# Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics Data

> **NIH NIH U24** · UNIVERSITY OF CALIFORNIA BERKELEY · 2020 · $685,480

## Abstract

Cancer begins with mutations of the genome that can include substitutions, indels,
duplications, gene fusions, and genome rearrangements. These mutational signatures
vary widely between tissues and, often, between individual tumors. To understand this
mutational landscape, cancer researchers need tools for visualizing the structural
variation in cancer DNA, and its impact on gene transcription and regulation. For greater
insight, these data should be augmented with gene annotations, results from functional
genomics project like ENCODE, and population-level data.
The classic tool for visualizing human gene annotations is the web-based genome
browser. However, genome browsers are not generally well-suited to visualizing
large-scale structural variation: for that, circular visualization tools (such as Circos) are
often used, but those tools are not very interactive (or web-based). Additionally, few
genome browsers allow analysis to be performed within the application itself.
JBrowse is the most popular genome browser built using JavaScript and dynamic web
technology. Originally aimed at model organism genome projects, it is the web-based
browser predominantly used by such projects, and yet its single largest user is now the
UK-based Cancer Genome Project. We have developed prototypes of an interactive
circular view for JBrowse, a data loading pipeline to import human genome annotations,
a framework for running interactive analyses from within the browser. We plan to extend
these prototypes to a fully-fledged system for visualizing structural variants and other
mutations in cancer genomes, and running analyses on those data. We will integrate
this software with the systems of the Cancer Genome Project, the International Cancer
Genome Consortium, and the Genomic Data Commons.

## Key facts

- **NIH application ID:** 9986722
- **Project number:** 5U24CA220441-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Ian H Holmes
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $685,480
- **Award type:** 5
- **Project period:** 2017-08-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9986722

## Citation

> US National Institutes of Health, RePORTER application 9986722, Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics Data (5U24CA220441-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9986722. Licensed CC0.

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