Genome-wide association studies have recently been given a shot in the arm thanks to a free online toolkit courtesy of the National Human Genome Research Institute. A product of NHGRI's three-year Consensus Measures for Phenotypes and eXposures, the PhenK toolkit aims to provide researchers with a grouping of standard measurements for physical characteristics and environmental exposures of research subjects. The impetus for the project arose from a desire to enable researchers to analyze results across a range of research studies.
"What we're finding is that a lot of these studies, while they may have some really good measures — for example, diabetes — do not always have great measures of cancer or heart disease, or conversely, a breast cancer study can be wonderful on breast cancer, and include histology and slides, but they might be really bad on diabetes measures," says Teri Manolio, director of the office of population genetics at NHGRI, who helps lead the initiative. "So we thought if you wanted to actually combine these studies, it would be a shame if you had to use some really limited measure."
The answer was to arrive at measures that, while perhaps not the gold standard, were valid, useful, and not terribly burdensome. This was easier said than done. "The challenge was really limiting the number of variables that we would look at, so you ask somebody to define metabolic disease or think of all the things we could study in metabolic disease, and they say it's hundreds if not thousands of variables," she says. "But for a study that would be a pooling study or an additional study, you can't measure thousands of variables or thousands of traits, so we decided that we really just need 15, and for most of them, we've been able to get close to that number."
Manolio says another challenge with getting PhenX off the ground was convincing the experts involved to sign off on the finished product, which often required them to make concessions with the way in which particular phenotypic traits might be measured.
The initiative eventually hopes to have 20 health and disease research categories for PhenX, as well as a Facebook-like social networking platform that will enable registered users of the PhenX website to collaborate with other researchers.