ASHG 2017 Interactive Invited Workshop: Accessing the Breadth of Data in Ensembl: A Worked Clinical Example

Date:

  Wednesday 18 October 2017

Venue: 

Orange County Convention Center - Orange County Convention Center, International Drive, Orlando, , FL,  FL 32819-1509, United States

Participation: 

First come, first served

Contact: 

Benjamin Moore

Registration closed

Dates additional information: 

This 'Interactive Invited Workshop' is ticketed event that is being held as part of the ASHG 2017 conference. Please see the ASHG 2017 website for further details: http://www.ashg.org/2017meeting/

Course Overview

The Ensembl genome browser (www.ensembl.org) provides visualisation and analysis of integrated genomic data, including genes, variants, comparative genomics and gene regulation, for over 100 species.

This workshop provides guidance for wet-lab scientists and clinicians who have not yet discovered the power and depth of this resource. A brief introduction to Ensembl will be followed by hands-on demonstrations and exercises that describe and demonstrate an adaptable workflow for exploring and exporting genomic data:

  • Use BioMart to export a list of genes falling within a clinically relevant genomic location (20min)

  • From the gene list exported from BioMart, explore a single gene in Ensembl, exporting its sequence and identifying variants, homologues and GO terms (20min)

  • Work through a deep dive exploration of a variant that falls within the gene of interest, finding functional consequences, population frequencies from the 1000 Genomes project, population transcript haplotypes and phenotypes (20min)

  • Explore GTEX eQTL data to discover relevant variants in the region surrounding the gene of interest, that affect its expression in various tissues (10min)

Workshop materials, including slides, demonstration screenshots, exercises and solutions will be made available before the workshop and will remain permanently online at our training portal: https://training.ensembl.org.

 

Audience

Clinicians and wet-lab scientists. New/intermediate Ensembl-users.

Learning outcomes

  • Gain confidence to explore a broad range of data types in Ensembl, and to export these data

  • Gain familiarity with typical workflows for exploring genomic annotation from Ensembl

  • Explore the GTEX eQTL data, which has recently been incorporated into Ensembl

  • Learn about transcript haplotypes predicted from phased 1000 Genomes variation