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Revision History

Document

Date

Description of Change

Document # 100000000110864 v02

August 2020

Update to support software version 1.5.1 release.

Added instructions for the following new features:

• Importing gene association data to a variant association.
• Automatic literature search and publication evidence queue.
• Opt-in selections for secondary findings, research consent, and DNA storage.
• Using unique custom annotation title/column heading names.
• Searching by case information.

Added partially duplicated transcript to transcript consequence filters.

Renamed Report Category to Report Section.

Added instructions for deleting FASTQ files.

Consolidated instructions for adding association data.

Noted that default BED files are included for each version of the reference genome.

Noted that the maximum number of custom annotation files per test is 10.

Added callability and coverage report names to report descriptions.

Noted that only original authors can edit comments.

Noted that large custom IGV files must be compressed before upload.

Document # 100000000110864 v01

June 2020

Update to support software version 1.5 release.

Consolidated instructions for adding association data.

Changed CaseLog gene expression histogram graph data from count of reads per kilobase per million mapped reads (RPKM) to transcripts per million (TPM).

Added instructions for the following new features:

• Setting up domain administrator and managing domain access.
• Adding and using custom STR annotation threshold files.
• Adding gene list files and using gene lists in filters.
• Applying active/inactive case status.
• Modifying phenotype after case is initiated.
• Adding custom report field and editing existing fields.
• Updating association details from reports page.
• Variant grid multi-level column sorting, flagging variants, and viewing by status.
• Adding SNV evidence and ACMG criteria when adding a new association.
• Enabled sharing variant comments across cases.
• Downloading the CLI tool from the account drop-down list.
• Using the --configFilePathcommand.
• New transcript consequence filters for CNV/SV
• Additional gene details.
• Changed classification options for for SVs and CNVs to use the same categories as SNVs.
• Usage data displayed in the dashboard, linked to detailed usage information.
• Added % SNV in ROH QC metric.
• Notes replaced by case-specific comments.
• Variant grid pedigree zygosity and scores across transcripts for consequence, pLI, and PrimateAI.

Document # 100000000110864 v00

April 2020

Initial release.