Web-based, participant-driven studies yield novel genetic associations for common traits. N. Eriksson1, J. M. Macpherson1, J. Tung1, L. Hon1, B. Naughton1, S. Saxonov1, L. Avey1, A. Wojcicki1, I. Pe'er2, J. Mountain1,3
1) 23andMe, Inc., Mountain View, CA; 2) Department of Computer Science, Columbia University, New York, NY; 3) Department of Anthropology, Stanford University, Stanford, CA.
Despite the recent, rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data.
We report on initial results from a participant-driven study of 22 common traits based on a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design.
We present novel associations for hair curl, "asparagus anosmia" (the inability to smell the methanethiol produced after eating asparagus), and photic sneeze reflex. For hair curl, we identify two independent SNPs: rs17646946 (p-value less than 10-28, near TCHH) and rs7349332 (p-value less than 10-8.4, in WNT10A). For asparagus anosmia, we identify one SNP in a region of olfactory receptors, rs4481887, with a p-value less than 10-16. For photic sneeze reflex, we identify one SNP, rs1040173, with a p-value less than 10-9.7. In order to validate the web-based, self-reporting design, we have in addition replicated associations in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, MC1R, TYR, TYRP1 and ASIP for hair color, eye color, and freckling.
The other traits analyzed in this study include laterality preferences (handedness, footedness, ocular dominance, and hand-clasp), simple physical characteristics (whether participants have had cavities, have worn braces, have had wisdom teeth removed, have astigmatism, wear glasses, have attached earlobes, and suffer from motion sickness while riding in a car), and personality traits and preferences (optimism, a preference for sweet versus salty food, and preference for night-time versus morning-time activity).
Secondly, even if it proves impossible to compete with academic researchers in the medical genomics space, 23andMe and deCODEme (but not Navigenics) do have a fairly good fall-back position: they can generate information about things that fascinate the public, but are difficult to get funding for in the public arena. I'm talking, of course, about both genealogy/ancestry testing and the genetics of normal variation (e.g. pigmentation, handedness, attached versus detached earlobes, that sort of thing).
Genetic genealogy and ancestry testing are huge markets, and 23andMe already seems to do them better than most other companies in the space - certainly their interface is slick, and their investment in this whole-genome analysis of almost 1,000 genetically diverse humans performed by Stanford University researchers demonstrates their commitment to this area. In addition, 23andMe's customer base will give it substantial power to uncover the genetic determinants of many variable traits that would seem trivial to a grant committee, but that customers would pay good money to explore - especially once scans become cheap enough to run on multiple family members.
"in Hawaii for most of the next couple of weeks"
I assume you mean days :)
Handedness in particular is a fascinating trait with some significant medical implications regarding lateralization of the heart. It should be ripe for this sort of analysis. A few years back, AJ Klar had an intriguing theory about handedness and hair whorl; ideas on this subject are under "Related articles" at the PubMed page of this 2007 paper.
Nice place for a conference.
they will eventually use genetics to predict shopping habits and feed personalized ads to the screen according to the alleles
The devil is in the details of that little abstract my friend.......
Have fun in Hawaii, I miss Lanai! And Kapalua.......
Hot and sunny? I'm sure I couldn't stand Hawaii. Hope you enjoy it~
@wei: How would they pull off personalized ads? You underestimate the effect the environment has on development
Here's a man-bites-dog story in today JAMA: "Implications of Hypertrophic Cardiomyopathy Transmitted by Sperm Donation", by BM Maron et al. This useful MedPage synopsis of the case says that the HCM was caused by a previously-unknown mutation in beta-myosin heavy chain, Arg169Gly.
When he donated sperm in 1990/91, the man was healthy and had no knowledge of underlying heart disease.
In an accompanying ethics piece, commenters recommend expanding donor screening to include markers of genetic diseases, and the establishment of a registry.