In the last 10 years the UCSC Genome Browser has become a standard resource in the field. The number of web hits and users continues to increase, more than doubling in the last four years. The browser is also widely featured in scientific papers and presentations. As genomics penetrates ever more deeply into science and medicine, the value of the browser's definitive collection of data sets mapped to reference genome, coordinated, and made interactively accessible, continues to grow. In the next five years we will tackle several key challenges: (1) Update the UCSC gene set to reflect recent dramatic progress in genomics methods with the widespread use of technologies such as next-generation genome sequencing, RNA-seq, and ChlP-seq;these have deepened our view of human genes, both coding and non-coding, including alternative splice variants, regulatory elements, and haplotype variants. (2) Enhance and unify in a common framework our linkages to functional elements of the genome that have been associated with known human variation by projects such as 1000 Genomes and dbSNP, with homologous elements in other species by projects such as Genome 10K, with experimental information by projects such as ENCODE and Roadmap Epigenomics, and with disease phenotypes by projects such as OMIM and COSMIC. The value to research of these linkages and the advanced integration we create increase sharply as they become more comprehensive and more accurate. (3) Continue the fundamental transition to a more distributed database that started with the development of browser data hubs. Broaden our reach with more remote mirror sites and increased training, and increase the security of data uploaded to the browser by users. These developments are essential for the transition from the era of reference genomics to the era of personal genomics, where the data sets are too large, too distributed, and too sensitive to be handled like reference genome data. Since these data still need to map to a reference genome, these innovations will make the browser more relevant than ever in the era of personal genomes.

Public Health Relevance

RELEVAN;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 Cooperative Agreements (U41)
Project #
2U41HG002371-13
Application #
8339088
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Felsenfeld, Adam
Project Start
2001-07-12
Project End
2017-06-30
Budget Start
2012-09-12
Budget End
2013-06-30
Support Year
13
Fiscal Year
2012
Total Cost
$3,380,016
Indirect Cost
$1,087,794
Name
University of California Santa Cruz
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
125084723
City
Santa Cruz
State
CA
Country
United States
Zip Code
95064
Zerbino, Daniel R; Ballinger, Tracy; Paten, Benedict et al. (2016) Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinformatics 17:400
Haeussler, Maximilian; Schönig, Kai; Eckert, Hélène et al. (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148
Speir, Matthew L; Zweig, Ann S; Rosenbloom, Kate R et al. (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res 44:D717-25
Qu, Kun; Garamszegi, Sara; Wu, Felix et al. (2016) Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods 13:245-7
Hinrichs, Angie S; Raney, Brian J; Speir, Matthew L et al. (2016) UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics 32:1430-2
Foote, Andrew D; Liu, Yue; Thomas, Gregg W C et al. (2015) Convergent evolution of the genomes of marine mammals. Nat Genet 47:272-5
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
1000 Genomes Project Consortium; Auton, Adam; Brooks, Lisa D et al. (2015) A global reference for human genetic variation. Nature 526:68-74
Miga, Karen H; Eisenhart, Christopher; Kent, W James (2015) Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res 43:e133

Showing the most recent 10 out of 24 publications