Report Builders

Reports is an interactive graphical interface designed to facilitate data analysis and is based on the GOR language. The Reports tab opens by default when the Sequence Miner application is opened from the Clinical Sequence Analyzer (CSA) dashboard, displaying a grid which lists all available report modules.

To open any one of the modules in Sequence Miner, click on the module in the grid. The grid can be sorted according to the category/type of module.

Using Report Builders

The Reports tab contains a set of predefined report modules, also known as report builders, which can be used to parameterize a variety of different types of reports. There are over forty different modules currently available which target variant and gene annotation, Mendelian inheritance analysis, and cohort analysis use cases.

The Reports tab displays all available report builders as tiles. Clicking on a tile opens the selected report builder in a new tab, where input parameters can be edited to run the report.

Saving favorites

To save a report builder to your favorites, toggle the star icon in the upper right-hand corner of the selected report builder tile. To show only your favorite report builders, toggle the star icon next to the search bar.

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Clicking the star icon on a report adds it to your favourites

Reordering and undocking tabs

To reorder open tabs in the Sequence Miner window, click on a tab and drag it to a new location.

To undock a tab from the window, by right-click on the tab title and select Undock. To redock the tab into Sequence Miner, close the undocked window.

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Right-click the tab title to undock

Renaming tabs

Tabs can be renamed by right-clicking the tab title and selecting Set Title.

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In the Set title dialog, enter a new title and click OK. Tab titles can include alphanumeric and underscore characters only.

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Generating reports

When you have completed the form associated with any report, the Create Report button changes color from grey to light blue, indicating that you have entered sufficient input arguments to run the report. Click the button to generate the report.

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Button changes color when sufficient data has been entered

Cancer Reports

The table below shows a list of the available report builders in Sequence Miner in the Cancer category with a short description of each. Note that Cancer modules are included only in selected installations of Sequence Miner and that your setup may be different.

A list of available Cancer report modules in Sequence Miner
Module Title Description
Cancer QC and statistics Calculates and reports variant statistics for tumor samples
CNV analyzer Annotates and summarizes copy number variation (CNV) calls from the CNVkit caller for tumor samples
Differential expression analysis using edgeR Determine differentially expressed genes between two or more groups of samples
Gene association cancer Gene-aggregated variant analysis
Methylation summary Provides the methylation status of samples at the individual probe level, gene level, or transcript level
mRNA summary Provides expression sequencing data information for samples
miRNA summary Provides miRNA expression sequencing data information for samples
Mutational signatures Count variants per VEP category
Sample map - TCGA Map samples across different data types available in the TCGA multi-omic dataset
Tumor mutation analysis Counts the number of heterozygous, homozygous, and compound heterozygous variants in case and control subjects that pass filtering parameters
Tumor mutation burden Generate input table for statistical tools

Case/Control Reports

The table below shows a list of the available report builders in Sequence Miner in the Case/Control category with a short description of each.

A list of available CaseControl report modules in Sequence Miner
Module Title Description
Gene analysis Count variants and variants in gene for a cohort
Gene association Gene-aggregated variant analysis
Gene count Count variants per VEP category
Phenogrid Generate input table for statistical tools
Recessive analysis Counts the number of heterozygous, homozygous, and compound heterozygous variants in case and control subjects that pass filtering parameters
Sequence Kernel Association Test (SKAT) Evaluate the effect of variants on continuous or dichotomous traits using the sequence kernel association test (SKAT).
Single point regression Apply linear or logistic regression to quantify the relationship between specified variants and phenotypic data
Variant association Single variant case-control association using Fisher Exact
Variant association ExAC (WES) Single variant case-control association using Fisher Exact for multiplactive (mm), recessive (rc), and dominant (dc) genetic models, using the Exome Aggregation Consortium (ExAC) database as controls.
Variant count Count variants in a cohort

Comments Reports

The table below shows a list of the available report builders in Sequence Miner in the Comments category with a short description of each.

A list of Comment report modules in Sequence Miner
Module Title Category Description
Internal annotations Comments Reports List variants with comments in local knowledgebase
Related comments Comments Reports Comments related to PN and gene

Gene Reports

The table below shows a list of the available report builders in Sequence Miner in the Gene category with a short description of each.

A list of available Gene report modules in Sequence Miner
Module Title Description
Annotate genes from list Cross-reference a report with a gene list
Gene carrier report Find carriers of variants in a genelist
Gene ontology association Quantify the association between a list of genes and categories in the Gene Ontology (GO) database
Gene ontology to genes Gene associated with Gene Ontology (GO) codes
Gene/protein ID converter Maps/converts gene and protein IDs from reference source to all others and provide gene/protein names and IDs in a set of user-provided genomic regions
Genes to paralogs Generate a report listing all paralogs of genes in a list
Genes to pathways Maps list of genes to corresponding pathway(s)
Paralog disease annotation Annotate variants with the disease(s) associated with genes and their paralogs
Pathways to genes Maps selected pathway(s) to a set of related genes in the same pathway(s)

Inheritance Reports

The table below shows a list of the available report builders in Sequence Miner in the Inheritance category with a short description of each.

A list of available Inheritance report modules in Sequence Miner
Module Title Description
Carrier Preconception disease gene carrier analysis for parents
De novo/CHZ for trios Trio de novo variant analysis and annotation
Mendelian analysis Single index case Mendelian disease analysis
Multi-family Mendelian analysis Zygosity analysis for cases versus controls

Quality Control (QC)

The table below shows a list of the available report builders in Sequence Miner in the Quality Control (QC) category with a short description of each.

A list of available QC report modules in Sequence Miner
Module Title Description
Exon coverage Calculate the exon coverage for one or more subjects using Ensembl transcripts
Gene coverage Calculate the gene coverage for one or more subjects
Sample QC and statistics Calculate quality statistics for multiple subjects
Sex check Check the sex of the samples
Sharing Calculate the kinship of individuals
Variant QC and statistics Generate a variant summary for subject(s)

Variant Reports

The table below shows a list of the available report builders in Sequence Miner in the Variant category with a short description of each.

A list of available Variants report modules in Sequence Miner
Module Title Description
Annotate variants Annotate variants in selected genes
Annotate variants from file Annotate variants with your own file
Compare GOR reports Compare two reports
Liftover Convert the genomic positions from one genome build to another
Loss of heterozygosity Identify regions of loss of heterozygosity
Overlapping variants Count the variants within a gene list
Risk SNPs Return SNP genotypes for rsIDs
Transcripts Variant transcript effect
Venn variant analysis Compare variant reports with Venn visualization