Scientists gathered for NIEHS Genomics Day May 10 to showcase the capabilities of the core laboratories and promote discussion of experiments underway at NIEHS.
Genomic and epigenomic studies are increasingly vital approaches to better understanding everything from embryonic development to the subtle impacts of environmental exposures that may lead to disease. Technologies in both fields are rapidly expanding. Genomics is the study of DNA changes, and epigenomics is the study of changes to DNA that do not affect the underlying genes.
The day was anchored by a keynote presentation from Stephanie London, M.D., Dr.P.H., head of the NIEHS Genetic Susceptibility and the Environment Group. Her talk was complemented by six oral presentations and 68 posters, presented by researchers and trainees in the NIEHS Division of Intramural Research, its Clinical Research Branch, the National Toxicology Program (NTP), and vendors.
Helping to streamline services
“Genomics day lets you pay attention to what people are doing at NIEHS, and the newest and best technologies offered, because genomics technology moves at light speed,” said lead organizer Kevin Gerrish, Ph.D., director of the NIEHS Molecular Genomics Core Laboratory. He highlighted his core’s newest technologies and techniques, including developing methods to isolate cell-free DNA from plasma and serum, and high-throughput extraction of nucleic acid from tissue samples.
Gerrish was followed by Guang Hu, Ph.D., from the Epigenomics Core, who discussed how the laboratory has streamlined its service by offering web-based project submissions. The core has also recently acquired the NOVA-Seq system, which increased its sequencing capacity ten times while allowing for deeper sequencing of these samples.
Hu also described the core’s support for studies throughout the institute that involved sequencing the genomes of single cells.
Each of these studies involves large amounts of data. Jian-Liang Li, Ph.D., director of the Integrative Bioinformatics Support Group, discussed the latest techniques developed by his group to handle data from these experiments. The bioinformatics group supports researchers at NIEHS by analyzing data and developing novel methods of analysis. For example, Li said they are developing deep-learning approaches to help better understand the data being generated.
Epigenetics as a biomarker of smoking exposure
DNA methylation, which is one type of epigenetic change, may be affected by substances an individual is exposed to. During her keynote talk, London discussed the changes in DNA methylation that her group has associated with smoking exposures.
London used large DNA sequencing data sets from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) and the Pregnancy and Childhood Epigenetics (PACE) consortia to compare methylation with exposure to smoking.
The researchers observed DNA methylation changes in adults who smoke. They also found distinct differences in newborns of mothers who smoked throughout their pregnancy.
That study established DNA methylation as an excellent biomarker of environmental exposure. The same approach is now being used to study whether DNA methylation may point to other exposures, such as heavy alcohol use and maternal folate exposure.
(Cody Nichols, Ph.D., is an Intramural Research Training Award fellow in the NIEHS Genetics, Environment, and Respiratory Disease Group.)