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Genome Analysis Module:�Variant Interpretation with Exomiser

Dr. Phillip Richmond�UBC MSc Genetic Counselling�November 14th, 2022

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Today’s Outline (November 14th)

  1. Visualize output from ProblemSet 4
  2. Exomiser Introduction and Human Phenotype Ontology
  3. Running Exomiser on Case #4
  4. ProblemSet 5

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Today’s Outline (November 14th)

  • Visualize output from ProblemSet 4
  • Exomiser Introduction and Human Phenotype Ontology
  • Running Exomiser on Case #4
  • ProblemSet 5

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LET’S GET GOING

  1. Activate the VPN (Mitch)
  2. Login to the GPCC
  3. Change to your workshop directory

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Today’s Outline (November 14th)

  • Visualize output from ProblemSet 4
  • Exomiser Introduction and Human Phenotype Ontology
  • Running Exomiser on Case #4
  • ProblemSet 5

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Exomiser

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Exomiser has been used on a large scale!

https://www.nejm.org/doi/full/10.1056/NEJMoa2035790

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Outcome of Exomiser on 100,000 genomes pilot

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Exomiser overview

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Variant prioritization: In silico metrics--CADD

CADD - combined annotation dependent depletion.

https://cadd.gs.washington.edu

In silico scoring metric to predict the potential pathogenicity of variants.

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Variant prioritization: Clinvar

ClinVar - https://www.ncbi.nlm.nih.gov/clinvar/

Allows you to search for pathogenic variants. Let’s explore ClinVar...

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Variant prioritization: population frequency--gnomAD

gnomAD - https://gnomad.broadinstitute.org �gnomAD (nature) - https://www.nature.com/collections/afbgiddede �Let’s explore gnomAD

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Curated disease-associated genes: OMIM

OMIM - https://www.omim.org�Let’s explore OMIM

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HPO - Human Phenotype Ontology

HPO - https://hpo.jax.org/app/

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Today’s Outline (November 14th)

  • Visualize output from ProblemSet 4
  • Exomiser Introduction and Human Phenotype Ontology
  • Running Exomiser on Case #4
  • ProblemSet 5

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Using Exomiser

Exomiser is very simple to use, you only need these things:

  1. Merged VCF for your trio
  2. PED file describing your trio
  3. Exomiser Config.yml file (pointers to VCF, PED, and a list of HPO terms).
  4. Script to call Exomiser Config.yml

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Let’s review Case #4

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Let’s get set up

$ cd /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/

$ cp Scripts/Case4_Exomiser.yml StudentSpaces/Sherlock

$ cp Scripts/RunExomiser_case4.sh StudentSpaces/Sherlock

$ cd StudentSpaces/Sherlock

$ cat Case4_Exomiser.yml

$ cat RunExomiser_case4.sh

$ nano Case4_Exomiser.yml

$ nano RunExomiser_case4.sh

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Walking through the Exomiser Script (places to change for the problemset and your own case analysis)

Always check your file paths!

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$ ls /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/CaseInformation/CaseFiles/Case4/Case4_Merged.vcf.gz

$ ls /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/CaseInformation/CaseFiles/Case4/Case4.ped

$ more /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/CaseInformation/CaseFiles/Case4/Case4.ped

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We also will change the output prefix, matching it to the assigned case

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The RunExomiser script: Make sure you adjust the CONFIG_YML accordingly

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Run Exomiser

$ cd /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/StudentSpaces/Sherlock/

$ nano RunExomiser_Case4.sh

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<Change your email>

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$ sbatch RunExomsier_Case4.sh

$ squeue

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Check for output

$ ls -lahtr

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Let’s use SSHFS to mount the GPCC onto our local machine!

  1. Mac: SSHFS - https://osxfuse.github.io
    1. Open fresh terminal
      1. sshfs <username>@gpcc-node01.bcrichwh.lan:/mnt/scratch/Public/TRAINING/GenomeAnalysisModule/ <somePathOnLocalMachine>
      2. sshfs prichmond@gpcc-node01.bcricwh.lan:/mnt/scratch/Public/TRAINING/GenomeAnalysisModule/ ~/Portal_GPCC/
    2. To close when done:
      • umount -f <somePathOnLocalMachine>
      • umount -f ~/Portal_GPCC/�
  2. PC: http://www.secfs.net/winfsp/
    • \\sshfs\<username>@gpcc-node01.bcricwh.lan/../../../mnt/scratch/Public/TRAINING/GenomeAnalysisModule/

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Open Exomiser HTML output in a web browser

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Summary about the filters applied

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Exomiser output: Prioritized genes

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Exomiser output: Details on the variants

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Inheritance description

  • Inheritance:
    • 0/1 - heterozygous
    • 1/1 - homozygous/hemizygous
    • 0/0 - homozygous reference
  • [Proband:Mother:Father]

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Inheritance description

  • Inheritance:
    • 0/1 - heterozygous
    • 1/1 - homozygous/hemizygous
    • 0/0 - homozygous reference
  • [Proband:Mother:Father]

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What is the mode of inheritance here?

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Exomiser output: Learn more about these pathogenic variants

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Take the rsID query gnomAD, ClinVar

Can also query based on the variant info:

  1. Gnomad: https://gnomad.broadinstitute.org
  2. Choose V3 (IMPORTANT!)
  3. Enter into search bar:

chr7-117530930-T-G

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Take the rsID query gnomAD, ClinVar

Can also query based on the variant info:

chr7-117530930-T-G

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But wait…it’s not there! Note: gnomad V3 and V2 are different sets of genomes/exomes!�

Check the rsID in gnomAD v2: rs397508490

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gnomAD resource growing population…meaning changing allele frequencies!

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Today’s Outline (November 14th)

  • Visualize output from ProblemSet 4
  • Exomiser Introduction and Human Phenotype Ontology
  • Running Exomiser on Case #4
  • ProblemSet 5

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Problem Set 5: Analysis of Case 3

$ cd /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/StudentSpaces/Sherlock/

$ mkdir ProblemSet5

$ cp /mnt/scratch/Public/TRAINING/GenomeAnalysisModule/Assignments/ProblemSet5/ProblemSet5.txt ProblemSet5/

$ cat ProblemSet5/ProblemSet5.txt