G2P VEP plugin

The G2P VEP plugin identifies likely disease causing genes based on the knowledge encoded in the G2P database and runs as part of the Variant Effect Predictor (VEP).

Ensembl Variant Effect Predictor

Ensembl VEP predicts the molecular consequence of a variant and reports further optional annotation.

How the plugin works:

The G2P VEP plugin adds further annotation to the line of output based on the individual's genotypes and the knowledge contained in the G2P database. The G2P VEP plugin uses a set of filters for identifying potentially causal variants. If the plugin counts a sufficient number of causal variants (variant hits) for a G2P gene it will report the gene as likely disease causing and all variants that passed the filters. The number of sufficient causal variants is derived from the allelic requirement of the gene which is stored in the G2P database.

By default the plugin adds certain information to the VEP output individual information, gene symbol or HGNC id, global allele frequency data from 1000 Genomes Phase 3 data for any colocated variant, SIFT predictions, Polyphen-2 predictions.

The plugin by default also checks for existing variants that are colocated with the given variants and will exclude those flagged as failed by Ensembl QC checks.

Filtering rules:

Consider the variant as potentially causal if the variant passes all filtering steps.

1. The variant overlaps a G2P gene
2. The variant consequence is in the list of severe consequences. The default list contains the following terms: splice_donor_variant, splice_acceptor_variant, stop_gained, frameshift_variant,stop_lost,initiator_codon_variant, inframe_insertion, inframe_deletion, missense_variant, coding_sequence_variant, start_lost, transcript_ablation, transcript_amplification, protein_altering_variant
3. All allele frequencies from co-located variants in reference populations (1000 Genomes project, gnomAD) need to be below a given threshold. The default frequency values for an allele in a bi-allelic gene is 0.005 and for an allele in a mono-allelic gene is 0.0001.

The sufficient number of variant hits is determined by the gene's allelic requirement.

G2P supports biallelic_autosomal, monoallelic_autosomal, mitochondrial, monoallelic_Y_hem, monoallelic_X_hem, monoallelic_X_het, monoallelic_PAR, biallelic_PAR as an allelic requirement. To ensure compatibility with our old terminologies, we still support the allelic requirements, monoallelic, biallelic, hemizygous, x-linked dominant, x-linked dominance.

af => 0.005, rules => {HET => 2, HOM => 1} 

 af => 0.0001, rules => {HET => 1, HOM => 1} 

Installing and running the VEP and G2P VEP plugin

For installation and running the VEP script please refer to the VEP GitHub repository and VEP documentation pages. Plugins are installed and configured during the VEP installation. The G2P VEP plugin is located in the VEP plugins repository.

To run the G2P VEP plugin add the following argument to the VEP command:

The file to be used for running G2P plugin is the panel file from G2P or PanelApp. The plugin can not be run without the file.

Options are passed to the plugin as key=value pairs

./vep -i input.vcf --plugin G2P,file='DDG2P.csv',af_monoallelic=0.00001

./vep -i input.vcf --plugin G2P,file='DDG2P.csv',af_biallelic=0.05

Allele frequencies

The G2P plugin filters input variants on allele frequencies. The allele frequencies are retrieved from major genotyping projects like the 1000 Genomes project and gnomAD. The VEP provides a cache which contains allele frequencies in order to speed up the variant annotation.

To use the VCF file for filtering, the G2P plugin option af_from_vcf needs to be set to 1.

./vep -i input.vcf --plugin G2P,file='DDG2P.csv,af_from_vcf=1'

Example input and output files

• run_vep_g2p_plugin
• input.vcf
• VEP TXT output
• report.html
• report.txt

Speed and Optimization

• VEP can look up existing annotations from locally installed cache files in order to increase the speed of computation. The VEP installation process will guide you through the cache file selection and installation process.
• More ways to make sure that your VEP installation is running as fast as possible.

PanelApp

The G2P VEP plugin accepts PanelApp data files as input. We use the following mappings to translate between the terminologies used by G2P and PanelApp.