Release notes¶
Releases for the Rare Disease pipeline are bundled with NGIS releases, details of which can be found here.
Mira¶
Release information
The major new features that are released in Mira are:
- Upgrade of the DRAGEN software utilised for mapping and variant calling from DRAGEN v3.2.22 to DRAGEN v4.0.5 (updates throughout user guide), including:
- updated internal allele frequency cohort used during assessment of population frequencies
- updated approach and thresholds for small variant 'PASS' filters and de novo variants
- updated approach for CNV detection (2-10Kb)
- Upgrade to ExpansionHunter v5 software (within DRAGEN), with introduction of REViewer software for short tandem repeat expansion visualisation
- Tiering of rare variants impacting non-coding green genes in the applied panel (altered biotypes and variant consequences included for consideration of Tier2 variants)
- Variants-with-pathogenic-associations in the Genomics England Clinical Variant Ark are only included as tiered variants if the internal allele frequency is less than 5%, or if variants are on the variant inclusion list
- Heterozygous variants which fulfill relevant tiering criteria are tiered in combination with alternate homozygous variants that impact the same gene and also fulfill relevant tiering criteria under compound heterozygote segregation filters
Minor updates subsequently added to original release of the Mira genome analysis user guide:
- modifications to variant inclusion list
- increased clarity about handling of de novo variants
- added details of Ensembl database version used in the pipeline
Lyra¶
Release information
The Lyra release of the online user guide is an early access release and replicates the v2.4.1 rare disease user guide available through the NHS Futures website under “NHS Genomic Medicine Service” > “Guidance” > “Genomics England Documentation”).
There are some minor changes of the content and presentation after migration of the PDF to the online user guide:
- "The Clinical Reporting Workflow" section renamed to "Variant Prioritisation Approaches"
- Reordering and joining of Sections 1-7 into "Background"
- Update of population allele frequency information used during small variant tiering
- Removal of Section 9.7 "Short SNV and Indel (small variant) Tiering guide for bioinformaticians"
- Changes in presentation format across all sections, including splitting up of larger sections of the guide and reorganisation of content where appropriate
Prior to Lyra¶
Release information prior to Lyra
- information about specific changes to releases prior to Lyra are available in previous versions of the Genomics England rare disease user guide (available as PDFs through the NHS Futures website under “NHS Genomic Medicine Service” > “Guidance” > “Genomics England Documentation”)