Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) Webinar Series

The Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) webinar series began 10 years ago (in November 2014). The series was designed to share lessons learned about the application of next generation sequencing to cancer epidemiology research. In this special webinar, organized to mark this milestone, Kimberly Doheny, PhD; Alexander Gusev, PhD; and Melissa Davis, PhD reflected on lessons learned, opportunities and challenges, and their vision for the future of sequencing in cancer epidemiology. The webinar was moderated by Fredrick Schumacher, PhD, MPH and Tabitha Harrison, MPH, who have been moderating this series since its inception.

Dr. Michael Gillette is a senior group leader in proteomics and biomarker discovery at the Broad Institute of MIT and Harvard. He is also a pulmonary and critical care medicine attending and associate physician at the Massachusetts General Hospital, an assistant professor of medicine at Harvard Medical School, and an associate editor for Molecular & Cellular Proteomics. Dr. Gillette’s interests include clinical proteomics and biomarker development. With other Broad colleagues, he was involved in the development and implementation of all aspects of a coherent biomarker discovery-to-verification pipeline. With Proteomics Platform director Steve Carr, he led Broad Institute efforts in breast and ovarian cancer proteomic biomarker discovery and in molecular characterization of infectious diseases of high international health import, including pediatric febrile illness and tuberculosis. In this webinar, Dr. Gillette presented on proteogenomic insights into non-small cell lung cancer biology and epidemiology.

Dr. Audrey E. Hendricks is an associate professor of biomedical informatics at the University of Colorado Anschutz Medical Campus. Her team at the Hendrick’s Lab serves as the lynch pin between biomedical research and statistical and machine learning method development. They develop and apply methods to improve the utility and equity of large, publicly available genetic data resources, identify the biological mechanisms of healthy diets, and elucidate the genomic underpinnings of conditions and traits. In this webinar, Dr. Hendricks presented on the opportunities and challenges of using common controls in sequencing studies as well as methods and applications in this area.

Dr. Philip Lupo is a professor of pediatrics and hematology-oncology at Baylor College of Medicine. His lab focuses on the molecular epidemiology of pediatric disease and conditions. Areas of interest include understanding the risk of cancer among children with structural birth defects; determining inherited genes underlying susceptibility to rhabdomyosarcoma; phenomic and genomic studies of structural birth defects; and addressing disparities in acute lymphoblastic leukemia susceptibility and outcomes. In this webinar, Dr. Lupo presented on leveraging population-based registries for genomic studies of pediatric cancer.

Dr. Ting Wang is a Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine at the McDonnell Genome Institute, Washington University School of Medicine in St. Louis. Dr. Wang’s lab investigates epigenetic determinants of cell fates in normal development and regeneration, in cancer, and in evolution, by integrating cutting-edge experimental and computational technologies. His lab developed widely used DNA methylomics technologies, algorithms to identify regulatory motifs and modules, and analytical and visualization tools to integrate large genomic and epigenomic data.

Dr. Karen Miga is an assistant professor in the Biomolecular Engineering Department at the University of California, Santa Cruz (UCSC). She is also the associate director of the UCSC Genomics Institute. In addition, she co-leads the Telomere-to-Telomere (T2T) Consortium and is the project director of the Human Pangenome Reference Consortium (HPRC) Production Center at UCSC. Her lab aims to uncover a new source of genetic and epigenetic variation in the human population, which is useful to investigate novel associations between genotype and phenotype of inherited traits and disease.

In this webinar, Drs. Wang and Miga presented on the human pangenome reference. They discussed resources that describe the tools and methods used in the pangenome and T2T, including the consortium website, the UCSC Genome Browser, and the WashU Epigenome Browser.

Dr. Kushal Dey is an assistant member and Josie Robertson investigator in the Department of Computational and Systems Biology at the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center. He is also an assistant professor at the Gerstner Sloan Kettering Graduate School of Biomedical Sciences. In this webinar, Dr. Dey discussed his work at the Kushal Dey Lab, which builds statistical and machine learning models that integrate genetic and genomic data to prioritize variants, genes, and cell types, and to decode the causal functional architecture underlying heritable complex diseases — including immune-related diseases, like Alzheimer’s and inflammatory bowel disease, and heritable cancers, like breast cancer.

Dr. Burcu F. Darst is an assistant professor in the Public Health Sciences Division at the Fred Hutchinson Cancer Center. Her research is focused on identifying and understanding genetic and multi-omic risk factors of prostate cancer in diverse populations. In this webinar, Dr. Darst presented on her effort to improve the utility of polygenic risk scores and rare genetic variants for the prediction of prostate cancer across patient populations.

Dr. Maximilian Haeussler is the co-PI for the UCSC Genome Browser, an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. Dr. Melissa Cline is program manager of the UCSC BRCA Exchange, a project which aims to advance the understanding of the genetic basis of breast, ovarian, pancreatic, and other cancers by pooling data on BRCA1/2 genetic variants and corresponding clinical data from around the world. In this webinar, Drs. Haeussler and Cline discussed these programs and data resources for clinical variant interpretation.