Researchers identify key gene variation linked to increased stroke risk

Dr. Stephen Williams, a postdoctoral fellow in CPHG and CVRC, and CPHG faculty Dr. Michèle Sale, Associate Professor, Dr. Brad Worrall, Professor of Neurology, and Dr. Wei-Min Chen, Associate Professor, are part of the research team that has made a breakthrough discovery that could have important implications for understanding stroke, as well as other diseases. In this study, which focused on the conversion of the enzyme methionine into homocysteine, the scientists conducted independent genome-wide association studies and a meta-analysis of methionine metabolism, in 2,710 participants from the Framingham Heart Study (FHS) and 2,100 participants from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial, and then examined the association of the identified loci with incident stroke in FHS. Based on their findings, the team subsequently developed a genetic risk score that predicts post-methionine load homocysteine levels, and also identified a novel association between ischemic stroke and ALDH1L1, both of which highlight the potential impact this discovery may have in clinical settings.

News of the researchers’ findings was reported in the March 27th issue of UVa Today. The full text of the paper, Genome-Wide Meta-Analysis of Homocysteine and Methionine Metabolism Identifies Five One Carbon Metabolism Loci and a Novel Association of ALDH1L1 with Ischemic Stroke, can be found in the March 20, 2014 issue of PLoS Genetics.

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Important implications found for design and analysis of rare variant GWAS studies

A study by researchers, including Dr. Stephen Rich, Director of the Center for Public Health Genomics, was published recently in PLoS One. The focus of the study was to advance understanding of the impact that population stratification has on rare variant association methods. The researchers performed exhaustive coalescent simulations with demographic parameters calibrated from exome sequence data to evaluate the performance of nine rare variant association methods in the presence of fine-scale population structure. They found that all methods have an inflated spurious association rate for parameter values that are consistent with levels of differentiation typical of European populations. The results have important implications for the design, analysis, and interpretation of rare variant genome-wide association studies. Fine-scale patterns of population stratification confound rare variant association tests can be read in full in the July 4, 2013 issue of PLoS One

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Quinlan and Hall inducted into Millipub Club

Dr. Aaron Quinlan, Assistant Professor, CPHG, and Dr. Ira Hall, Assistant Professor, Biochemistry and Molecular Genetics, and affiliate faculty member of CPHG, were among a group of ten researchers who were inducted into the UVa SOM Millipub Club for 2013. This club which was created in 2012 with an initial group of 33 members, was formed to specifically recognize researchers who reach the milestone of having a single paper cited over 1000 times. Dr. Quinlan was recognized for his work on A map of human genome variation from population-scale sequencing, the first publication from The 1000 Genomes Project, and Dr. Hall was recognized for Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi published in Science in 2002. The complete list of Millipub members can be seen on a plaque in the lobby of the Claude Moore Health Sciences Library.

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Study focuses on role of microRNAs in ischemia-induced angiogenesis

A group of researchers including Charles Farber, PhD (CPHG) and Brian Annex, MD (Dept. of Medicine-Cardiovascular Medicine) have published findings from a study that explored the role of microRNAs in ischemia-induced angiogenesis, such as in peripheral arterial disease. The resulting data indicate that miR-93 enhances perfusion recovery from hindlimb ischemia and is a strong potential target for pharmacological modulation to promote angiogenesis in ischemic tissue. MicroRNA-93 Controls Perfusion Recovery After Hindlimb Ischemia by Modulating Expression of Multiple Genes in the Cell Cycle Pathway was published in the April 30, 2013 issue of Circulation.



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Mosaic CNV Study published in Science magazine

Michael McConnell, Assistant Professor in the Department of Biochemistry & Molecular Genetics, and affiliate faculty member of CPHG, along with his colleagues just published a new study featured in Science magazine. In this research, two recently developed single-cell genomic approaches to map DNA copy number variations (CNVs) were applied to single human neurons. The study revealed that 13 to 41% of neurons have at least one megabase-scale de novo CNV, and that deletions are more common than duplications. The results show that mosaic CNV is abundant in human neurons. Mosaic copy number variation in human neurons was published in the Nov 1, 2013 issue of Science.

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CPHG team volunteers at Fluvanna Middle School

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.

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CPHG hosts visiting scholar Caroline Brorsson

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.

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CPHG grad student invited to speak at the Mammalian Research Council at Harwell

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.

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Quinlan discusses computational genomics at Big Data Summit 2

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 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.

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Manichaikul awarded Emerging Research Grant from HHF

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.

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