Mountain View hasn’t exploded from sheer intellect yet.

So yeah, plenty to write about, sometime. I saw Pete Binfield of PLoS at the SC Salon and he joked that I was falling behind, reposting things that he’d posted a whole four days ago. Makes me want to start the Slow Blog movement…

Those posts will probably keep simmering for a little while. In the meantime, I haven’t been completely idle – in the last three weeks, I’ve written three blog posts for 23andMe‘s Spittoon on genetic association studies on glaucoma, bone mineral density, and blood-related traits. Another one is set to come out early next week. So if you haven’t been tuning in regularly to the Spittoon, now you know where else to find me!

New job and curation 101

It’s been several weeks now since I started working at 23andMe, a personal genomics company located in Mountain View, CA. Perhaps not coincidentally, it’s also been several weeks since I last blogged. The transition hasn’t been difficult, but it did take some getting used to, mentally and physically. I mean, leaving for work by 8:30am? Regular hours? Commuting??

Ok, so I really have nothing to complain about. 8:30 isn’t that early, and I could shave half an hour off each end of my commute if I didn’t choose to take advantage of bike-friendly roads, good weather, and a company-sponsored free train pass (OMG benefits!?). All in all, things are pretty much fantastic. The work environment is friendly, flexible, and laid-back; we have plenty of food and drink to keep us fueled throughout the day, and regular workouts/yoga if we need to get fired up or mellowed down (and to keep the “Free Food 15” at bay). Plus, personal genomics is a super interesting and rapidly evolving industry, so there’s really never a dull moment.

So what is personal genomics, anyway? We’ve known for a while that genetics – the sequence of DNA inside our cells – plays an important role in our form and functioning. Many diseases are caused by changes in DNA (often in genes, parts of DNA that code for proteins) that alter the normal functioning of cells, though not all genetic differences lead to negative changes. (Genetics can also tell us about ancestry – who is related to whom and the history of populations – but I won’t be addressing that in this post.) Where it gets personal is when you apply it to individuals, such as when someone gets a genetic test to determine whether they have or are at risk of developing or passing on a particular disease. Where it gets genomics is when we use high-throughput technologies to do what is essentially thousands of genetics tests at once. Put them together, and you get personal genomics.

How do we know what genetic “pieces” correspond to what conditions or diseases? The general strategy is to compare the DNA of a whole bunch of individuals that have that condition (cases) to a whole bunch of individuals that don’t (controls). As long as both groups are similar save for their case-control status, any significant genetic differences between them should have something to do with that condition. We call this a genetic association.

It turns out that there are millions of single locations in the human genome where the exact sequence of the DNA might differ between two people, and these places, called single nucleotide polymorphisms, or SNPs, can contribute to differences we can observe, such as whether you flush when you drink alcohol or how easily you put on weight. 23andMe personal genomics kit determines what your sequence is for a representative subset of SNPs. Many are already known to be associated with certain conditions, and new research is being done every day to uncover more and more of these associations.

So what exactly do I do at 23andMe? My official job title is “Scientist, Content Curation”. Curation, I’ve found, is not very familiar to most people. Most people probably know that there is such a thing as a museum curator, but might not know what they do. Hardly anyone has ever heard of scientific curation. (And I thought explaining what I was studying as a grad student was hard! Biomedical informatics, anyone?)

But it’s really not that complicated. The essence of curation is almost always the same: the selection, acquisition, and management of content. What that content is differs depending on the field – for example, an art curator might look for and organize artwork for exhibition in a gallery, while a curator in the “Ancient Civilizations” department of a museum may be in charge of acquiring, managing, and presenting archaeological artifacts.

In science, curation involves organization of scientific knowledge and data. An area where this has been especially important is the life sciences, as the amount of information being generated by high-throughput experiments, large-scale projects, and scholarly publishing has skyrocketed. In order to manage this information and render it useful to others, the field of biocuration was born. Any database that organizes scientific knowledge – UniProt (the Universal Protein resource), FlyBase (database for that very important model organism, Drosophila), PharmGKB (a database focused on how genes and drugs interact), etc – depends on curators to keep the information up to date and easy to use.

And so it is with 23andMe. The genetic testing kit is one part of the product, but the other part is information – what knowledge is there about associations between the SNPs on our platform and health traits or conditions? What does your particular data mean? The science is far from exhausted on this subject, and in order to stay up to date with the research, 23andMe spends a lot of effort on curating the scientific literature for new genetic associations and presenting the information on our website for our customers.

Day to day, this means that we keep track of papers recently published in scientific journals, skim through to find ones that may have promising findings, and then vet these more thoroughly to see if they pass our stringent scientific standards. If they do, we extract the bits of information we need and put the bits together in reports that will eventually become part of the content on the website. It’s a job that definitely benefits from an organized system and an eye for detail – as well as a sense of curiosity.

After three weeks on the job, I think I’m starting to get the hang of the day to day work. Since my work is even more directly tied to the literature than it was as a graduate student in academia, I’m also developing an enhanced awareness of issues surrounding scientific publishing – those related to standardization and metadata, publication bias towards positive results, and closed vs. open access. The hardest aspect of transitioning from academia to industry hasn’t been the regular schedule, or the work environment, or the work itself, it’s been getting used to being on the other side of the pay-wall of scientific journals.

But that’s a rant for another time. ;)

The home stretch, and next steps

Photo by zizzy on Flickr

Photo by zizzy on Flickr

I’ve been neglecting my blog lately, through no fault of its own. There’s been lots going on, and lots not going on as a result, so I just wanted to post a quick update.

I’m a little over a month away from handing in my dissertation, which means many hours that might have gone towards writing blog posts instead went towards writing the darn thing. Learning LaTeX wasn’t nearly as bad as I thought it would be, especially with a handy Stanford thesis template and some web resources. I just handed a copy of the draft to my committee for comments and hoped for a brief respite to take care of some random bits (like all those appendices, code documentation, etc…).

Of course, my advisor says, “Now that you have nothing to do, why don’t you write a paper?” So now I’m writing a paper… which is probably a good thing, since there does seem to be enough material for a paper, and I might as well write it while I’m in so-called “writing mode”. I have the feeling by the time this is over, though, even Twitter will seem like too much writing!

Most of the rest of the time is spent on activities related to Ultimate, which started up about a month ago. There’s been two tournaments, some practices, various pickup games which are pseudo-mandatory for me, and various workouts to get in shape for the season.

Even with those two things, there’s probably ample time to squeeze in a post or two. But the mental energy isn’t quite there. And maybe it’s also because I still spend a couple hours cooking and get 8-9 hours of sleep most nights. Some things just can’t be sacrificed. Like home made strawberry shortcake with freshly whipped cream. :)

So that’s mostly what I’ve been up to the last couple months. The next month will probably be much the same. And then?

Well, I think it’s official enough now that I can announce it: I’ve accepted an offer to join 23andMe as a scientific curator in late August! I’m very excited about working with them and hopefully will be able to contribute across multiple facets of the company.

The end – and a new beginning – is in sight!

Health information in an information age

From NYC DOHMH website

From NYC DOHMH website

A colleague of mine presented an interesting bioethics issue for our lunch time seminar today. It was a discussion motivated by the New York City Department of Health’s recent initiative for diabetes prevention, which adds an amendment to the health code requiring laboratories to report results from a blood sugar test called A1C to the Dept of Health and Mental Hygiene*. High A1C corresponds to high blood sugar. Test results are entered into the A1C registry; medical providers will receive quarterly reports listing patients and their A1C level and patients with high A1C levels might be notified in the mail about the finding.

This initiative is striking in two ways. First, it collects and distributes patient health information without knowledge or consent from the patient. This isn’t necessarily new – a lot of health information is collected and used in the name of public health. Either the NYC DOH is casting diabetes prevention as a public health concern or it is setting a new precedent for the use of health information. Second, it circumvents the usual transmission of health information from provider to patient by sending the patient test results directly, and there’s a question whether it is ethical to send patients this information without the context that their health provider could give.

As part of the discussion, we looked at examples of an emerging grey area for patient health data. GoogleHealth, Microsoft HealthVault, and 23andMe are all services that collect information about a person’s health (or genetics) through that person’s consent, but they reserve the right to use that information for reasons they see fit, nominally research. There then becomes what looks increasingly to be a slippery slope. Medical providers at one end who are bound by HIPAA rules, public health activities, and at the other end, commercial companies who do not provide medical services but handle patient health data. How important are medical providers when you dispense health information? Should these companies be regulated by HIPAA (or some variation), i.e. is health information qualitatively different from other types of data? Is it ok for the government to monitor your health and distribute that information without your knowledge (especially in situations of low public health risk, at least to others)?

Obviously, we are moving towards more access and more information. But there seem to be many complex issues when health information is involved. Should it be treated differently?

* By the way, does anyone else think the term “mental hygiene” sounds dated?