Using drill in reports

The Drill in function in Sequence Miner enables quick variant and gene annotation on the fly. For example, if you have list of variants and want to know if the gene carrying the variants has been associated with a disease, you can select the drill in under Associated gene with that is called Associated human phenotypes (HGMD, OMIM, ClinVar).

To access drill in reports, open a grid in Sequence Miner (e.g., by running a report builder analysis) and highlight one or more rows of interest.

Right-click on the highlighted row(s) and select Drill in Reports to open a list of available drill ins for variant and gene annotations, grouped by category of analysis. Variant-specific drill ins are available only if columns Chrom, Pos, Reference, and Call are present in the grid. Gene-specific drill ins are available only if the Gene_symbol column is present.

Select a drill in report from the list. A new Sequence Miner window opens to display the original grid with new columns containing the selected annotation appended to the right-hand side.

Note

If the original grid does not contain the required columns for a particular drill in report table to be joined, that drill in report is greyed out in the context menu and cannot be selected.

Available drill in reports

The following table contains a list of available drill-in reports with a description of each.

Drill in reports in Sequence Miner

Category of analysis	Drill in report	Description
Annotate variant with	Gene symbol and info	Annotates each selected variant with 7 gene annotation columns prefixed with Gene_, including the gene symbol, Ensembl gene ID, biotype, strand of transcription, gene description, and the coding sequence start and stop position.
	Allele frequency	Annotates each selected variant with AF (allele frequency) information from 1000GP3, EVS, and gnomad databases.
	dbSNP - rsID	Annotates each selected variant with the rsID from the dbSNP database.
Predict effect of variant with	VEP - summary annotation	Annotates each selected variant with 9 summary Ensembl VEP columns prefixed with VEP_, including the maximum predicted impact and consequence of the variant, biotype, gene symbol, total number of predicted transcripts, altered amino acid (if coding variant), protein position, coding sequence position, and Refgene transcript ID.
	VEP - detailed annotation	Adds comprehensive annotation in 24 new columns from VEP Ensembl columns including the maximum predicted consequence, RefSeq gene, transcript and protein ID; cDNA, coding sequence and protein position; altered amino acid (if coding variant); altered codon sequence; existing matching variations in dbSNP/COSMIC; exon/intron altered; HGNC symbol; distance; maximum allele frequency; protein domain affected; HGVS transcript and protein annotation; biotype; RefSeq transcript ID; protein amino acid size; and gene symbol.
	Refseq - detailed annotation	Adds comprehensive annotation in 24 new columns from VEP RefSeq including the maximum predicted consequence, Ensembl gene, transcript and protein ID; cDNA, coding sequence and protein position; altered amino acid (if coding variant); altered codon sequence; existing matching variations in dbSNP/COSMIC; exon/intron altered; HGNC symbol; distance; maximum allele frequency; protein domain affected; HGVS transcript and protein annotation; biotype; RefSeq transcript ID; protein amino acid size; and gene symbol.
	DeepCODE scores	Annotates each selected variant with the likelihood that the variant is deleterious.
List variant associated with human phenotype/traits	Human Gene Mutation Database	Annotates each selected variant with information from the HGMD professional database about the variant’s relationship with human phenotypes, including the following: HGMD curator comments and confidence levels; HGMD accession number; associated disease annotations; HGMD variant consequence (mutation_type); HGMD pathogenicity score (variant_type); genomic sequence flanking the variant position; smomed ct ID; OMIM ID; pubmid ID; rsID; uniprot ID; Ensembl ID; Entrez ID; and population allele frequency (AF) from 1000GP3, EVS, EXAC, Genomes of the Netherlands (GONL), Japan (Kyoto_JPT) and Iceland (DECODE_AF). Annotation available from ref/hgmd/hgmd_hgmd.gorz.
	Clinical variant databases (HGMD, OMIM, ClinVar)	Annotates each selected variant with clinical information about the variant(s) from HGMD, OMIM, AND ClinVar.
	Published GWAS	Lists the variants that have been previously described in a GWAS study and reported as associated with a disease_trait.
	Cohort specific phenotypes	Joins the selected variant(s) to the source/var/wgs_varcall.gord file to extract all carriers, counts the number of distinct sample_id’s for carriers of the selected variant(s), and then maps each carrier to the Phenotypes.rep file to extract each carrier’s phenotype-taxonomy, -code and -description (a Phenotypes.rep file must be open in a tab).
List carriers and zygosity status	Patients carrying selected variants	Lists the samples that carry the selected variant(s) in two columns: set_PN: A comma-delimited list of samples that contains this variant. dis_PN: The number of distinct sample IDs for carriers of the variant.
Annotate gene with	Predicted pathway membership via domain signature	Maps the selected gene_symbol(s) to the ref/ensgenes/ensgenes_gene2pathway.mmap file and annotates each selected gene_symbol with related pathway information.
	Exome aggregation consortium (ExAC)	Annotates each selected gene with the likelihood of the gene causing a disease if mutated (e.g., genes like olfactory receptors are not likely to cause a disease).
	Associated human phenotypes (HGMD, OMIM, ClinVar)	Maps the selected gene_symbol(s) to the ref/clinical_genes.gorz file and extracts the annotation columns for the selected gene_symbol(s). Added columns are KNOWN Gene_diseases, lis_disease (a comma-delimited list of associated diseases), MaxClinImpact, and lis_dbSourceMaxClinImpact (comma-delimited list of databases sources of MaxClinImpact reports).