Future Opportunities for Genome Sequencing -- Planning Workshop

 

Future Opportunities for Genome Sequencing and Beyond:
A Planning Workshop for the National Human Genome Research Institute

Overview of NHGRI and NIH Programs and Consortia Mentioned in this Summary

BD2K (Big Data to Knowledge) - Trans-NIH initiative to enable biomedical scientists to capitalize more fully on the Big Data being generated by those research communities, by developing new approaches, standards, methods, tools, software, and competencies. Supports research, implementation, and training in data science and other relevant fields. http://bd2k.nih.gov/#sthash.IBHWmnj4.dpbs           

ClinGen (Clinical Genome Resource) - NHGRI project which aims to collect phenotypic and clinical information on variants across the genome, develop a consensus approach to identify clinically relevant genetic variants, and disseminate information about the variants to researchers and clinicians. http://www.clinicalgenome.org/ 

eMERGE (The Electronic Medical Records and Genomics Network) - NHGRI program to explore the best avenues to incorporate genetic variants into EMR for use in clinical care and study related issues such as consent, education, regulation and consultation. eMERGE also discovers genomic variants associated with clinical conditions identified using EMRs and develops algorithms for electronic phenotyping. http://www.genome.gov/27540473/electronic-medical-records-and-genomics-emerge-network/ or http://emerge.mc.vanderbilt.edu/

ENCODE (Encyclopedia of DNA Elements) - NHGRI international consortium which aims to identify all functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. http://www.genome.gov/encode/ or https://www.encodeproject.org/

FunVar (Functional Variation) - NHGRI program on Interpreting Variation in Human Non-Coding Genomic Regions Using Computational Approaches and Experimental Assessment (R01) https://grants.nih.gov/grants/guide/rfa-files/RFA-HG-13-013.html

GGR (Genomics of Gene Regulation) - NHGRI program that will explore genomic approaches to understand the role of DNA sequence in gene regulatory networks. (U01) http://grants.nih.gov/grants/guide/rfa-files/RFA-HG-13-012.html

GSP (Genome Sequencing Program) - NHGRI program http://www.genome.gov/10001691/nhgri-genome-sequencing-program-gsp/consisting of:

LSAC (Large Scale Sequencing and Analysis Centers) - NHGRI program aimed at providing large-scale genome sequence datasets in pursuit of multiple long-term goals of high significance to a broad range of the biomedical research community. These include identifying somatic mutations associated with cancer, characterizing variation underlying complex disease, pursuing questions about basic genomic variation and how it relates to biology and disease, exploring basic questions in comparative and evolutionary genomics through sequencing many organismal genomes, adding value to model organism research by providing reference genome sequences, and other areas. http://www.genome.gov/27546191

CMG (Centers for Mendelian Genomics) - NHGRI program which aims to make major contributions to the discovery of the genetic basis of most, or all, Mendelian disorders by using genome-wide sequencing and other genomic approaches to discover the genetic basis underlying as many Mendelian traits as possible, spanning the various Mendelian inheritance patterns. The centers accelerate the discovery by disseminating the obtained knowledge and effective approaches, reaching out to individual investigators, and coordinating with other rare disease programs worldwide. http://www.genome.gov/27546192/centers-for-mendelian-genomics-cmg/

CSER (Clinical Sequencing Exploratory Research) - NHGRI program which aims to examine the methods development needed to integrate sequencing into the clinic, and the ethical, legal, and psychosocial research required to responsibly apply personal genomic sequence data to medical care. The consortium of grantees will also cooperate to evaluate best practices in this rapidly advancing field and communicate these to the community. http://www.genome.gov/27546194/clinical-sequencing-evidencegenerating-research-cser2/ or https://cser-consortium.org/

GS-IT (Genome Sequencing Informatics Tools) - NHGRI program to provide "researcher friendly" sequence analysis tools and software to a broad community of independent scientists who increasingly rely on genomics in their biological, biomedical and clinical research, thus democratizing access to useful analysis software for these researchers. http://www.genome.gov/27546195/genome-sequencing-informatics-tools-gsit/ or http://iseqtools.org/

GTEx (Genotype-Tissue Expression) - Common Fund program which aims to study human gene expression and regulation in multiple tissues, providing valuable insights into the mechanisms of gene regulation and, in the future, its disease-related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. http://commonfund.nih.gov/GTEx/index or http://www.gtexportal.org/home/

IGNITE (Implementing Genomics in Practice) - NHGRI consortium created to enhance the use of genomic medicine by supporting the development of methods for incorporating genomic information into clinical care and exploration of the methods for effective implementation, diffusion and sustainability in diverse clinical settings. The project will incorporate genomic information into the electronic medical record (EMR) and provide clinical decision support (CDS) for implementation of appropriate interventions or clinical advice, as well as develop new methods and projects to disseminate their findings to the public. http://www.genome.gov/27554264/implementing-genomics-in-practice-ignite/

LINCS (Library of Integrated Network-based Cellular Signatures) - Common Fund program which aims to develop a "library" of molecular signatures, based on gene expression and other cellular changes that describe the response that different types of cells elicit when exposed to various perturbing agents, including siRNAs and small bioactive molecules, collected in a standardized, integrated, and coordinated manner to promote consistency and comparison across different cell types. http://www.lincsproject.org/ or http://commonfund.nih.gov/LINCS/index

NSIGHT (Newborn Sequencing In Genomic medicine and public HealTh) - NHGRI program exploring, in a limited but deliberate manner, the implications, challenges and opportunities associated with the possible use of genomic sequence information in the newborn period. http://www.genome.gov/27558493/newborn-sequencing-in-genomic-medicine-and-public-health-nsight/

Roadmap Epigenomics Project - Common Fund program which proposes to: (1) create an international committee; (2) develop standardized platforms, procedures, and reagents for epigenomics research; (3) conduct demonstration projects to evaluate how epigenomes change; (4) develop new technologies for single cell epigenomic analysis and in vivo imaging of epigenetic activity; and (5) create a public data resource to accelerate the application of epigenomics approaches. Includes the NIH Roadmap Epigenomics Mapping Consortium, which was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. http://www.roadmapepigenomics.org/

UDN (Undiagnosed Diseases Network) - Common Fund program to promote the use of genomic data in disease diagnosis and will engage basic researchers to elucidate the mechanisms underlying the diseases so that treatments may be identified. The program will also train clinicians in the use of contemporary genomic approaches so that genomic methods can increasingly be brought to bear on myriad diseases. http://commonfund.nih.gov/Diseases/index

Posted: October 14, 2014