General
Purpose
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Software release notes
Moon version 4.0.2
26 September 2022 • 21b741c6fb95b3, e8a03535c0a5842
Features
Only laboratory admins will be able to initiate a payment [MOON-453]
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The manual was updated to version 4.0.2 (release date 26-09-2022).
Moon version 4.0.1
20 June 2022 • 3eafe9a1028583ede46403301d6c743e666dc076, 951ab6b7acd1908d584c383c517808b401bbade6
Features
Variant ID field from the VCF is now also displayed in the Moon API output (MOON-489)
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The manual was updated to version 4.0.1 (release date 20-06-2022).
Moon version 4.0.0
1 May 2022 • 87c5011, ef88598
New features
Addition of a Quality page for SV/CNV input files (MOON-277)
Addition of a Filter view for SV/CNVs (MOON-254; MOON-416; MOON-441)
Annotation and analysis of BND calls in automated pipeline and Filter view (MOON-188)
Addition of gnomAD SV as annotation source for deletions and duplications (MOON-211)
Updates to family segregation filtering in SV/CNV pipeline (MOON-259)
Addition of SV/CNV to exon-level visualisation in the SV/CNV genome browser (MOON-275)
Compound heterozygosity of a carrier SNV with an SV/CNV variant is now also indicated for the variant in the Carrier tab (MOON-99)
Support detection of SV/CNVs overlapping non-protein coding genes; change requirement for exonic overlap in automated SV/CNV pipeline (MOON-257)
Display known SV/CNV syndromes in the SV/CNV Shortlist and variant cards (MOON-411)
Add zygosity-inheritance filtering for SV/CNVs affecting single genes (MOON-216)
Allow to upload gzipped VCF files for SV/CNV input (MOON-415)
Annotate 'updated' label if differences in reanalysis results for SVs (MOON-412)
Add SV/CNVs to the Shortlist download (MOON-414)
Addition of ACMG classification support in the KB (MOON-33)
Addition of Moon favicon (MOON-409)
Addition of an API endpoint for updating Patient information (MOON-413)
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The manual was updated to version 4.0.0 (release date 1-05-2022).
Moon version 3.6.0
18 February 2022 • 041c06c, 5b2b5f5
New features
Addition of EVE predictions (2021-11-17) as annotation (Frazer et al., 2021), contributing to variant ranking in the Shortlist. EVE scores are highlighted in red if the value is > 0.762 (PPV80 threshold based on internal testing) (MOON-343)
Warning for non-existing/recognised genes when adding/editing a Panel (MOON-242)
Warning for non-existing/non-recognised genes in the Genes filter in the Filter view (MOON-235)
Possibility to open a variant in Alamut Visual Plus via the position menu, or c. notation in the variant card (MOON-327)
Newsletter is now displayed in Moon after a new version is released and the most recent Newsletter can be reviewed at any time through the help menu (MOON-348)
Filter view now allows to only display variants with an associated Apollo disorder annotation (MOON-208)
On the Samples overview screen, it is now also possible to filter samples based on not being part of a Project (MOON-392)
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The manual was updated to version 3.6.0 (release date 18-02-2022).
Moon version 3.5.1
6 December 2021 • b270ca8
Bug fixes
Fix for HPO extraction from referral notes for non-English text, with empty lines at beginning or end of the inputted text (MOON-71)
Fix for use of annotation source InvitaeKB (GRCh37 samples only). In Moon 3.5.0, version 2021-06-04 was still in use. This has now been fixed in order to use version 2021-10-06. Variants classified as LB/B by Invitae based on this latest version of the data source, will now be filtered out of the automated analysis (if not overruled by a classification in the lab’s KB). Variants with LP/P classifications will be less stringently assessed for inclusion in the Shortlist based on classifications in this most recent version as of Moon 3.5.1 (MOON-306).
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The manual was updated to version 3.5.1 (release date 06-12-2021).
Moon version 3.5.0
23 November 2021 • commit 6c77d9a
New features
Addition of SpliceAI annotation for variants within disease-associated genes located within exons or 200 nt flanking intronic regions and covering SNVs and 1-2 nt indels. Use of SpliceAI annotations in the automated pipeline, and possibility to filter on SpliceAI annotation in the Filter view (MOON-300)
HPOs can automatically be extracted from a Referral note on the Patient info screen (MOON-71)
Addition of gnomAD MT as annotation source for MT variants. This annotation is now used during automated analysis of MT variants (MOON-155).
All variants in the KB now have a source indication, which can be seen and changed in the KB UI (MOON-313)
The KB UI opens in a new tab when clicking the KB icon for a variant (MOON-320)
After adding a Shortlisted variant to the KB, the KB icon remains visible with an indication that the variant has been added to the KB (MOON-319)
In the Shortlist, a message is shown if there were updates to the KB classification of currently shortlisted variants. The sample needs to be reanalysed to display this new annotation, and take advantage of the updated KB classifications during analysis (MOON-323)
Performance improvements for retrieving the KB trough the API (MOON-311)
Added the possibility to request the KB logs through the API (MOON-312)
Improved filtering for variants expected to cause loss-of-function based on effect and location within the gene and for which the annotated disorder is known to be caused by a loss of function pathogenic mechanism (MOON-41)
De novo splice variants can be selected for the Shortlist even if splice predictions are not significant, although other requirements (eg. frequency, effect, phenotype match) still need to be met (MOON-98)
The Segregation filter in the Filter view now also provides the option to filter for De novo, Paternal, Maternal or biparentally inherited variants (MOON-321)
Downloads:
Addition of a ‘Parental origin’ column to all downloadable files (options: maternal, paternal, biparental, de novo, inconclusive)(MOON-315)
CSV Shortlist download: Addition of the Shortlist category in which the variant was reported (SNV, Carrier, Manually filtered)(MOON-338)
Use of MANE for translation of ENSTs to NM IDs for GRCh38. For GRCh37 samples, a lift-over from MANE is used to improve ENST to NM translation (MOON-240)
Addition of the possibility to remove applied Filter sets from the Report. Removing a Filter set from the report is logged in the Sample logs (MOON-331)
Update of the list of common pathogenic variants, which are also annotated and considered during analysis in Moon, despite having a gnomAD frequency > 2% (addition of NM_000155.2(GALT):c.-119_-116delGTCA and NM_000140.5(FECH):c.315-48T>C) (MOON-333)
Digitally signing or authorising reports is now logged in Sample logs (MOON-10)
Samples are now searchable based on HPO IDs in the samples search box (MOON-161)
Files with .VCF as extension are now also accepted for upload (in addition to .vcf files) (MOON-310)
Based on the input HPOs, only 10 suggestions are shown anymore (MOON-314)
Haplotypes/patch chromosomes are not annotated or considered during analysis (MOON-196)
In the Filter view, the exclusion reason for Carriers is now shown as “Shortlisted by Moon, carrier” (MOON-322)
When signing up for Moon, a disclaimer is added to make sure users want to create a new lab instead of joining an existing lab (MOON-318)
2FA setup and login in Moon are now improved (MOON-326)
Update to sample upload allowing parallel file uploads and improved display of upload status on upload screen (MOON-328)
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The manual was updated to version 3.5.0 (release date 23-11-2021).
Moon version 3.4.0
28 June 2021 • commit 1115d2a, 093f8cfbb5e482ed06db6d6e87528c53ad086ab4
New features
Addition of a case repository feature in Moon’s UI (MOON-47, MOON-281)
The search field in Moon now also allows to search for genes that are shortlisted in the SV/CNV tab (MOON-234)
Moon’s API for updating or adding variants to the internal knowledge base has now been improved (MOON-282, MOON-288)
Moon’s system security has been further enhanced, including password policy and server time-out updates (MOON-269, MOON-285, MOON-287, MOON-290, MOON-291)
Moon now supports generic authenticator apps in addition to Authy for 2FA (MOON-294)
You can now have the possibility to disable 2FA once enabled (MOON-292)
You can now assign samples back to “Nobody” after initially assigned to someone (MOON-293)
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The manual was updated to version 3.4.0 (release date 28-06-2021).
Moon version 3.3.4
27 April 2021 • commit be49c7a
Bug fixes
Performance optimisation, allowing for 15 min time savings for WGS analysis (MOON-276)
Nexus files with SV/CNV calls can now be imported regardless of their format (MOON-279)
Checklists are now correctly reflecting matches with parent and grandparent HPO terms. All matches up to 2 levels up and down in the HPO as compared to the input HPO terms are now checked in the variant card (MOON-273)
Corrected the exclusion filter in the Filter view, for variants excluded based on ‘Benign/Likely benign on ClinVar or in InvitaeKB or in KB’ (MOON-262)
Fix for allowing to conduct a family analysis in which a sample indicated as family member has previously been analysed as proband (MOON-280)
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The manual was updated to version 3.3.4 (release date 27-04-2021).
Moon version 3.3.3
24 March 2021 • commit 702f9ca
New features
Addition of an integrated SV/CNV genome browser (MOON-163)
Improvements to the automated pipeline:
Variants with a Benign/Likely Benign classification in InvitaeKB are now filtered out from the automated pipeline (MOON-246)
Additions/improvements to Filter view functionality:
Introduction of ‘Exclusion’ filter option, allowing to filter variants based on Moon’s reason for exclusion from the Shortlist (MOON-134)
Addition of ‘Non coding transcript exon’ option to the Effects filter, allowing more specific filtering for variants in non-protein coding genes (MOON-179)
Addition of an ‘Export’ button to download the list of variants resulting from a given combination of filter settings, as a .txt csv file (MOON-201)
Extension of the Frequency filter, allowing to lower the gnomAD/Diploid frequency below 0.1% and to set any desired frequency threshold with the slider or free input (MOON-202)
Improvements/additions to the UI:
The version of the annotation sources used by Moon at the time of analysis is now also included in the PDF report as an Appendix (MOON-123)
HPO lists are now expandable in case of a large number (>10) of input HPO terms (MOON-150)
Clickable HP IDs are now also shown next to the HPO terms in the Shortlist and PDF report (MOON-243)
The c.notation of variants in transcripts that have a RefSeq ID, now link out to Alamut Visual, allowing to immediately open the specific mutation in Alamut Visual (MOON-239)
Added support for the option to share Knowledge Bases among labs using the same server (MOON-189)
Samples analysed by the Autopilot now have the lowest priority (MOON-207)
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The manual was updated to version 3.3.3 (release date 24-03-2021).
Moon version 3.3.2
14 December 2020 • commit 786c61c
New features
Use of gnomAD v3.1 for frequency annotations in GRCh38 samples, including the possibility to click out to the gnomAD v3.1 webpage from within Moon (MOON-96)
Additions to Autopilot functionality (MOON-116, MOON-197):
The Autopilot is now also able to flag cases with updated variant classifications from the lab’s internal Knowledge base, ClinVar, or both, based on user preferences.
As part of the Autopilot settings, users can now decide to only compare updates within the top n variants in the Shortlist.
Samples with updates after an Autopilot reanalysis can now be found in the Autopilot page for all users.
User interface improvements:
Primary findings in MT genes are now displayed in a separate Shortlist tab, which will only be displayed in case of Shortlisted variants in MT genes (MOON-169)
Knowledge Base entries now have a “Source” field to indicate the origin of an entry (MOON-133). The source can be indicated when uploading Knowledge Base variants through the API.
The API output for variants now contains a “in_report” field to indicate whether a variant has been reported (true/false), per analysis (MOON-114)
Moon now allows BND calls (translocations) in SV/CNV VCFs (MOON-183). These BND calls are however not yet annotated or included for the interpretation.
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The manual was updated to version 3.3.2 (release date 14-12-2020).
Moon version 3.3.1
6 September 2020 • commit b9acc16
Bug fixes
Fixed issue with annotation sources without Grch38 version (MOON-164)
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The manual was updated to version 3.3.1 (release date 06-09-2020).
Moon version 3.3.0
2 September 2020 • commit 47d98b0
New features
Improvements to automated variant filtering and ranking: Addition of InvitaeKB variant classifications (Nykamp et al., 2017) as a new annotation source (MOON-137)
Addition of functional protein annotations to the Genome browser (MOON-154)
Improvements to family analysis:
Addition of an automated Family relations check feature for confirmation of relationships between family members (MOON-144)
Addition of the family information provided through the patient info screen (family relations and status) to the pedigree in variant card and PDF report (MOON-135)
Ability to retrieve HPO checklists through the API (MOON-140)
Updates to the automated report note:
Addition of chromosomal location, gnomAD frequency for all variants including variants in ClinVar/KB, and RefSeq ID to the automated report notes (MOON-88)
It is now possible to indicate the language in which the automated report notes should be generated within an analysis (English/Dutch) (MOON-149)
Removal of the “More variants” button: The full list of variants in the shortlist SNV tab is now directly displayed (MOON-148)
Addition of ENST transcript ID, RefSeq ID and family information fields in the All rare variants download file (MOON-151)
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The manual was updated to version 3.3.0 (release date 02-09-2020).
Moon version 3.2.4
6 April 2020 • commit b450066
New features
Filter Sets: Possibility to save a set of filters in the Filter view, and apply these on future samples (ticket MOON-70)
Error handling: improved notifications in case of analysis failures (MOON-112)
Additions to the API to allow removal of KB entries, add the ability to specify a source for each KB entry (MOON-109)
Effect filter in Filter view: Both ‘non-synonymous’ coding and ‘splicing’ are now selected as Effect with default filter settings (ticket MOON-124)
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The manual was updated to version 3.2.4 (release date 06-04-2020).
Moon version 3.2.3
3 February 2020 • commit d4273b0
Bug fixes
ClinVar annotations not shown for variants with Conflicting interpretations on ClinVar (MOON-119)
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The manual was updated to version 3.2.3 (release date 03-02-2020).
Moon version 3.2.2
16 December 2019 • commit 18b131e
Annotation sources:
The following database was updated to the most recent version (ticket MOON-104)
Apollo (2019-12-12)
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The manual was updated to version 3.2.2 (release date 16-12-2019).
Moon version 3.2.1
10 December 2019 • commit a88632f
New features:
Urgent samples: Added the possibility to prioritise samples for analysis on the Patient info screen (ticket MOON-93)
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The manual was updated to version 3.2.1 (release date 10-12-2019).
Moon version 3.2.0
7 October 2019 • commit f06b64f
New features:
Addition of support for annotation and analysis of GRCh38 VCF files with the following versions of annotation sources (ticket MOON-79):
ClinVar: 2019-10-03
dbNSFP: 4.0
dbSNP: 151
dbscSNV: 1.1
Apollo: 2019-10-06
RefSeq: 38
gnomAD: 2.1.1
HPO: 2019-02-12
KB: 2019-10-06
DGV: 2016-03-01
dbVar: 2019-07-07
Mitomap: 2019-01-14
Mitimpact: 2.9.1
Mastermind: 2019-09-27
Addition of a Genome Browser functionality for SNVs (ticket MOON-80)
Prediction of gender based on the VCF file, shown on the patient info screen (ticket MOON-83)
Bug fixes:
Correction in the annotation of the number of X-linked heterozygotes on gnomAD (ticket MOON-15)
Improvements in handling variants with multiple (superfluous) ALT alleles in the VCF (tickets MOON-17/18)
Correction of 0% gnomAD frequency annotation for variants with multiple Alt alleles (ticket MOON-20)
Improvements in handling haploid GT fields in the VCF (ticket MOON-22)
The following GRCh37 databases were updated to their most recent version (ticket MOON-78)
ClinVar: 2019-10-03
dbNSFP: 4.0
dbSNP: 151
Apollo: 2019-10-06
gnomAD: 2.1.1
dbVar: 2019-07-07
Mastermind: 2019-09-27
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The manual was updated to version 3.2.0 (release date 07-10-2019).
Moon version 3.1.2
19 July 2019 • commit c47740e
New features:
The following databases were updated to their most recent version (ticket MOON-23)
Apollo (2019-07-19)
ClinVar (2019-07-01)
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The manual was updated to version 3.1.2 (release date 19-07-2019).
Moon version 3.1.1
25 June 2019 • commit 182d3cd
New features:
CE IVD marking on the European market
Bug fixes:
Improved handling of variants with multiple Alt alleles (ticket MOON-2)
Improved handling of known (likely) pathogenic multi-allelic sites in automated analysis (ticket MOON-6)
Updated the list of common pathogenic variants (ticket MOON-16)
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