The genome.ucsc.edu web site provides the primary point of access to the reference human genome sequence for many tens of thousands of scientists and medical researchers worldwide. It is used over the World Wide Web by more than 5,000 scientists each day, servicing more than 150,000 requests for information. The site includes human gene sequences, their location in the genome, expression levels in different tissues, alternatively spliced transcripts, and protein products. Users get quick links to other databases. There is an integrated view that provides information on each gene's function in normal and diseased states. The site supports 31 genomes in addition to human, and produces multiple genome alignments and other comparative genomics analysis. This analysis, along with other large scale data such as ChlP/CHIP, sheds light on regulatory as well as coding regions. Expansions to the project are needed to handle the flood of additional genomes and other large data sets, to further develop comparative genomics, to improve the gene sets, to increase interactions with other databases, and to add additional support for transgenic studies in model organisms. We also propose three new projects to help link together genomics and more medically oriented research: (1) a suite of tools for working with SNP association studies and other genomic scans, (2) tools to support medical sequencing and identify causative mutations, and (3) support for new representations of human polymorphism both in the germ line and in cancerous and aging cells. By helping scientists tie changes in the genome to medically relevant phenotypes, these new projects will greatly facilitate the next generation of disease studies. Relevance: At least half of all diseases have a substantial genomic component. This work will help scientists better understand these diseases, and develop new treatments.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Biotechnology Resource Grants (P41)
Project #
5P41HG002371-11
Application #
7885247
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Felsenfeld, Adam
Project Start
2001-07-12
Project End
2012-06-30
Budget Start
2010-07-01
Budget End
2011-06-30
Support Year
11
Fiscal Year
2010
Total Cost
$3,796,698
Indirect Cost
Name
University of California Santa Cruz
Department
Biostatistics & Other Math Sci
Type
Schools of Engineering
DUNS #
125084723
City
Santa Cruz
State
CA
Country
United States
Zip Code
95064
Lincoln, Stephen E; Yang, Shan; Cline, Melissa S et al. (2017) Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. JCO Precis Oncol 1:
Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res 43:D670-81
Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S et al. (2015) Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics 31:764-6
Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R et al. (2015) Building a pan-genome reference for a population. J Comput Biol 22:387-401
Karolchik, Donna; Barber, Galt P; Casper, Jonathan et al. (2014) The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 42:D764-70
Raney, Brian J; Dreszer, Timothy R; Barber, Galt P et al. (2014) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30:1003-5
Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn et al. (2014) A unifying model of genome evolution under parsimony. BMC Bioinformatics 15:206
Rosenbloom, Kate R; Sloan, Cricket A; Malladi, Venkat S et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res 41:D56-63
Ewing, Adam D; Ballinger, Tracy J; Earl, Dent et al. (2013) Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol 14:R22
Kuhn, Robert M; Haussler, David; Kent, W James (2013) The UCSC genome browser and associated tools. Brief Bioinform 14:144-61

Showing the most recent 10 out of 71 publications