The UCSC Genome Browser 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, requesting more than a total of 150,000 pages of information. Scientists retrieve direct information about the sequences of human genes, their location in the genome, their normal expression levels in different tissues, the alternatively spliced mRNAs they produce, the protein products they make, and the genetic variations that exist within them in the human population. Users get quick links to other databases at NIH and elsewhere that provide detailed information on each gene's function, its association with human disease, and known disease-causing variants of the gene. ? ? Genes make up only approximately 1.5% of our genome. The remaining parts of our genome harbor important non-protein-coding functional elements that control gene expression and other important cellular processes, such as DNA packaging and replication. The UCSC Genome Browser is one of the first tools that allows scientists to begin to explore the vast uncharted landscape of these non-protein-coding functional elements in our genome, and to determine how they affect our health. Like the genes, these other functional elements are evolutionary conserved between different mammals. We identify these elements through their exceptional patterns of evolutionary conservation, using comparisons between the human genome and the genomes of other mammals, including the experimental model organisms, mouse and rat. Our cross-species DNA mappings provide researchers a chance to study individual functional elements in mammalian model organisms that correspond to particular functional elements in the human genome. Through such research, we will learn the functions of both the human genes and the non-coding functional elements in our genome. ? ? By mapping the important genetic differences between people and understanding their functional consequences, we lay the groundwork for a future of individualized medicine, where treatment is increasingly tailored to the individual. ? ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Biotechnology Resource Grants (P41)
Project #
5P41HG002371-07
Application #
7279997
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M2))
Program Officer
Felsenfeld, Adam
Project Start
2001-07-12
Project End
2007-08-31
Budget Start
2007-08-01
Budget End
2007-08-31
Support Year
7
Fiscal Year
2007
Total Cost
$139,994
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:
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
Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res 43:D670-81
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

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