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Document # 1000000001129 v13
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March 2022
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Removed National Comprehensive Cancer Network from Guideline Organization selection drop-down menu.
Updated VCF file requirements to specify that the genome assembly must be included in the reference metadata header row.
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Document # 1000000001129 v12
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June 2020
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Updated software descriptions for release 2.10.0, which includes the following changes:
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AddedDRAGEN to variant caller analysis pipeline. |
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Merged GnomAD Exome database with GnomAD database. |
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Document # 1000000001129 v11
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January 2020
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Updated software descriptions for release 2.9.0, which includes the following changes:
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Added Date option to case registry filters. |
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Combined descriptions for merged Created Date and Last Updated Date columns. |
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Document # 1000000001129 v10
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September 2019
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Updated software descriptions for release 2.8.0, which includes the following changes:
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Added Project column to Cases list. |
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Added case search and filter descriptions. |
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Document # 1000000001129 v09
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August 2019
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Removed bidirectional support from Structural Variant fusion consequence filter.
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Document # 1000000001129 v08
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June 2019
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Updated software descriptions for release 2.7.0, which includes the following changes:
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Added probability of loss of function (pLI) scores to gene column and gene filters. |
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Added GnomAD Genome, GnomAD Exome, and TOPMed population database descriptions. |
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Removed ExAC population frequencies, which are included in the GnomAD Exome cohort. |
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Removed obsolete transcript amplification, transcript ablation, and transcript truncation CNV consequence filters. |
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Added MaxMQ0Frac metrics filter. |
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Document # 1000000001129 v07
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February 2019
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Updated software descriptions for release 2.6.0, which includes the following changes:
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Added the ability to view Tumor Type in the Data Type column. |
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Added the ability to expand column width in the Cases tab. |
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Added Tumor Type and Assembly as Sample Metadata Manifest table. |
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Updated Metrics Filters table. |
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Updated the dbSNP, COSMIC, Variant Length, and Number of Copies variant and gene filter descriptions. |
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Document # 1000000001129 v06
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September 2018
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Updated software descriptions for release 2.5.0, which includes the following changes:
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Transcript source selection moved from variant grid to Settings. |
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Added trio analysis setup. |
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Added reciprocal overlap threshold. |
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Add option to upload a gene-level preferred transcript specification. |
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Added IGV track preferences. |
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Added option to select a different transcript for small variants on the variant grid. |
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Added variant length, number of copies, and OMIM to variant and gene filters. |
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Added protein altering consequence filter. |
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Added filter definitions for zygosity. |
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Added SNV and MNV variant filters. |
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Updated procedures for adding and managing gene lists. |
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Clarified definitions for On and Off status. |
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Combined zygosity and metrics columns. |
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Renamed canonical transcript filtering to selected transcript. |
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Updated instructions for adding curations in the curation portal. |
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Added option to send variant for curation. |
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Added option to specify an ACMG tag to publication or miscellaneous evidence types in Mendelian associations. |
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Noted that only privileged users can close cases. |
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Noted that hs37d5 can be used as a synonym for GRCh37 in VCF reference lines. |
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Document # 1000000001129 v05
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February 2018
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Updated software descriptions for release 2.4.1, which includes the following changes:
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Added new case filters for flagged variants, interpreted variants, and variants included in report |
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Unified SNV/Indels, CNV, and SV tabs into a single tab view |
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Reorganized filter tab groups |
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Added case creation date, case updated date, and status filtering to cases tab |
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Added Primary association flag for direct interpretations |
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Database versions added to More Info popup in Case metadata panel |
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Variant Caller column on Cases page is renamed to Genome Build |
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Document # 1000000001129 v04
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September 2017
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Updated the following software descriptions:
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Updated maximum variant exports to 10K |
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Report appendix now includes database versions |
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Document # 1000000001129 v03
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August 2017
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Updated software descriptions to1.0.19963, which includes the following changes:
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Transcript-aware interpretation |
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New interpretation options for Penetrance and Validation |
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Add Knowledge Base associations to report |
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Bulk input of phenotype identifiers in sample metadata manifest |
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Custom annotation support for multiple custom annotations and advanced filtering |
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Family information in read metrics popup |
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Tumor Normal paired & split-read display and filtering |
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Bulk case operations to apply filter, assign owner, reanalyze, and delete |
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Document # 1000000001129 v02
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April 2017
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Updated software descriptions to v1.0.16980, which includes the following changes:
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Added descriptions for the following new features:
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Germline annotation Phenotype contribution |
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Oncology variant Include association type |
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Annotation database notation as allele-especific or position-specific |
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Added new term definitions |
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Removed instructions for auditing a subject |
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Improved description of filters |
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Pipeline renamed to Variant Caller |
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Somatic Variant Caller renamed to Pisces |
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# of Variants renamed to Type of Variants |
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Set Preferences renamed to General |
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New icon renamed to Import |
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Add Interpretation renamed to Case Interpretations |
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Oncology interpretation categories (L1-L4) |
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Germline and Oncology report tabs |
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Read column renamed to Metrics |
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Max Allele Freq renamed to Population Frequency |
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Document # 1000000001129 v01
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September 2016
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Updated software descriptions to v1.0.10580, which includes the following changes:
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Updates to variant grid |
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Added instructions for interpreting and curating variants |
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Document # 1000000001129 v00
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April 2016
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Initial release.
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