NHGRI funds researchers to evaluate standard measures in genomic studies

NHGRI funds researchers to evaluate standard measures in genomic studies

By Geoff Spencer
Associate Director of Communications for Extramural Research

Standards can make our lives better. We have standards for manufacturing many items - from car parts to nuts and bolts - that improve the reliability and compatibility of all sorts of widgets that we use in our daily lives. Without them, many tasks would be difficult, a bit like trying to fit a square peg into a round hole. There are even standard measures to collect information from participants of large population genomic studies that can be downloaded for free from the Consensus Measures for Phenotype and eXposures (PhenX) Toolkit [phenxtoolkit.org]. However, researchers will only adopt such standard measures if they can be used easily.

That is why the NHGRI's Office of Population Genomics has launched a new effort called the PhenX Real-world Implementation and Sharing (PhenX RISING) program. The National Human Genome Research Institute (NHGRI) has awarded nearly $900,000, with an additional $100,000 from NIH Office of Behavioral and Social Sciences Research (OBSSR), to seven investigators to use and evaluate the standards. Each investigator will incorporate a variety of PhenX measures into their ongoing genome-wide association or large population study. These researchers will also make recommendations as to how to fine-tune the PhenX Toolkit.

"We want to ensure the PhenX measures are of the highest quality so that the research community uses them to expand the scope and value of their studies. Use of these standard measures will enable researchers involved in large population and Genome-Wide Association Studies (GWAS) to pinpoint the genetic and environmental contributions to diseases faster and with greater accuracy," said Erin Ramos, Ph.D., an epidemiologist in NHGRI's Office of Population Genomics and an NIH project scientist with the PhenX project. RTI International of Research Triangle, N.C. leads the PhenX Toolkit project through a cooperative agreement with NHGRI.

GWAS have identified more than a thousand associations between genetic variants and common diseases such as cancer and heart disease, but the majority of the studies do not share standard measures. PhenX standard measures are important because they allow researchers to more easily combine data from different studies to see if there are overlapping genetic factors between or among different diseases. This ability will improve researchers' understanding of disease and may eventually be used to assess a patient's genetic risk of getting a disease such as diabetes or cancer and to customize treatment.

More than 200 scientists from a variety of scientific and health disciplines selected nearly 300 standardized measures and protocols across 21 research domains for the toolkit. Research areas include demographics, cancer, cardiovascular, diabetes, environmental exposures, social environments and oral health. Currently, some of the measures most frequently downloaded by researchers include age, weight, tobacco-smoking status, air contaminants in the home environment and lipid profile.

"PhenX RISING will promote the use of PhenX measures within the genomics research community and provide us with valuable feedback about the overall usefulness of the Toolkit in real-world research settings," said Carol M. Hamilton, Ph.D., director of Bioinformatics at RTI and the project's principal investigator. "For instance, we want to know whether the standard measures can be easily integrated into ongoing studies and how we might improve the resources and tools provided by the PhenX Toolkit."

PhenX RISING investigators will also provide feedback about how likely they would be to use the standard measures again or if they would recommend the Toolkit to colleagues. PhenX RISING investigators also plan to perform data analyses across their studies, something that would not have been feasible without using standard measures.

The studies that have been funded for PhenX RISING and the NIH institute that primarily fund the existing study are:

• Ecologic Stressors, Post-Traumatic Stress Disorder, and Drug Use in Detroit
  University of Michigan, Ann Arbor, Allison Aiello, Ph.D.
  National Institute on Drug Abuse
   
• Human Translational Applications Core
  University of California, Los Angeles, Robert Bilder, Ph.D.
  National Institute of Mental Health
   
• Creating a Pediatric Imaging-Genomics Data Resource
  University of California, San Diego, Terry Jernigan, Ph.D.
  National Institute on Drug Abuse
   
• Genome-Wide Study of Cataract and Low HDL in Personalized Medicine Research Project
  Essentia Institute of Rural Health, Duluth, Minn., Catherine McCarty, Ph.D.
  National Human Genome Research Institute
   
• Genome-Wide Association Scan to Identify Risk Genes for Type 2 Diabetes in Asian Indians
  University of Oklahoma, Oklahoma City, Dharambir Sanghera, Ph.D.
  National Institute of Diabetes and Digestive and Kidney Diseases
   
• Self-Regulation Failure: Identifying and Modifying a Risk Phenotype
  Duke University, Durham, N.C., Timothy Strauman, Ph.D., and Ahmad Hariri, Ph.D.
  National Institute on Drug Abuse
   
• Determinants of Healthy Longevity in China
  Duke University, Durham, N.C., Zeng Yi, Ph.D.
  National Institute on Aging

In spring 2012, PhenX RISING investigators will meet to talk about their experiences using the PhenX Toolkit and to report the findings gleaned from their data analyses.

For general information about the PhenX program, please contact the Project Scientist Erin Ramos at ramoser@mail.nih.gov or 301-451-3706. For more information about supplemental funding, please contact Heather Junkins at junkinsh@mail.nih.gov or 301-402-0343.

Posted: December 19, 2011