Gene carrier report¶

The Gene carrier report builder finds carriers of variants in a user-designated genelist among subjects in a user-designated list. The user may limit the report to variants that meet VEP_consequence and quality thresholds.

Example Use Case¶

An investigator has a list of candidate genes for autism and wishes to identify all carriers among a subset of patients (samples in the project) of variants with HIGH and MODERATE VEP_consequence in the genelist. The investigator creates a grid of the subject PNs of interest (the SUBJECTS) and a grid of the genelist of interest, sets the desired VEP_consequence threshold, and creates the report.

Description of the algorithm¶

All variants in the user-designated genes/genelist that meet the desired thresholds for VEP_max_consequence, allele frequency, and quality filters are reported in the output with a total count of the carriers for each reported variant.

Interpreting the output¶

This report returns a PN_count column and a lis_PN column. The PN_count column displays the number of samples carrying the variant in that row. The lis_PN column displays a comma-delimited list of the samples (PNs) carrying the variant in that row.

Column descriptions¶

Report output columns and descriptions¶
Group	Column	Description
Basic	Call
	Chrom
	Pos
	Reference
Max	AF	Maximum allele frequency from public databases (1000Genomes, Exome Variant server, etc.)
	consequence	Consequence type reported for this variant having the greatest impact
	Impact	Classification of the level of severity of the transcript consequence type assigned by VEP
Other columns	Amino_Acids	The amino acid with and without variant (provided only if the variation affects the protein-coding sequence), otherwise “.”
	Biotype	Biological class of transcript or regulatory feature
	CDS_position	Position of the base pair in the coding sequence; a value is given for each transcript
	Gene_Symbol	Based on HGNC when it exists, otherwise it is the Ensembl internal alias
	lis_PN	A comma-delimited list of the samples containing this variant
	PN_count	The number of samples containing this variant
	Protein_Position	Position of the amino acid in the protein sequence (only if the variant falls within a coding sequence); a value is given for each corresponding transcript specified in the CDS position field
	Refgene	The accession number from NCBI of the affected transcripts
	Transcript_count	Number of different transcripts in which the variant is found