On the Day of Caring this year, CPHG volunteers headed out to spend the morning working on a project at Fluvanna Middle School. Since their move in 2012 into the old high school building, FMS has been gradually working towards reclaiming the old Flying Flucos football stadium. No longer used for high school football games, the press boxes and other structures around the stadium needed to be updated with a fresh coat of paint. The school supplied the paint, rollers, and brushes, the CPHG volunteers supplied the labor, and so together they accomplished the goal. The team left that day with the stadium area looking much better than they found it.
Caroline Brorsson, a post doctoral research fellow at the University Hospital Herlev in Copenhagen, Denmark spent 3 months this summer as a visiting scholar at the Center. Brorsson’s work involved collaborating with other researchers at UVa, and analyzing ImmunoChip genotyping data on Danish type 1 diabetes cohorts. The cohorts included almost 3400 diabetic cases and 2000 healthy control individuals. The samples included in this study have been collected from different Danish sources. The largest cohort consists of samples from a nation-wide biobank for children who are diagnosed with diabetes before the age of 17 years. The biobank is connected to the national diabetes register, which collects baseline and follow-up data from all diabetes clinics in Denmark. A second cohort consists of long-standing diabetic cases with and without diabetic complications. This cohort has electronic medical records (EMRs) available and will be part of an ongoing collaboration with the Technical University of Denmark with the focus to mine the data of the EMRs and combine with genetic data. The last cohort consists of a unique multi-ethnic and Danish collection of children with diabetes who have been followed closely for the first year after disease onset. Brorsson’s research focus is to correlate genetic variation with baseline and longitudinal clinical and biochemical data for these cohorts with the aim to better understand differences in disease phenotypes and disease progression.
During her visit, Brorsson also had the opportunity to explore Charlottesville and the surrounding area. She especially enjoyed the local restaurants and micro-breweries, the Farmers’ Market, Fridays after Five concerts, and hiking the mountains of Shenandoah National Park. Since returning home, Brorsson continues her work at University Hospital Herlev in the research group of Professor Flemming Pociot, focusing primarily on the genetics of type 1 diabetes.
Kaity Allen (second from right) presented two papers at the 7th Extraordinary International Symposium on Recent Advances in Otitis Media in Stockholm, Sweden.
Kaity Allen, a CPHG/BMBG graduate student, was invited to speak to the Deafness group at the Mammalian Research Council at Harwell, in Harwell, England. Allen presented the project “Honing in on genetic determinants of chronic otitis media with effusion.” The Mammalian Research Council is an international center for mouse genetics that utilize mouse genetics and functional genomics to study human disease. From there, Allen attended the 7th Extraordinary International Symposium on Recent Advances in Otitis Media in Stockholm, Sweden. This biennial Symposium was held June 12-16 and addressed topics concerning research and patient care of otitis media and deafness. Allen presented two talks entitled “Fine mapping risk variants of chronic otitis media: targeted resequencing approach with follow up genotyping” and “Replication of SNPs from the Raine cohort GWAS of OM in a family population of chronic otitis media with effusion and/or recurrent otitis media (COME/ROM).” Finally, Allen attended the Keystone Symposia on Human Genomics and Personalized Medicine held also in Stockholm, Sweden June 17-21 which addressed topics concerning clinical genomics, personalized medicine, pharmacogenomics, microbial genomics, and more. Allen presented a poster entitled “Bacteria in the nose of young adults during wellness and rhinovirus colds- detection by culture and microarray methods in 100 nasal lavage specimens.”
Since Allen’s return to the U.S., papers from two of the presentations have been published. A Genome-Wide Association Study of Chronic Otitis Media with Effusion and Recurrent Otitis Media Identifies a Novel Susceptibility Locus on Chromosome 2 appears in the August 23rd electronic edition of Journal of the Association for Research in Otolaryngology : JARO. This GWAS study was also featured on MDLinx, an online resource that helps healthcare professionals stay current with the latest articles relevant to their work. The paper from Allen’s poster presentation Bacteria in the nose of young adults during wellness and rhinovirus colds: detection by culture and microarray methods in 100 nasal lavage specimens was published electronically June 25, 2013 in International Forum of Allergy & Rhinology.
The recent Big Data Summit 2 held at UVa, and hosted by UVACSE and the Office of the Vice President for Research, included a talk on computational genomics by CPHG Assistant Professor Aaron Quinlan. The purpose of the summit was to address the issues of data, answer questions about plans for data management, analysis, and visualization, and to create opportunities for collaboration among the UVa big data community. Dr. Quinlan also recently taught a course on Informatics for High-Throughput Sequencing Data as part of the Canadian Bioinformatics Workshops (CBW) series offered by Bioinformatics.ca in Toronto, Ontario. Held in June, this course was geared for graduate students, post-doctoral fellows, clinical fellows and investigators involved in analyzing data from HT sequencing platforms. Lastly, Dr. Quinlan presented a talk on the Quinlan Lab’s new GEMINI software, a flexible Python analysis framework for exploring human genetic variation, at SciPy 2013, the 12th annual Scientific Computing with Python conference. The conference was held in Austin, Texas and gave attendees the opportunity to present their current projects, and to learn and collaborate with others who use open source Python software in the fields of mathematics, science, and engineering.
Assistant Professor Ani Manichaikul was awarded second year funding of an Emerging Research Grant from the Hearing Health Foundation. The goal of Dr. Manichaikul’s study, “Susceptibility to chronic otitis media: translating gene to function,” is to find genetic factors that increase risk for chronic otitis media with effusion and/or recurrent otitis media (COME/ROM) in children. The discovery of causal variants would increase knowledge of novel genes and pathways involved in COME/ROM pathogenesis. In the long term, the research findings are expected to improve the clinical prevention of chronic infections, thus decreasing pediatric antibiotic use, surgery, and deafness. Dr. Manichaikul is working on this study in collaboration with her colleagues in the Center, Associate Professor Michele Sale, and graduate student Kaity Allen.
The Hearing Health Foundation is the largest private funder of hearing research with a mission to prevent and cure hearing loss by advancing research efforts. Since being established in 1958, HHF has awarded almost $30 million to hearing and balance research with many of their grantees becoming leaders in the field.
Congratulations go out to Wei-Min Chen, PhD, a resident faculty member of the Center, on his promotion to Associate Professor of Public Health Sciences! Dr. Chen’s leadership in the area of statistical genetics analysis has earned him this well-deserved recognition. A number of the CPHG affiliate faculty have also received promotions including Ira M. Hall, PhD, promoted to Associate Professor of Biochemistry and Molecular Genetics; Jeffrey J. Saucerman, PhD, promoted to Associate Professor of Biomedical Engineering and awarded tenure; and Bradford B. Worrall, MD, promoted to Professor of Neurology.
Aaron Mackey, PhD of the CPHG and his colleagues published Sequencing of mRNA identifies re-expression of fetal splice variants in cardiac hypertrophy in the May 17th online edtion of the Journal of Molecular and Cellular Cardiology. This study hypothesized that patterns of alternative splicing occurring during heart development recur during cardiac hypertrophy. The researchers used high-throughput sequencing of mRNA isolated from fetal rats, adult sham-operated rats, and adult rats subjected to 10 days of pressure overload. A noteworthy degree of overlap between changes in both gene and isoform expression in TAC and fetal hearts relative to sham was found. The resulting data supports the concept that mRNA splicing patterns typically associated with heart development recur as part of the hypertrophic response to pressure overload.
To investigate the role of the gut microbiome in kwashiorkor, an enigmatic form of severe acute malnutrition, researchers performed a longitudinal comparative study of the fecal microbiomes of monozygotic (MZ) and dizygotic (DZ) twin pairs born in Malawi who became discordant for kwashiorkor. The study also included dietary experiments in gnotobiotic mice that had received gut microbiota transplants from twins discordant for kwashiorkor. Authors of the paper include CPHG faculty Pat Concannon, PhD, Josyf Mychaleckyj, MA, DPhil, and Steve Rich, PhD. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor was published online in the January 30, 2013 issue of Science.
A research team, led by the Farber lab in the Center for Public Health Genomics and collaborators at UCLA and the University of Namur in Belgium, has used a systems-based approach to identify gene networks that govern the activity of bone cells. The group used genome-wide gene expression data across a large panel of inbred mouse strains to identify a network of genes that are involved in the function of bone-forming osteoblasts, one of the key cell types in determining bone strength. The authors went on to use the network to elucidate novel genes that are involved in osteoblast-mediated bone formation. The study revealed novel regulatory mechanisms governing bone formation that may one day be targets of therapies designed to prevent and treat osteoporotic fractures. Systems Genetic Analysis of Osteoblast-Lineage Cells was published online in PLoS Genetics on December 27, 2012.