- Collaborative Opportunities, Consortia, and Networks
- Knowledge Synthesis Resources
- Presentations and Reports
The resources on this page provides links to resources that may be of interest to cancer researchers interested in the area of pharmacogenomics, but is not exhaustive.
Collaborative Opportunities, Consortia and Networks
- Clinical and Translational Science Awards (CTSAs)
A national consortium, funded through Clinical and Translational Science Awards (CTSAs), is transforming how clinical and translational research is conducted, ultimately enabling researchers to provide new treatments more efficiently and quickly to patients. The consortium now comprises 46 medical research institutions in 26 states. The consortium ultimately will link about 60 institutions together to energize the discipline of clinical and translational science.
- Critical Path Institute (C-Path)
The Critical Path Institute (C-Path) was created to support the Food and Drug Administration (FDA) in its effort to implement the Critical Path Initiative. It is an independent non-profit institute, unaffiliated with any single entity or interest group, that develops innovative collaborative projects in research and education to enable the safe acceleration of medical product development.
- Electronic Medical Records and Genomics (eMerge) Network
The Electronic Medical Records and Genomics (eMERGE) Network, organized by the National Human Genome Research Institute (NHGRI), is a national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record systems for large-scale, high-throughput genetic research. Each center participating in the consortium has proposed studying the relationship between genome-wide genetic variation and a common human trait. Such studies commonly involve testing hundreds of thousands of single nucleotide polymorphisms (SNPs) throughout the genome in people with and without the trait.
The consortium also includes a focus on ethical issues such as privacy, confidentiality, and interactions with the broader community. To address ethical concerns, the consortium conducts research and then recommends best practices for Institutional Review Board interactions, participants' consent, and reporting results to the broader community.
- Human Genome Epidemiology Network (HuGENet)
Initiated by the Centers for Disease Control and Prevention (CDC), the Human Genome Epidemiology Network, or HuGENet™, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. The goals of HuGENet are to:
- establish an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention;
- provide training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice;
- develop an updated and accessible knowledge base on the web; and
- promote the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion.
- Pharmacogenetics Research Network (PGRN)
The NIH Pharmacogenetics Research Network (PGRN), led by the National Institute of General Medical Sciences (NIGMS), was formed in 2000 to enable a network of multidisciplinary research groups to conduct studies addressing research questions in pharmacogenetics and pharmacogenomics and to populate a knowledge base (PharmGKB). The latter will be used as a research tool to enable future pharmacogenetics studies and should serve as the premier knowledge base in the field. The PGRN is comprised of 12 independently funded interactive research groups, including the knowledge base group, and each research group has a focus in an identified area of pharmacogenetics. The long-term goal of the PGRN is to advance knowledge of the genetic basis for variable drug responses and identify safe and effective drug therapies designed for individual patients. The PGRN is accomplishing its mission by conducting studies of variation in human genes relevant to pharmacokinetics (drug disposition) and pharmacodynamics (drug action), and the relationship of such variation to drug response phenotypes.
- Serious Adverse Events Consortium (SAEC)
The international Serious Adverse Events Consortium (SAEC) is a global, non-profit partnership between leading pharmaceutical companies, the Food and Drug Administration (FDA), and academic institutions which is identifying and validating genetic markers that may help predict which individuals are at risk for serious adverse drug events. The goal of the consortium is to publish a set of predictive single nucleotide polymorphisms (SNPs) for all drug-related serious adverse events (SAEs), reducing significant patient and economic costs as well as improving the flow of safe and effective medical advances by addressing safety issues of new drugs before they reach the market.
- Database of Genotypes and Phenotypes (dbGaP)
The database of Genotypes and Phenotypes (dbGaP) is a database initiated by the NIH's National Library of Medicine (NLM). It is part of the National Center for Biotechnology Information (NCBI) and was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as studies of associations between genotype and non-clinical traits. The advent of high-throughput, cost-effective methods for genotyping and sequencing has provided powerful tools that allow for the generation of the massive amount of genotypic data required to make these analyses possible.
dbGaP provides two levels of access -- open and controlled -- in order to allow broad release of non-sensitive data, while providing oversight and investigator accountability for sensitive data sets involving personal health information. Summaries of studies and the contents of measured variables as well as original study document text are generally available to the public, while access to individual-level data including phenotypic data tables and genotypes require varying levels of authorization. Learn more about specific genomic datasets for cancer research.
- Database of Single Base Nucleotide Substitutions (dbSNP)
The Database of Single Base Nucleotide Substitutions (dbSNP) is the National Center for Biotechnology Information (NCBI) central repository for single base nucleotide substitutions (SNPs) and short deletion and insertion polymorphisms. NCBI is part of NIH's National Library of Medicine (NLM).
- Drug Gene Interaction Database (DGIdb)
A research resource that can be used to search candidate genes or drugs against the known and potentially druggable genome in order to advance personalized medicine.
Eudragene is a European collaboration that established a collection of DNA samples as a resource for studying genes which influence serious or adverse drug reactions (ADRs). The group will study an initial set of six ADRs that are important because they cause serious illness in a small number of those exposed to drugs that are otherwise more effective than any alternative, and that are easily identified because they produce distinctive conditions that are not related to the disease for which the drug was prescribed. The coordinating centre will manage the database, and will make samples freely available to academic and industry-based researchers throughout Europe. The collection will be extended to include more ADRs after the first 1-2 years, based on problems of current concern.
My Cancer Genome is a precision cancer medicine knowledge resource for physicians, patients, caregivers and researchers. Users can match tumor mutations to therapies and find up-to-date information on which mutations make cancers grow and related therapeutic implications.
- Pharmacogenomics Knowledge Base (PharmGKB)
PharmGKB is a publicly available Internet research tool developed by Stanford University with funding from the NIH and is part of the NIH Pharmacogenetics Research Network (PGRN). Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs.
The PharmGKB database is a central repository for genetic, genomic, molecular, and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data include, but are not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic, and transporter domains. The contributors tab contains the links to all of the projects submitting data to the PharmGKB. The PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes.
Knowledge Synthesis Resources
- Genotype-Tissue Expression (GTEx) Project
This program aims to study human gene expression and regulation in multiple tissues, providing valuable insights into the mechanisms of gene regulation and, in the futute, its disease-related perturbations. A database of existing GTEx-generated eQTL data will allow users to view and download computed eQTL results and provide a controlled access system for de-indetified individual-level genotype, expression, and clinical data.
- Evaluation of Genomic Applications in Practice and Prevention (EGAPP)
Evaluation of Genomic Applications in Practice and Prevention (EGAPP) is a project initiated by the Centers for Disease Control and Prevention's (CDC) National Office of Public Health Genomics that utilizes a systematic, evidence-based process for assessing genetic tests and other applications of genomic technology in transition from research to clinical and public health practice. EGAPP aims to integrate:
- existing recommendations on implementation of genetic tests from professional organizations and advisory committees; and
- knowledge and experience gained from existing processes for evaluation and appraisal, previous CDC initiatives, and the international health technology assessment experience
Presentations and Reports
- Cancer Pharmacogenomics: Setting a Research Agenda to Accelerate Translation
Links to published commentary and presentations from 2009 Workshop, sponsored by the Trans-NCI Pharmacogenomics and Pharmacoepidemiology Working Group.
- NIH Office of Biotechnology Activities: Pharmacogenomics Web Page
This page provides a link to the report "Realizing the Potential of Pharmacogenomics: Opportunities and Challenges," and related meeting transcripts, presentation materials, and Webcasts from the Secretary's Advisory Committee on Genetics, Health, and Society (SACGHS).
PhenX is a project led by RTI International, in collaboration with the National Human Genome Research Institute (NHGRI), to contribute to the integration of genetics and epidemiologic research. The PhenX Toolkit provides background information on measures recommended for genome-wide association studies (GWAS) and other large-scale genomic research efforts, along with standard operating procedures, common data elements, controlled vocabularies, a glossary of terms, standard analytic procedures to harmonize similar measures, and an outline of suggested protocols and methods for analyzing GWAS data.