Genome Overview

The Genome View Tab, available from V37.0 and up, is a powerful feature designed to give users a clear, visual overview of the genome and chromosomes in their cases. This feature is especially useful for analyzing large Copy Number Variation (CNV) events and regions of homozygosity/loss of heterozygosity (ROH/LOH) across the genome, providing intuitive filtering and interactive insights for researchers and clinicians.

What is the Genome View Tab?

The Genome View tab is a dedicated section within the Case Page for Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), and Array data. This tab offers a graphical visualization of genomic data, focusing on CNV and LOH/ROH analysis for proband cases. Users can access this tab directly from the Case Page.

Key Features

Chromosome Ideogram

The chromosome ideogram offers a visual representation of all 23 human chromosomes, with CNV and LOH/ROH events highlighted for intuitive analysis. Here's what you can expect:

Variant types:

• Deletions (DEL): Marked in red, displayed to the left of the chromosome.

• Duplications (DUP): Marked in blue, displayed to the right of the chromosome.

• LOH/ROH (Regions of Homozygosity/Loss of Heterozygosity): Marked in gold, displayed over the chromosome.

Note: Variants with no coverage or reference (Ref) are excluded.

Filtering Options:

• Users can filter segments by size, using a range selector with the following options: 50 bp,1 KB, 10 KB, 50 KB, 100 KB, 1 MB, 10 MB, Max (no filter).

• The default filter is set from 50 KB to Max.

• Limitation: Only the 500 largest variants are displayed in this tab in v37.0.

Hover and Click Interactions:

• Hovering over a variant displays

  • Chromosome number, start and end positions, and size (e.g., chr1:100000-200000 (100 KB))

  • Cytoband range (e.g., p12.3 - q11.2) based on ISCN nomenclature

  • Variant type (DEL/DUP/LOH/ROH)

  • Number of genes affected

• Clicking on a chromosome refines the genome view below to that chromosome.

• Clicking on a variant opens a detailed Variant Page where many actions and further review can be made.

• Legend: A clear legend explains color coding and icons for DEL, DUP, and LOH/ROH variants for quick reference.

Genome Viewer

The genome viewer provides a deeper dive into the genomic data through three interactive tracks:

• Log R / TNS Track:

  • Displays copy number intensity data using values from the TNS BigWig file or LogR bedgraph.

  • Y-axis ranges from -3 to 3, with increments of 0.4.

  • X-axis displays the genome (whole genome view) or chromosome segments (whole chromosome view).

• BAF Track:

  • Displays B Allele Frequency (BAF) data using values from the BAF BigWig file or BAFbedgraph.

  • Y-axis ranges from 0 to 1, with increments of 0.1.

  • X-axis aligns with the Log R track.

• ROH Track:

  • Indicates regions of homozygosity for further analysis.

Zoom and navigation

• Default View: Displays the entire genome.

• Zoom-In Options: Users can zoom in to view individual chromosomes by clicking on them.

• Interactive Navigation: Clickable chromosomes on the ideogram allow seamless switching between views.