The Dress, and other blogging and articles about genetics (mostly)

Posted by Sappho on March 30th, 2015 filed in Blogwatch, DNA

Sometimes it’s as interesting to find out where an odd difference probably isn’t strongly influenced by genetics as to know when it does. A month ago, when the Dress swept the Internet, 23andMe customers asked whether their friends’ perverse inability to see the fact that the Dress was blue and black/white and gold/blue and gold (I’m #TeamBlueAndGold, but I’m in the minority) might have something to do with genetics. 23andMe obliged with a survey of selected customers who had agreed to participate in research, and reported on the results here and here (including a white paper on the survey). Because 23andMe has already collected a bunch of survey information from customers who have agreed to participate in research, they were able to correlate responses to a few simple questions about the Dress (what colors do you see in this picture, what colors did you see when you first saw the Dress, do you see the colors as constant or do they shift) not only with the customers’ genes (or at least the subset that 23andMe samples), but also with other survey responses. Here is what they found.

… About 25,000 people responded, and this is some of what our researchers learned.

For one, there was no clear genetic association with seeing either a blue and black dress versus seeing a white and gold one, according to Fah Sathirapongsasuti, PhD, a computational biologist here at 23andMe.

That doesn’t mean there is no association, it just means that we didn’t find one that met our threshold for a strong association. We did see a small effect size for a genetic variant in the gene ANO6. While this may or may not be significant, it’s interesting because ANO6 is in the anoctamins gene family, which includes the gene ANO2. The gene ANO2 is involved in light perception, so this might be something that warrants further study. But as we said, the association we saw did not show a big effect. Others who’ve looked at the possible genetic influence of how people perceive the color of the dress also did not find a strong genetic association, finding, for instance, that identical twins also reported seeing different colors.

While we first looked at genetic associations with different color perceptions, we went on to see if there were other associations related to different phenotypes. The strongest association we found was with age. Our researchers found that the effect of age comes in two phases — for people up to 60 years old and for those who are over 60. According to our data the proportion of those who see white and gold increased up until the age of 60, but after 60 the proportion of those who see white and gold starts to decrease.

The white paper reports that they also found associations with where people had grown up and whether they had done shift work.

For a genetic genealogy hobbyist blogger like me, the 23andMe white paper on The Dress is fun. But the bigger financial news is 23andMe’s announcement that they will be adding a division to mine their genetic database for drug discovery

Metabolic and immune system disorders, eye disease and cancer are among conditions the company will seek to address through searching the database. Among other things, it hopes to learn from what Ms. Wojcicki calls “escapers,” people who carry a potentially deleterious mutation but don’t have any disease symptoms.

Because they aren’t sick, such people don’t show up in the doctor’s office, but they can be found in the company’s database, Ms. Wojcicki said. Determining what traits seem to protect them from disease could reveal targets, for instance, to treat people with the mutation who do get sick.

At Bio IT World, Aaron Krol reflects on this new development.

23andMe is closely associated with Silicon Valley — its most steadfast investors have been Google and Google Ventures — and that feeds into a couple of narratives about the company. One is that its business can’t be as straightforward as engaging customers in genetic research. Think of the old maxim about Google and Facebook: the user is the product. It’s tempting to level the same charge against 23andMe, which sells its Personal Genome Service (PGS) kits at little more than break-even prices.

I’ve given in to this temptation myself, suggesting in a previous feature on the company that 23andMe’s customers might not know what they’re getting into when they agree to have their data used for research. The cynical angle is that customers are being duped into sharing valuable data, and paying for the privilege. Then 23andMe spins around and sells that data to Pfizer for a handsome profit….

At the same time, it’s pretty ungenerous to 23andMe’s customer base — 80% of whom consented to participate in research, and many of whom sign in regularly to take new surveys about their health and lifestyle — to say they’re all pawns on big pharma’s chessboard….

As someone who bought my 23andMe kit at a time when I was undergoing treatment for cancer, and for whom the ability to assist in research (even, yes, research that may bring 23andMe a profit), I’m on the side of “if we’re the product, here, we’re a quite willing product.” And I’ve run into DNA cousins who are there more for the research than for the genealogy. If there are ethical issues here, they’re not ones that pit profit seeking 23andMe against naive customers, but more ones that cross lines among customers. (For instance, adoptees looking for birth families have sometimes pushed for less privacy protection, but, given that 23andMe is in the medical research business and wants willing participants, that’s not something they can get.)

Perhaps the biggest news of the past week, on the genetics front, has been the largest set of full genomes from a single population: Iceland.

Katie M. Palmer, at Wired, writes about Why Iceland Is the World’s Greatest Genetics Laboratory.

In these latest studies, deCODE sequenced the full genomes of 2,636 Icelanders, along with less detailed genetic information from more than 100,000 others, in the form of genotyping microarrays like the ones used by 23andMe that look at every 10,000 or so of the genome’s 3 billion letters. That covers almost a third of the entire population—and Iceland’s genealogical and medical records are famously exquisite. “The Icelandic system is the perfect system to do this in,” says Lisa Brooks, director of the genetic variation program at the National Human Genome Research Institute. Established by Norsemen and Celts in 9 A.D., Iceland has a remarkably homogenous population that can trace its lineage to just a few common ancestors, according to Kári Stefánsson, deCODE’s founder and CEO. That means that there’s less genetic variation, which in turn means less background noise to interfere with the identification of meaningful gene variants. In the new papers, the tally is 20 million variants, some of which have already been linked to diseases.

The Social Issues Committee of the American Society of Human Genetics and the Public and Professional Policy Committee of the European Society of Human Genetics have issued recommendations for fetal DNA tests.

A team at Johns Hopkins University has discovered a new genetic variant that causes autism.

“In genetics, we all believe that you have to sequence endlessly before you can find anything,” says Aravinda Chakravarti, a professor in the Johns Hopkins University School of Medicine’s McKusick-Nathans Institute of Genetic Medicine. “I think whom you sequence is as important—if not more so—than how many people are sequenced.”

With that idea, Chakravarti and his collaborators identified families in which more than one female has autism spectrum disorder, a condition first described at Johns Hopkins in 1943. For reasons that are not understood, girls are far less likely than boys to have autism. When girls do have the condition, however, their symptoms tend to be severe. Chakravarti reasoned that females with autism, particularly those with a close female relative who is also affected, must carry very potent genetic variants for the disease, and he wanted to find out what those were.

A sweet reflection on genetics and autism by a parent.

In Cameroon, hunter-gatherer people have more diverse microbiomes than neighboring agricultural people.

Kitty Cooper explains the basics of using your DNA test results for genetic genealogy.

DNA provides more evidence of infidelity in Richard III’s family tree.

This has nothing at all to do with genetics, but I love the Maccabeats’ version of D’ror Yikra.