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.

Opening Reports

The Reports tab can also be opened by clicking on this icon in the toolbar on the left-hand side of the Sequence Miner window.

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.

Filtering and search

Report builders can be filtered by report type by clicking the arrow to open the drop-down menu. You can also search for individual report builders by entering keywords into the search bar, which searches report builder names, parameter names, and text descriptions.

Filtering the Reports tab

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.

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.

Right-click the tab title to undock

Renaming tabs

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

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

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.

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
Create Case/Control Grid	Generate a case-control grid from sets of subjects, for one or more phenotypes.
dynamic_gwas	GWAS analysis performed for the selected gene(s) or variant input, using genotypes from the selected freeze dataset.
Gene analysis	Count variants and variants in gene for a cohort.
Gene association	Gene-aggregated variant analysis.
Gene count	Count variants per VEP category.
list_casecontrol_counts	In a set of cases and controls, identify the count of ref, het, hom, and NA genotypes.
list_subject_genotypes	In a set of cases and controls, given a list of alleles (defined by variant or gene input), list the genotype for each individuals in each case/control category.
Phenogrid	Generate input table for statistical tools.
Recessive analysis	Count 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).
skat_sequencing	This report performs association tests between genotypes and a phenotype using the SKAT R package.
Single point regression	Apply linear or logistic regression to quantify the relationship between specified variants and phenotypic data.
single_point_regression_sequencing	This report performs association tests between genotypes and phenotype(s) using the generalized linear model, which accepts continuous (e.g. glucose, IQ) as well as binary (e.g. case/control) variables.
Variant association	Single variant case-control association using Fisher Exact.
Variant association ExAC (WES)	Single variant case-control association using Fisher Exact for multiplicative (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)

Samples Reports

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

A list of available Samples report modules in Sequence Miner

Module Title	Description
Create Case/Control Grid	Generate a case-control grid from sets of subjects, for one or more phenotypes.
venn_diagram	Venn comparison among up to ten grids containing a first column of sample identifiers.

Search

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

A list of available Search report modules in Sequence Miner

Module Title	Description
Sample search	Identify subjects with information that matches the input keywords

UKBB Reports

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

A list of available UKBB report modules in Sequence Miner

Module Title	Description
covariate_grid	Produce covariate grids for use as input to subsequent analysis.
phewas_lookup	Finds records from genomic regions of interest with specified variant effect and p-value thresholds.
uk_biobank_sets	Search for relevant UKB fields and identify individuals with specific criteria for use as input to subsequent analysis.

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