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


Purpose

The Epidemiology and Genomics Research Program hosts a webinar series entitled "Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE)." The purpose of this forum is to provide an opportunity for our grantees and other interested individuals to share lessons learned and practical information regarding the application of next generation sequencing to cancer epidemiology studies.

By sharing lessons learned across funded projects, EGRP aims to facilitate higher quality research and more interpretable genetic research studies for the future. In addition, the webinar participants may work together to establish best practices for epidemiology research.

Any interested individual is invited to participate, however pre-registration is required. Each presentation will be about 30 minutes in length and allow for 30 minutes of discussion. Instructions for connecting to the webinars will be sent via e-mail to individuals who register for the webinars.

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Background

The past decade has seen a transformation in genetic epidemiology of complex diseases, from linkage to association studies, which progressed from investigating single variants in candidate genes, to genome-wide approaches, including genome-wide association studies (GWAS). GWAS have successfully identified hundreds of common genetic variants associated with cancer and other complex diseases, however with the advent of next-generation parallel DNA sequencing technologies, there is a renewed interest in examining the role of rare variants and other forms of genetic variation in complex disease etiology. While sequencing of thousands of cancer-normal genomes is estimated to be completed worldwide by the end of 2014, germline sequencing in epidemiologic studies of cancer risk are relatively nascent.

Sequencing technology is more technically difficult than genotyping using GWAS arrays and requires unique considerations related to the study design and techniques used for sequencing and analysis. Quality control standards are needed for sequencing across samples, platforms, and institutions. GWAS arrays had high reproducibility and concordance, but this is not yet the case for sequencing data. In addition, combining data from different studies is more challenging in sequencing studies than GWAS. Poorly designed studies will result in uninterpretable or even biased results.

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Upcoming Topics and Speakers

September 27, 2017 3:00 p.m. to 4:30 p.m. ET

Analyzing Large Scale Sequenced Based Epidemiological Studies

Suzanne Margaret Leal, Ph.D.External Web Site Policy
Professor, Molecular and Human Genetics, Baylor College of Medicine
Adjunct Professor, Department of Statistics, Rice University
Senior Research Associate, The Rockefeller University


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Dr. Suzanne Leal is a Professor in the Department of Molecular and Human Genetics at Baylor College of Medicine and Director of the Center for Statistical Genetics, an Adjunct Professor in the Department of Statistics at Rice University, and a Senior Research Associate at The Rockefeller University. Her primary research interests are statistical genetics and genetic epidemiology. Currently, Dr. Leal's concentration is in the development of methods to analyze rare variants. In addition to applied work, mapping disease\trait loci, she has worked extensively in developing methods to aid in gene identification and understanding disease etiology. Dr. Leal will be presenting on software for analyzing sequencing-based epidemiological studies and rare variant aggregation association tests.


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November 14, 2017 1:00 p.m. to 2:30 p.m. ET

Informatics Tools for Analysis of Next Generation Sequencing Studies Supported by the NCI ITCR Program

Aviv Regev, Ph.D.External Web Site Policy
Professor of Biology, MIT; Core Member, Broad Institute; Investigator, Howard Hughes Medical Institute
Informatic Tool: TRINITYExternal Web Site Policy, a toolkit for analysis of RNA sequencing data and cancer transcriptomes.

Michael Ryan, Ph.D.External Web Site Policy
Founder, In Silico Solutions
Informatic Tools: CRAVATExternal Web Site Policy and MuPITExternal Web Site Policy, tools to use and integrate a variety of functional annotations and structural information for interpretation of genetic variants.

Obi Griffith, Ph.D.External Web Site Policy
Assistant Professor of Medicine, Washington University; Assistant Director, McDonnell Genome Institute
Informatic Tool: CIViCExternal Web Site Policy, a resource for the clinical interpretation of variants in cancer.


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NCI's Information Technology for Cancer ResearchExternal Web Site Policy (ITCR) program promotes research-driven informatics technology across the development lifecycle to address priority needs in cancer research. ITCR supports a wide range of informatics tools to serve current and emerging needs across the cancer research continuum. We invite you to join us for a SeqSPACE panel of speakers that will highlight several of the informatics tools from ITCR useful for next generation sequencing applications including transcriptomics, functional and clinical interpretation of variants.


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Note: Additional speakers and topics may be added in the future.

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Past Topics and Speakers


2017

June 21, 2017 2:00 p.m. to 3:30 p.m. ET

Lessons Learned in the Application of Next Generation Sequencing to Pancreatic Cancer

Alison Klein, M.H.S., Ph.D.External Web Site Policy
Professor of Oncology, School of Medicine, Epidemiology, Genetic Epidemiology, Johns Hopkins University


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Dr. Alison Klein is a Professor of Oncology at Johns Hopkins School of Medicine. She is the Director of the National Familial Pancreas Tumor RegistryExternal Web Site Policy, the largest pancreatic cancer family registry in the world. Her current work focuses on the identification the genetic and environmental risk factors for pancreatic cancer as well as other complex genetic diseases. As part of this work, she developed PancPROExternal Web Site Policy, a clinical risk assessment tool for high-risk pancreatic cancer families, that facilitates the translation of her research findings into the clinical setting. Dr. Klein presented on lessons learned in the application of next generation sequencing to pancreatic cancer.


March 9, 2017 3:00 p.m. to 4:30 p.m. EST

The Application of Next Generation Sequencing Technologies in Diverse Populations and Methods for Evaluating the Pathogenicity of Variants

Carlos Bustamante, Ph.D.External Web Site Policy
Professor of Biomedical Data Science, of Genetics, and, by courtesy, of Biology
Founding Director, Stanford Center for Computational, Evolutionary, and Human Genomics


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Dr. Carlos Bustamante is a Professor of Biomedical Data Science, of Genetics, and, by courtesy, of Biology. Additionally, he is the Founding Director of the Stanford Center for Computational, Evolutionary, and Human Genomics and the Director of Informatics at the Stanford Center for Genomics and Personalized Medicine. He is a population geneticist whose research focuses on analyzing genome wide patterns of variation within and between species to address fundamental questions in biology, anthropology, and medicine. Dr. Bustamante presented on next generation sequencing in diverse populations and evaluated pathogenicity of variants using different methods.


February 6, 2017 3:00 p.m. to 4:30 p.m. EST

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes – Relationships Between Germline and Somatic Mutations

Jan Korbel, Ph.D.External Web Site Policy
Group Leader, Korbel Lab, GenomeBiology Unit
European Molecular Biology Laboratory (EMBL)


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Dr. Jan Korbel is the Group Leader of the Korbel Lab in the GenomeBiology Unit of the European Molecular Biology Laboratory (EMBL). His research applies experimental and computational genomics approaches to study the extent, functional impact, as well as mutational and evolutionary origins of genetic variants. In addition, Dr. Korbel's group plays a leadership role in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. Integrating data from somatic and germline whole genomes, DNA methylomes, transcriptomes, and clinical data from more than 2800 cancer patients, this group aims to unravel commonalities and discrepancies between the emergence of cancer types and subtypes, to facilitate molecular classification of malignancies with impact on diagnostics and treatment, and uncover causalities linking genotype, environment, and phenotype. Dr Korbel presented on the PCAWG and results from whole genome sequencing germline studies.


January 13, 2017 2:00 p.m. to 3:30 p.m. ET

Deep Sequencing of 10,000 Human Genomes and Sequencing Quality Standards for Human Variation Discovery

Amalio Telenti, M.D., Ph.D.External Web Site Policy
Chief Data Scientist, Human Longevity, Inc.
Adjunct Scientist, J. Craig Venter Institute
Professor, The Skaggs School of Pharmaceutical Sciences, University of California, San Diego


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Dr. Amalio Telenti is the Chief Data Scientist at Human Longevity, Inc. and Adjunct Scientist at J. Craig Venter Institute, as well as a Professor at the Skaggs School of Pharmaceutical Sciences at the University of California, San Diego. He directs HLI-X, the unit at Human Longevity, Inc. that develops advanced analytics in genomics and data sciences. He recently led the analysis of the first 10,000 deep sequenced human genomes, as well as the definition of the complete map of conservation of the regulatory structures in the human genome. Dr. Telenti presented on his experience deep sequencing 10,000 human genomes with an emphasis on the importance of sequencing quality standards for human variation discovery.



2016

November 1, 2016 3:00 p.m. to 4:30 p.m. EST

Lessons Learned in the Application of Exome Sequencing to Cancer Epidemiology Studies

Chad Huff, Ph.D.External Web Site Policy
Assistant Professor, Department of Epidemiology
The University of Texas MD Anderson Cancer Center


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Dr. Chad Huff is an Assistant Professor in the Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences at The University of Texas MD Anderson Cancer Center. His research concentrates on understanding human evolution and the genetic basis of human disease through statistical, computational, and population genomics and spans a number of human genetics subdisciplines, including disease-gene identification, mutation rate estimation, detection of recent positive selection, and reconstruction of demographic history. Dr. Huff presented on lessons learned and best practices in the application of exome sequencing to cancer epidemiology studies.


June 7, 2016 3:00 p.m. to 4:30 p.m. EDT

Lessons Learned in Applying Functional-Annotation for Rare Variant Analysis

Bogdan Pasaniuc, Ph.D.External Web Site Policy
Assistant Professor, Pathology and Laboratory Medicine
University of California, Los Angeles, David Geffen School of Medicine


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Dr. Bogdan Pasaniuc is an Assistant Professor of Pathology and Laboratory Medicine at the University of California, Los Angeles (UCLA), David Geffen School of Medicine. His primary research interests are statistical and computational methods for understanding genetic risk factors for common diseases with a particular focus on the study of admixed populations. Dr. Pasaniuc presented on lessons learned and best practices in applying functional-annotation for rare variant analysis.


May 3, 2016 3:00 p.m. to 4:30 p.m. EDT

PrediXcan and Genotype-Tissue Expression (GTEx) Program: Use for Interpretation of Genetic Associations

Nancy Cox, Ph.D.External Web Site Policy
Director, Vanderbilt Genetics Institute
Research Professor, Division of Genetic Medicine, Vanderbilt University, School of Medicine


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Dr. Nancy Cox is the Founding Director of the Vanderbilt Genetics Institute and is a quantitative human geneticist with a long-standing research program in identifying and characterizing the genetic component to common human diseases. Her current research is focused on large-scale integration of genomic with other "-omics" data as well as biobank and electronic medical records data. Dr. Cox presented on using PrediXcanExternal Web Site Policy, a computational method that links genetic variation and gene activity to disease traits. In addition, she provided updates on the Genotype-Tissue Expression (GTEx)External Web Site Policy project and using this data to aid in the interpretation of genetic association studies.


March 1, 2016 3:00 p.m. to 4:30 p.m. EST

ACMG Guidelines for Interpreting Sequence Variants

Carolyn Sue Richards, Ph.D., FACMGExternal Web Site Policy
Professor, Department of Molecular and Medical Genetics, Oregon Health & Science University


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Dr. Richards is a Professor within the Department of Molecular and Medical Genetics at Oregon Health & Science University. The focus of her clinical research laboratory is to develop sequence-based testing for rare disorders, develop custom analysis to address copy number variants, design algorithms using analysis tools for interpretation of sequence variations, and translation of these products into clinical practice. Dr. Richards presented on the American College of Medical Genetics guidelines for interpretationExternal Web Site Policy.


February 9, 2016 3:00 p.m. to 4:30 p.m. EST

Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene

Melissa Rotunno, Ph.D.
Program Director, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute


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Dr. Rotunno is a Program Director in the Genomic Epidemiology Branch of the Epidemiology and Genomics Research Program in NCI's Division of Cancer Control and Population Sciences and holds an adjunct appointment to the Genetic Epidemiology Branch, of NCI's intramural Division of Cancer Epidemiology and Genetics. Her grant portfolio and research area focus on the many analytic and computational challenges accompanying the application of next generation sequencing technologies to large scale epidemiology studies. Dr. Rotunno described a study of whole exome sequencing in families at high risk for Hodgkin lymphoma which led to the identification of a predisposing mutation in the KDR gene. She described methodological aspects related to family sequencing studies and prioritization of variants.



2015

December 1, 2015 3:00 p.m. to 4:30 p.m. EST

Targeted Sequencing Of GWAS-Identified Cancer Loci In Multiethnic Populations: Lessons (Re)Learned

Peter Kraft, Ph.D.External Web Site Policy
Professor, Department of Epidemiology and Department of Biostatistics, Harvard School of Public Health


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Dr. Peter Kraft is a Professor within the Department of Epidemiology and the Department of Biostatistics at the Harvard T.H. Chan School of Public Health. He played a leading role in the design and analysis of genome-wide association studies (GWAS) of breast, prostate, and pancreatic cancers as part of the NCI's Cancer Genetic Markers of SusceptibilityExternal Web Site Policy (CGEMS) and PanScan projects. Dr. Kraft's current research focuses on methods that link low-frequency variation, emerging functional annotation, and risk of complex disease and genetic risk prediction using common and rare genetic variation, as well as clinical and environmental risk factors. During this webinar, Dr. Kraft discussed his experience with targeted sequencing in breast cancer genetic epidemiology studies.


November 3, 2015 3:00 p.m. to 4:30 p.m. EST

Considerations in Design of Sequencing Studies – Lessons Learned from the Center for Inherited Disease Research

Kim Doheny, Ph.D.External Web Site Policy
Lead Co-Principal Investigator & Director, Center for Inherited Disease Research, Johns Hopkins University


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Dr. Kim Doheny is the Lead Co-Principal Investigator and Director of the Center for Inherited Disease ResearchExternal Web Site Policy (CIDR) at Johns Hopkins University. CIDR provides high quality next generation sequencing and genotyping services to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide valuable insight into analysis issues as they relate to study design, data production and quality control. Completed studies encompass more than 180 phenotypes across 750 projects and 800,000 samples. The impact is evidenced by more than 600 peer-reviewed papers published in 160 journals. Dr. Doheny presented on considerations regarding study design (e.g. coverage, selection of technologies) and lessons learned from CIDR regarding quality control and data cleaning.


July 7, 2015 3:00 p.m. to 4:30 p.m. EST

Considerations in Design of Sequencing Studies – Lessons Learned from The Genome Institute

Elaine R. Mardis, Ph.D.External Web Site Policy
Co-Director, The Genome Institute, Washington University
Professor, Department of Genetics, Washington University


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Dr. Elaine Mardis is the Co-Director of The Genome Institute and Professor of Genetics at Washington University. She also serves as an editorial board member of Molecular Cancer Research, Disease Models and Mechanisms and Annals of Oncology, and as a reviewer for Nature, the New England Journal of Medicine, Cell, and Genome Research. Dr. Mardis' research focuses on the application of next-generation sequencing to characterize cancer genomes and transcriptions, and using these data to support therapeutic decision-making. She presented on considerations regarding the design of whole genome and exome sequencing studies, including such topics as balancing sample size and coverage, comparisons between sequencing capture technologies, and new technologies. She also discussed experiences and lessons learned on data quality control and cleaning from The Genome Institute.


June 2, 2015 3:00 p.m. to 4:30 p.m. EST

Update and Lessons Learned from Haplotype Reference Consortium

Goncalo Abecasis, D.Phil.External Web Site Policy
Chair, Department of Biostatistics, University of Michigan School of Public Health


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Dr. Goncalo Abecasis is Chair of the Department of Biostatistics at University of Michigan's School of Public Health. His research focuses on the development of statistical tools for identification and study of genetic variants important in human disease, and has developed gene-mapping software that has been used in hundreds of gene-mapping projects around the world. Dr. Abecasis presented an update from the Haplotype Reference ConsortiumExternal Web Site Policy related to the imputation panel, and discussed methods of combining sequencing data from different studies and sources.


May 5, 2015 3:00 p.m. to 4:30 p.m. EST

Experience Using Next Generation Sequencing at NCI Division of Cancer Epidemiology and Genetics (DCEG)

Stephen J. Chanock, M.D.External Web Site Policy
Director, Division of Cancer Epidemiology & Genetics, National Cancer Institute


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Dr. Stephen Chanock is the Director of the Division of Cancer Epidemiology & GeneticsExternal Web Site Policy (DCEG) at the National Cancer Institute. He is a leading expert in the discovery and characterization of cancer susceptibility regions in the human genome. Before becoming director of DCEG, Dr. Chanock co-led the Cancer Genetic Markers of Susceptibility projectExternal Web Site Policy, served as Chief of both the Laboratory of Translational Genomics and the Cancer Genomics Research Laboratory, and co-directed the NCI Center for Cancer Genomics. Dr. Chanock discussed the utilization of next generation sequencing by DCEG researchers to provide insights into future studies.


April 7, 2015 3:00 p.m. to 4:30 p.m. EST

Genomic Approaches to Defining Inherited Basis of Childhood Cancer

Sharon E. Plon, M.D., Ph.D.External Web Site Policy
Director, Cancer Genetics Clinical and Research Programs & Neurofibromatosis Clinic, Texas Children's Hospital
Professor, Baylor College of Medicine


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Dr. Sharon Plon is a medical geneticist who is the Director of both the Cancer Genetics Clinical and Research Programs, and the Neurofibromatosis Clinic at Texas Children's Hospital. In addition, she is a Professor of Pediatrics-Oncology and Molecular and Human Genetics at Baylor College of Medicine, and a Professor at Baylor's Human Genome Sequencing Center. Her professional interests include cancer predisposition syndromes, mechanisms of genomic instability, and the use of genome sequencing in clinical medicine. Recently, Dr. Plon's lab initiated a project in collaboration with the Human Genome Sequencing Center to develop a large-scale sequencing to identify the causative mutation or chromosome imbalance in families with unusual patterns of childhood cancer. Dr. Plon's presentation provided an update of her NCI-funded study sequencing childhood cancer families for discovery of loci associated with childhood cancerExternal Web Site Policy. Her talk covered topics ranging from study design, population selection, sequencing strategy, and analytic approach.


March 3, 2015 3:00 p.m. to 4:30 p.m. EST

Epigenomics and Networks of Variants Underlying Common Disease and Cancer

Manolis Kellis, Ph.D.External Web Site Policy
Associate Professor, Computer Science, Massachusetts Institute of Technology


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Dr. Manolis Kellis is an Associate Professor of Computer Science at MIT, a member of the Computer Science and Artificial Intelligence Laboratory, and is the director of the MIT Computational Biology Group within the Broad Institute of MIT and Harvard. Recently, the Computational Biology Group was awarded funding to lead integrative analysis efforts of the modENCODE projectExternal Web Site Policy and the NIH Roadmap Epigenomics ProjectExternal Web Site Policy. Dr. Kellis presented on his experience interpreting results from sequencing data by using functional annotation obtained from data sources such as ENCODE and the Roadmap Epigenomics Project. He also discussed how these methods relate to interpretation of variants from non-coding regions during whole genome sequencing.



2014

December 4, 2014 12:00 p.m. to 1:00 p.m. EST

Experience Sequencing FFPE Tumor Specimens and Implications for Integrative Studies of Germline and Somatic Variation

Tom Hudson, M.D.External Web Site Policy
President and Scientific Director, Ontario Institute for Cancer Research


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Dr. Tom Hudson is President and Scientific Director of the Ontario Institute of Cancer Research (OICR). He is also Co-Founder and Member of the Executive Committee for the International Cancer Genome Consortium (ICGC). Dr. Hudson is internationally renowned for his work in genomics and human genome variation. Dr. Hudson's laboratory at OICR is involved in the study of genome variation that affects cancer predisposition, progression, and response to therapy. His main project focuses on the genetic architecture of loci associated with risk to colorectal cancer. In this presentation, Dr. Hudson spoke about OICR experience with targeted resequencing from tumor specimens stored as FFPE, lessons learned in developing a large scale colon cancer tumor sequencing project and germline-somatic integration, and commented on recent ICGC-TCGA DREAM Mutation Calling challenges.


November 4, 2014 2:00 p.m. to 3:00 p.m. EST

Introduction of SeqSPACE Forum and Brainstorming Key Issues

Leah Mechanic, Ph.D., M.P.H.
Program Director, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, NCI


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The Epidemiology and Genomics Research Program currently supports a portfolio of sequencing grants that use a wide range of study designs to investigate genetic susceptibility for a number of cancers across diverse populations. As reported at our workshop, "Making Sense of the Sequence," and in several recent publications about next generation sequencing, a clear challenge identified is the multiple approaches for applying sequencing to epidemiology studies and lack of standardized pipeline and best practices for next generation sequencing studies. This webinar series serves as a discussion forum to share lessons learned in research performed by next generation sequencing in cancer epidemiology studies. The inaugural webinar is an informal discussion where participants can brainstorm and suggest future topics and speakers for the SeqSPACE webinar series.



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SeqSPACE Co-Chairs

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SeqSPACE Planning Committee

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Contact

Questions about individual webinars, or the series, may be submitted via e-mail to the Planning Committee at seqspace@mail.nih.gov.

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