Peter Kraft is co-author on a recently published paper in Nature, “Directional dominance on stature and cognition in diverse human populations.” The study examined runs of homozygosity of 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and found statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment. The full article can be accessed here.
A new paper on “Modeling linkage disequilibrium increases accuracy of polygenic risk scores” has been accepted by AJHG. Led by former PGSG postdoc Bjarni Vilhjalmsson, this work introduces a new method of calculating polygenic risk scores, LDpred, which infers the posterior mean effect size of each marker using a prior on effect sizes and LD information from an external reference panel. Numerous PGSGers, past and present, were closely involved in this work.
Over a dozen PGSGers have been selected to present their work at this year’s ASHG conference in Baltimore. In addition, postdoc Sasha Gusev has been selected as a finalist for the ASHG Epstein Trainee Award for Excellence in Human Genetics Research; and Gaurav Bhatia, Pier Palamara, Po-Ru Loh and doctoral students Kevin Galinsky and Tris Hayeck were all selected as semi-finalists. Click here to see detailed talk and poster information. Congratulations to all!
Two papers written by Price lab members have recently been accepted by Nature Genetics. Finucane et al., in press, is titled “Partitioning heritability by functional category using GWAS summary statistics”; and Bulik-Sullivan et al. in press, is written on “An atlas of genetic correlations across human diseases and traits.”
Congratulations to Drs. Akweley Ablorh, Alexis Carere, Zhonghua Liu, and Shasha Meng, who all graduated and received their doctoral degrees today after years of hard work. We know they will continue to do great research in the future and we wish them the best of luck.
Welcome to Lori Chibnik
Dr. Lori Chibnik, PhD, MPH, is the newest PGSG faculty member. She is an Assistant Professor of Neurology at HMS and Brigham and Women’s Hospital, with a secondary appointment in HSPH-Epidemiology. Her research focuses on genetics and epigenetics of Alzheimer’s disease, cognitive decline, and multiple sclerosis; and longitudinal data analysis and risk prediction. She and Peter Kraft co-teach EPI 215: Advanced Topics in Case-Control & Cohort Studies (aka “Big data for Epidemiologists”) in the Fall semester. Dr. Chibnik also developed and leads an interactive biostatistics course at the KwaZulu-Natal Research Institute for Tuberculosis and HIV in Durban, South Africa.
Peter Kraft, David Hunter, and Sara Lindstroem are authors on a new paper out in JNCI in April 2015 that identifies new genetic markers of breast cancer survival. Survival after diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. This research is currently the largest study investigating genetic variation associated with breast cancer survival. The full article can be read here.
Liming Liang is first author of a new EWAS study published in Nature, “An epigenome-wide association study of total serum immunoglobulin E concentration,” featured on the HSPH news website. The researchers have discovered more than 30 genes that have strong effects on Immunoglobulin E (IgE- the antibody that triggers allergic responses), allergies and asthma. Amongst the genes are promising novel drug targets for treating allergies and asthma. The full article can be read here.
Immaculata De Vivo and collaborators have a paper just out in JAMA which found that patients who receive bone marrow transplants from donors with longer telomeres have a higher probability of survival over a 5-year period. The results of this observational study suggest that donor leukocyte telomere length may have a role in long-term post-transplant survival. Read the full article here.
Alkes Price is featured in the HSPH News for his recent work on “Leveraging population admixture to characterize the heritability of complex traits,” published in Nature Genetics. Read the full profile here.
Immaculata De Vivo and Marta Crous Bou have a new paper featured in the December edition of the British Medical Journal. Their work examines genetic factors that may contribute to the link between the Mediterranean diet and longer telomeres, using data from the Nurses’ Health Study. The full editorial can be read here.
PGSGers have had an impressive number of papers published recently in high-impact journals. Sara Lindström and Rulla Tamimi are first and last authors on a new paper in Nature Communications that identified multiple loci associated with both mammographic density and breast cancer risk; Price lab members have a new paper, “Leveraging population admixture to characterize the heritability of complex traits,” published in Nature Genetics; Postdoc Gaurav Bhatia had his paper on directional selection in African-Americans published in AJHG; Amit Joshi and Peter Kraft are first and last authors on their work published in the American Journal of Epidemiology examining additive interactions and breast cancer risk; “Variation in Predictive Ability of Common Genetic Variants by Established Strata: The Example of Breast Cancer and Age,” now published in Epidemiology, has an all-PGSG author list, led by Hugo Aschard; Jennifer Prescott is first author on a paper recently published in Frontiers in Oncology analyzing Vitamin D and ovarian cancer risk; Postdoc Sasha Gusev’s work on “Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases” was published in AJHG; Liming Liang is first author of a paper in press at Nature, “An Epigenome-Wide Association Study of Total Serum Immunoglobulin E Concentration” and co-first author of a paper in press at Human Molecular Genetics, “Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci”; Marta Crous Bou and Immaculata De Vivo’s paper, “Mediterranean diet and telomere length in the Nurses’ Health Study: Population-based cohort study,” is in press at BMJ; and postdoc Po-Ru Loh just had his paper on Bayesian mixed model analysis accepted in Nature Genetics.
Congratulations to Alkes Price, who received the NSF CAREER Award for his work on “Resources for mixed model association mapping of complex traits.” The CAREER program is one of the National Science Foundation’s most prestigious awards; it supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations.
Po-Ru Loh received a PQG Student/Postdoc Travel Award to attend the Fall 2014 ASHG conference. The awards are funded by HSPH’s Program in Quantitative Genomics and are used to support travel to present research at professional meetings. In addition, Po-Ru has been selected as a semi-finalist for the 2014 ASHG Charles J. Epstein Trainee Award, for his work on “Efficient Bayesian mixed model analysis increases association power in large cohorts.”
Alexis Carere has received a Doctoral Foreign Study Award from the Canadian Institutes of Health Research. Dr. Peter Kraft and Dr. Robert Green co-supervise her project, titled, “A prospective cohort of direct-to-consumer genetic testing customers: Consumer motivations, behavioral responses, and their impact on the health care system.”
After founding the Program in Molecular and Genetic Epidemiology (now the Program in Genetic Epidemiology and Statistical Genetics or PGSG) and overseeing its rapid growth (it has more than doubled in number of faculty, staff and trainees over the last 10 years) Professor David Hunter has stepped down as PGSG director to focus on his duties as Dean for Academic Affairs. Professor Peter Kraft is the new PGSG Director. Professor Kraft was deputy director of the PGSG from 2010 to 2014.
Congratulations to Alkes Price, who was recently promoted to Associate Professor of Statistical Genetics. Dr. Price has been at HSPH since 2008; his research focuses on the development of statistical methods for uncovering the genetic basis of human disease, and on the population genetics underlying these methods.
PGSG welcomes Wonil Chung and Yunhua Xiang, our two newest group members. Wonil is a Postdoctoral Fellow who recently received his Ph.D. from the University of North Carolina at Chapel Hill, while Yunhua is a Visiting Student from the Renmin University School of Statistics in Beijing. Both are working with Dr. Liming Liang.
PGSGers will have a strong showing at the major genetics conferences this Fall. Several students and researchers have been invited to showcase their work as poster and platform presentations at the annual American Society of Human Genetics Meeting, among others. Presentation details can be found here.
PGSG Deputy Director to Co-Direct AACR workshop
For the second year in a row, Peter Kraft will be Co-Director of an exciting workshop this summer in Boston, MA. The AACR’s Integrative Molecular Epidemiology Workshop is designed to accelerate the training of the next generation of cancer researchers. The workshop is primarily targeted toward molecular epidemiologists, but will also be a valuable experience for geneticists, statisticians, bioinformaticians, molecular biologists, physician scientists and others who have done basic course work in epidemiology. As Co-Director and member of the planning committee, Dr. Kraft has been very closely involved in organizing this event; Dr. Lorelei Mucci, Associate Professor of Epidemiology at HSPH, is also a workshop faculty member and member of the planning committee. The workshop was a great success when it was first held last year, and the organizers are working hard to put together another exciting learning experience for attendees.
The workshop is from August 11-15, 2014, in Boston. For more details visit the event website.
Epi in Space
An exciting new study led by NASA’s Human Research Program and the National Space Biomedical Research Institute will fund several investigations into the molecular, physiological and psychological effects of spaceflight in an effort to better understand the health impacts of human space exploration. Identical twins Scott and Mark Kelly, both veteran astronauts, will be the focus of this study. Scott Kelly will live aboard the International Space Station for one year while his twin brother, Mark Kelly, remains on Earth as a control. PI Immaculata De Vivo and lab manager Pati Soule are collaborating with researchers at Colorado State University to analyze the effect of spaceflight on telomeres. Telomeres are stretches of DNA found at the end of chromosomes; they shorten over time as cells divide and are associated with aging, cancer, and a higher risk of death. The project, “Differential effects on telomeres and telomerase in twin astronauts associated with spaceflight” will study astronaut Scott Kelly’s telomeres during his year in space and compare them to his twin. The researchers are excited to be a part of this first-of-its-kind investigation.
Symposium on Advances in Endometrial Cancer Epidemiology and Biology at HSPH
On March 17-18th Immaculata De Vivo hosted the Advances in Endometrial Cancer Epidemiology and Biology Symposium. The overall goal of the symposium was to identify priorities for future research that will have a strong impact on risk of and outcomes from endometrial cancer. Dr. De Vivo gave the opening and closing remarks, and also gave a presentation of her work on GWAS and XWAS results. Other notable speakers included Drs. David Hunter, Peter Kraft, and Jennifer Prescott, all members of PGSG. Many other researchers from multiple disciplines (epidemiologists, clinicians, and medical doctors) traveled from all over the country to attend the symposium. Karen Lu from MD Anderson Cancer Center, Sara Olson of Memorial Sloan-Kettering Cancer Center, and Wendy Setiawan from the University of Southern California were all co-organizers. The event was a huge success, and there is already talk of planning the next one!
PGSG research scientist Sara Lindstroem is PI of a new R21 grant, “Prioritizing Follow-up of GWAS Loci using Genetic and Functional Annotation Data.”
Rulla Tamimi is Co-PI on a new grant funded by Susan G. Komen for the Cure. The study, “Environmental exposures, early proliferative changes and breast cancer risk,” will evaluate if environmental exposures and geographic variation over the life course are related to mammographic density, proliferative BBD and breast cancer risk, independent of individual level risk factors. In addition, it also examines the associations of air pollution and UV-B with gene expression in normal (benign) breast tissue. Dr. Tamimi will be working with Co-PI Francince Laden, Associate Professor of Epidemiology and Environmental Health at HSPH.
Postdoctoral Fellow Bjarni Vilhjalmsson received a DFF-Individual postdoctoral grant to support his research.
Alkes Price and Peter Kraft, in collaboration with Ben Neale and Shamil Sunyaev of the Broad Institute, received an R01 to develop statistical methods for studies of rare variants.
Jennifer Prescott, who has worked with Dr. De Vivo for several years as a research fellow and now an instructor, was awarded a new grant from the Harvard Transdisciplinary Research on Energetics and Cancer (TREC) Center. The title of the project is “Influence of a family history of Type 2 Diabetes on colorectal cancer risk and mortality, and on biomarkers of glycemic control, plasma lipids, and inflammatory biomarkers.” The researchers hypothesize that increased insulin signaling increases the risk of colorectal cancer, based on previous studies that have shown healthy first-degree relatives of type 2 diabetics to have reduced insulin secretion due to impaired beta-cell function. The project will explore whether a family history of type 2 diabetes is associated with reduced risk of colorectal cancer incidence and mortality, and/or alters biomarkers associated with insulin action in the NHS and HPFS cohorts. Dr. Prescott will also explore whether a genetic risk score for type 2 diabetes is associated with colorectal cancer risk.
Postdoctoral fellow Amit Joshi also received grant funding from the TREC Center. Dr. Joshi’s research project is entitled “Effect modification of association of GWAS-identified susceptibility SNPs for body mass index with post-menopausal breast cancer risk by physical activity.” He will use data from the Nurses’ Health Study, which is one of the largest and longest running investigations of factors that influence women’s health.
Dr. Hugues Aschard, postdoctoral fellow under Dr. Kraft, was recently awarded grant 1R03HG006720-01A1, “Relaxing genetic models to identify genetic variants involved in gene-gene and gene-environment interactions.” Dr. Aschard and his colleagues developed a non-parametric test of association that compares phenotypic distribution by genotypic classes, which aims to identify quantitative trait loci involved in interactions. The aims of his grant are to identify potential technical improvements of the proposed method and to conduct real data application to identify genetic variants that have been missed by standard genome-wide association screening.