introduction to genome trax

With 3-4 million variants identified per sequenced human genome, it can be difficult to determine the few that count. Genome Trax™ enables you to positively identify variants of functional significance by mapping the NGS data to known elements such as disease mutations and regulatory sites. It can also filter out common variants, identify novel mutations that result in protein changes, or provide predictions on the functional impact of such variants.

If you are analyzing whole genome or exome sequencing data — Genome Trax™ is the tool to use. Genome Trax™ makes it easy to upload a complete genome’s worth of variations and, within an hour, identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. This is the only resource that provides public content as well as proprietary data from HGMD®, TRANSFAC® and PROTEOME™.

Genome Trax™ provides a simple, easy-to-use online interface for biologists, geneticists and pathologists working with variant files. For bioinformaticians and computational biologists, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax™ data is already optimized to work with many other software packages, such as CLC bio, Avadis NGS, Alamut, SimulConsult, GeneData, and Cartagenia.

Benefits

  • Prioritize mutations from large-scale sequencing
  • Identify disease-causing mutations
  • Sequence genome of interest, reduce cost and time on trio comparisons
  • Reduce the amount of mutations you have to investigate
  • Identify novel mutations not previously reported in the literature
  • Predict if novel mutations are deleterious, result in protein changes or affect disease genes
  • Find diseases, drugs, and pathways linked to variants

Key Features

  • Positively identifies relevant variants, not just filtering
  • Fast turnaround time: whole genome analysis in under an hour, whole exome in minutes
  • Over 150,000,000 annotated features total
    • HGMD® Professional disease mutations and genes
    • Pharmacogenomic variants
    • TRANSFAC® gene regulatory elements: miRNAs, experimental transcription factor binding sites (TFBS), refined ENCODE ChIP-seq TFBS, refined ENCODE DNase hypersensitivity region TFBS, microsatellites, CpG islands
    • PROTEOMETM disease biomarkers, drug targets, pathway memberships
    • Up-to-date, unified access to annotation from dbSNP, COSMIC, GWAS catalogue, ClinVar
  • Integrated variant effect prediction for novel variants based on machine learning, conservation, allele frequency, effect on protein sequence, and curated functional annotation
  • Fully compatible with ANNOVAR, UCSC Genome Browser, Galaxy, CLC Genomics Workbench, Avadis NGS, Alamut®, GeneData, SimulConsult, Cartagenia BENCH, Microsoft Excel
  • VCF, tab-delimited, BED, UCSC, and Complete Genomics variant file format support

 

Access Options

Online
An online subscription provides access to the Genome Trax web interface. Online subscriptions are available at the single named user, concurrent user, and institution-wide level. All subscription levels require IP plus username/password authentication.

Download
A download subscription provides access to all Genome Trax annotations in the form of .bed and .gff formatted files and MySQL relational database dump. In this way, the complete Genome Trax data can be integrated into your own, or 3rd party, NGS analysis pipelines or tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent. A download subscription does not provide access to the Genome Trax web interface.

Resources

Support Documents


Training

Release 2012.4 – Available on-demand
>> Watch it on YouTube


Video Tutorials

Analysis Steps
Perform various annotation features.
>> Watch video

Results
View mapped feature stats, table output and UCSC browser.
>> Watch video

File Formats
Various input formats and the download options.
>> Watch video

Identify Disease Variants
Using Alzheimer disease as an example.
>> Watch video


Archived Webinars

ANNOVAR: How to Annotate Genetic Variants
Integrating HGMD® and Genome Trax Data in a Large Scale Variant Analysis Platform
NGS Variant Analysis
Understanding Diseases and Pathways through NGS Data Analysis
Next Generation Sequencing in Clinical Research “Results and Lessons Learned”

>> View all webinars