Variation resources at UC Santa Cruz

The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in the context of other genomic annotations. Primary data from dbSNP is included for many organisms, with added information including genomic alleles and orthologous alleles for closely related organisms. Display filtering and coloring is available by variant type, functional class or other annotations. Annotation of potential errors is highlighted and a genomic alignment of the variant's flanking sequence is displayed. HapMap allele frequencies and linkage disequilibrium (LD) are available for each HapMap population, along with non-human primate alleles. The browsing and analysis tools, downloadable data files and links to documentation and other information can be found at

Presymptomatic risk assessment for chronic non-communicable diseases

The prevalence of common chronic non-communicable diseases (CNCDs) far overshadows the prevalence of both monogenic and infectious diseases combined. All CNCDs, also called complex genetic diseases, have a heritable genetic component that can be used for pre-symptomatic risk assessment. Common single nucleotide polymorphisms (SNPs) that tag risk haplotypes across the genome currently account for a non-trivial portion of the germ-line genetic risk and we will likely continue to identify the remaining missing heritability in the form of rare variants, copy number variants and epigenetic modifications. Here, we describe a novel measure for calculating the lifetime risk of a disease, called the genetic composite index (GCI), and demonstrate its predictive value as a clinical classifier. The GCI only considers summary statistics of the effects of genetic variation and hence does not require the results of large-scale studies simultaneously assessing multiple risk factors. Combining GCI scores with environmental risk information provides an additional tool for clinical decision-making. The GCI can be populated with heritable risk information of any type, and thus represents a framework for CNCD pre-symptomatic risk assessment that can be populated as additional risk information is identified through next-generation technologies.Comment: Plos ONE paper. Previous version was withdrawn to be updated by the journal's pdf versio

The ENCODE Project at UC Santa Cruz

The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website () is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Exploring relationships and mining data with the UCSC Gene Sorter

In parallel with the human genome sequencing and assembly effort, many tools have been developed to examine the structure and function of the human gene set. The University of California Santa Cruz (UCSC) Gene Sorter has been created as a gene-based counterpart to the chromosome-oriented UCSC Genome Browser to facilitate the study of gene function and evolution. This simple, but powerful tool provides a graphical display of related genes that can be sorted and filtered based on a variety of criteria. Genes may be ordered based on such characteristics as expression profiles, proximity in genome, shared Gene Ontology (GO) terms, and protein similarity. The display can be restricted to a gene set meeting a specific set of constraints by filtering on expression levels, gene name or ID, chromosomal position, and so on. The default set of information for each gene entry—gene name, selected expression data, a BLASTP E-value, genomic position, and a description—can be configured to include many other types of data, including expanded expression data, related accession numbers and IDs, orthologs in other species, GO terms, and much more. The Gene Sorter, a CGI-based Web application written in C with a MySQL database, is tightly integrated with the other applications in the UCSC Genome Browser suite. Available on a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set in interactive genomic exploration and analysis

Neuromuscular constraints on muscle coordination during overground walking in persons with chronic incomplete spinal cord injury

h i g h l i g h t s Persons with chronic incomplete spinal cord injury (iSCI) exhibit significant reduced muscle coordination during overground walking as compared to age-matched adults. Neuromuscular constraints following iSCI contribute to person-specific deficits in overground walking. Neuromuscular mechanisms underlying gait deficits may provide guidance for targeted SCI rehabilitation. a b s t r a c t Objective: Incomplete spinal cord injury (iSCI) disrupts motor control and limits the ability to coordinate muscles for overground walking. Inappropriate muscle activity has been proposed as a source of clinically observed walking deficits after iSCI. We hypothesized that persons with iSCI exhibit lower locomotor complexity compared to able-body (AB) controls as reflected by fewer motor modules, as well as, altered module composition and activation. Methods: Eight persons with iSCI and eight age-matched AB controls walked overground at prescribed cadences. Electromyograms of fourteen single leg muscles were recorded. Non-negative matrix factorization was used to identify the composition and activation of motor modules, which represent groups of consistently co-activated muscles that accounted for 90% of variability in muscle activity. Results: Motor module number, composition, and activation were significantly altered in persons with iSCI as compared to AB controls during overground walking at self-selected cadences. However, there was no significant difference in module number between persons with iSCI and AB controls when cadence and assistive device were matched. Conclusions: Muscle coordination during overground walking is impaired after chronic iSCI. Significance: Our results are indicative of neuromuscular constraints on muscle coordination after iSCI. Altered muscle coordination contributes to person-specific gait deficits during overground walking

ROC curves for the WTCCC dataset.

<p><b>A</b>. Crohn's Disease. <b>B</b>. Type 2 Diabetes. <b>C</b>. Rheumatoid Arthritis. In each plot, the black line corresponds to random expectation, the blue lines correspond to theoretical expectations (under the two disease models described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014338#s4" target="_blank">Methods</a>) when the genetic variable is known, the red line corresponds to GCI, and the green line corresponds to logistic regression.</p