2.7. Genome Browser

jMorp has a genome browser that allows you to browse the whole genome reference panel, Japonica array marker locations, and GWAS results while checking their positional relationships on the genome. This genome browser is built on JBrowse2.

2.7.1. Open Genome Browser

The genome browser can be opened from the “Explore with genome browser” panel on the top page. The three assemblies: “GRCh38/hg38”, “GRCh37/hg19”, and “JG2.1.0” are available.

../../_images/genomebrowser-top.en.png

Each assembly provides different data. Examples are shown below.

Assembly

Provided Data

GRCh38/hg38

  • Whole genome reference panel (14KJPN to 54KJPN; refer to 54KJPN-SNV/INDEL for more details)

  • Structural Variation Reference Panel based on long read sequencing (See JSV1 )

  • Copy Number Variation Reference Panel

  • Japonica Array Marker

  • Accessibility(HiSeq 2500, NovaSeq 6000, DNBSeq G400, DNBSeq T7)

GRCh37/hg19

  • Whole Genome Reference Panel (3.5KJPN to 8.3KJPN)

  • Structural Variation Reference Panel based on short read sequencing (See 8.3KJPN-SV )

  • Structural Variation Reference Panel based on long read sequencing (See JSV1 )

  • Japonica Array Marker

  • Accessibility (HiSeq 2500)

  • Genetic Map

  • GWAS

  • IMM Methylome (See IMM 3cell analysis and IMM cord blood)

JG2.1.0

  • Whole genome reference panel (converted from GRCh38)

  • GRCh38 derived region

When the genome browser is successfully loaded, the following display will appear.

../../_images/genomebrowser-initial-view.en.png

2.7.2. The list of tracks

When you opened the genome browser, some limited number of contents are shown. We provide a lot of data about TMM and other annotation and can be shown in the genome browser.

To display the list of tracks, please click a red rectangle shown in the below.

../../_images/genomebrowser-track-selector-open.en.png

The list of tracks is opened as shown in the below.

../../_images/genomebrowser-track-selector.en.png

In this panel, you can select tracks to display. There tracks are classified by categories. The list of categories are shown in the below.

Category name

Contents

Assembly

Annotation

  • External annotation data, such as gene annotation, ClinVar, dbSNP and Repeat Masker.

  • The variants in the ClinVar track are colored by clinical significance.

  • The variants in the dbSNP track are colored by snpEff impact.

  • The variants in the gnomAD track are colored by variant frequency.

  • The tracks in JG2.1.0 assembly is not colored.

GRCh38/hg38, GRCh37/hg19, JG2.1.0

TMM Genome Variation

  • Whole genome reference panel

  • A variant is colored by frequency.

  • The tracks in JG2.1.0 assembly is not colored.

GRCh38/hg38, GRCh37/hg19, JG2.1.0

TMM Genome Variation (Colored by snpEff Impact)

  • Whole genome reference panel

  • A variant is colored by snpEff impact

GRCh38/hg38, GRCh37/hg19

Japonica Array

  • The list of Japonica Array.

  • There is a problem that the current JBrowse version does not display correctly when trying to display a large area, so please zoom in.

GRCh38/hg38, GRCh37/hg19

Accessibility

  • Accessibility in various sequencers.

GRCh38/hg38, GRCh37/hg19

Variant co-occurrence

  • Variant co-occurrence

GRCh38/hg38, GRCh37/hg19

2.7.2.1. Color legend for variants

../../_images/color-legend.en.png

2.7.3. Region search

You can search a region by gene name, dbSNP ID, or amino acid change described with HGVS variant nomenclature. Searches can be performed from the box where the chromosome name and position are displayed, as shown in the image below.

../../_images/genomebrowser-search-box.en.png

Possible search items and examples are as follows

Search Item

Example

Note

Gene symbol

  • KRAS

  • BRCA2

  • NFE2L2

Searching by synonym (e.g. NRF2) is not supported.

dbSNP ID

rs671

amino acid change described with HGVS variant nomenclature

  • TP53 P72R

  • BRAF p.Val600Glu

  • Both 3-letter and 1-letter notation are available.

  • Searching by synonym (e.g. NRF2) is not supported.

When multiple areas are hit, the selection dialog will look like this.

../../_images/genomebrowser-search-result.en.png

Searching by dbSNP ID and amino acid change described with HGVS variant nomenclature is only available for GRCh37/hg19 or GRCh38/hg38 and is unique to jMorp’s JBrowse2.

2.7.4. Overlay your data.

JBrowse2 allows you to overlay your own data on top of the data at your local machine. Your data will not be uploaded to the server, nor will Tohoku Medical Megabank Organization be notified of what data is being displayed.

To overlay your data, select “Open track…” from the “FILE” menu from the “FILE” menu to display your data.

../../_images/genomebrowser-new-track1.en.png

Next, enter the URL or select a file in the “Add a track” panel displayed on the right side. If the format requires an index file, it will not be loaded automatically like IGV, so you will need to select it manually. Click “NEXT” when done.

../../_images/genomebrowser-new-track2.en.png

The settings are automatically suggested based on the contents of the file. If all is well, click “ADD”.

../../_images/genomebrowser-new-track3.en.png

After performing the above operations, you can overlay the data at your local machine as shown below. In this example, a CRAM file is displayed, but BED and GFF files can also be displayed.

../../_images/genomebrowser-new-track4.en.png

2.7.5. How to display variant co-occurrence

Variant co-occurrence can only be displayed correctly when a large enough area is displayed. If individual SNVs or INDELs are enlarged enough to be displayed, they should be reduced in size. If it is displayed correctly, it will look like this

../../_images/genomebrowser-co-occurrence.en.png

2.7.6. Share the contents of the display with others

JBrowse2 allows you to share the current display with others. When you do this, encrypted data of the current display is sent to the JBrowse developer. To share, click the “SHARE” button in the top header as shown below.

../../_images/genomebrowser-share1.en.png

After a short wait when the dialog box appears, the URL for sharing will appear as shown below. Click “COPY TO CLIPBOARD” to copy the URL and share it.

../../_images/genomebrowser-share2.en.png

2.7.7. JBrowse official document

Please refer JBrowse2 user guide for general use of JBrowse 2.