FEATURE / This article was originally published in the fall 2020 issue of West Virginia Science & Research's Neuron magazine.
Each genome tells a story. Genome sequencing chronicles the ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) that carry an individual’s genetic information.
In the Genomics and Bioinformatics Core (GABC) at the Marshall University Joan C. Edwards School of Medicine, researchers use advanced sequencing technology to accurately measure the abundance of messenger RNA (mRNA) in whole transcriptome analyses and discover genetic variants in genomic sequencing studies.
“Findings from studies like these can ultimately lead to new therapeutics or lifestyle modifications that could reverse or mitigate the disease process,” said James Denvir, Ph.D., associate professor of biomedical sciences at Marshall and co-director of the GABC. “This type of research also opens the door to more personalized medicine that specifically treats the underlying genetic cause.”
The GABC primarily focuses on next generation sequencing, which includes RNA sequencing, whole exome/genome and chromatin studies. Whole transcriptome studies allow investigators to determine the abundance of all mRNAs in a cell or tissue, and therefore, are very useful in discovering genes and metabolic pathways whose regulation is changed by genetic factors, diet or exposure to drugs or other environmental factors. Whole exome and whole genome sequencing can be used to identify genetic variants (e.g. single nucleotide polymorphisms, insertions and deletions) that are present in some individuals but absent in others.
This year, the GABC acquired an Illumina NextSeq 2000 high throughput sequencer with support from West Virginia IDeA Network of Biomedical Research Excellence (WV-INBRE), a National Institutes of Health (NIH) funded program.
“The NextSeq 2000 really puts us on the forefront of high throughput sequencing technology,” said Donald A. Primerano, Ph.D., professor and vice chair of biomedical sciences at Marshall and co-director of the GABC. “We’re now able to sequence 100 RNA samples, known as libraries, in 19 hours that previously took six days with an older system. The NextSeq 2000 system also allows us to sequence samples at a much lower cost, which is essential in furthering genomic research throughout our state.”
The scope of services provided by GABC, however, goes far beyond the advanced technology. Before work begins, investigators meet with GABC staff to discuss experimental design and objectives, technical issues (e.g. biological replicates and input DNA/RNA quality and quantity), probable sequence yields, methods of data analysis and outcomes and overall cost.
The GABC is supported by funding from WV-INBRE grant P20GM103434, COBRE ACCORD grant 1P20GM121299 and the West Virginia Clinical and Translational Science Institute grant 2U54GM104942.
Photo caption: (left to right) Donald Primerano, Ph.D., Jun Fan, Ph.D., and Robin Turner, M.S., with the Next Seq2000.
Date Posted: Wednesday, December 30, 2020