Variant annotations¶
Cases are processed via the bioinformatics pipeline and annotations are added by CellBase. Once a case arrives to the RDDSS, additional annotations are added from resources that are currently unavailable in CellBase.
Please note, that when annotating CNVs, CellBase applies ±2 kb padding to the CNV, which is intentional and is designed to account for uncertainty in CNV breakpoint coordinates. Without this padding, a CNV close to an exon boundary could be annotated as intronic or non-coding even where the true breakpoint overlaps the exon. This could make a potentially relevant CNV less likely to be reviewed and introduces a risk of false-negative interpretation. Applying padding prioritises sensitivity, at the cost of a small reduction in specificity. As a result, some CNVs close to exon boundaries may be labelled as exonic in the RDDSS even where the reported CNV coordinates do not directly overlap an exon in other resources such as DECIPHER.
SNVs¶
| Annotation | Description | Source | Static / Live |
|---|---|---|---|
| Tiering results | Tier, segregation, mode of inheritance, penetrance, GMS PanelApp panels, gene and source are annotated for Tiered SNVs | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| Exomiser results | Exomiser-prioritised SNVs | Exomiser prioritisation results, with associated scores, ranks and allele frequencies | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline |
| Gene, transcript and protein annotations (ID, flags, consequences) | Gene, transcript and associated annotations | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| Latest PanelApp panels | For genes - Panel name and version, gene status, gene mode of inheritance | PanelApp | Static (Annotated at case ingestion. The underlying dataset used for annotation is updated with the most recent PanelApp data every hour). |
| OMIM | Associated diseases and gene-phenotype mode of inheritance | OMIM (data stored internally) | Static (Annotated at the point of case ingestion. The underlying data used for annotation is updated with the most recent OMIM data with every RDDSS release). |
| REVEL | An in-silico prediction score used to estimate the likelihood that a missense variant is disease-causing. Scores range from 0 to 1, with higher scores indicating a greater predicted likelihood that the variant is pathogenic. | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| GEL population frequency | Internal germline allele frequency database | Genomics England dataset | Static (Annotated at the point of case ingestion. Also used within the Genomics England Rare Disease pipeline) |
| gnomAD population frequency | Population germline allele frequency database | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| CVA | CVA entr(y/ies) for the variant, with classification and count | CVA | Live |
| ClinVar submissions | ClinVar Germline Database - accession, review status, submissions, classification, interpretation, latest submission | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| DQ score | Posterior probability scores calculated from the possible genotypes within the family. Indicate the level of confidence that a variant represents a genuine de novo event. Higher scores indicate greater confidence in the supporting evidence. | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) | Static (Annotated at case ingestion, using the VCF file) |
| Segregation, MOI, penetrance | Segregation, MOI and penetrance groupings from the Tiering prioritisation results (previously known as Report Events) | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| Zygosity | SNVs | Variant zygosity | Variant genotype, from the variant VCF file (generated by the Genomics England Rare Disease pipeline) |
| Ref / alt / total reads | SNVs | Reference / alternative / total read counts | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) |
| QC filter data | All | Indicates whether the variant passed QC filters applied during the analysis | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) |
CNVs¶
| Annotation | Description | Source | Static / Live |
|---|---|---|---|
| Tiering results | Tier, entity, and GMS PanelApp panels are annotated for Tiered CNVs | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| Size and Type | CNVs | Size and type (Loss / Gain) | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) |
| Gene, transcript, exonic overlap, and protein annotations (ID, flags, consequences) | Gene, transcript, exonic overlap, and associated annotations | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| Latest PanelApp panels | For genes - Panel name and version, gene status, gene mode of inheritance | PanelApp | Static (Annotated at case ingestion. The underlying dataset used for annotation is updated with the most recent PanelApp data every hour). |
| OMIM | Associated diseases and gene-phenotype mode of inheritance | CellBase | Static (Annotated at the point of case ingestion. The underlying data used for annotation is updated with the most recent OMIM data with every RDDSS release). |
| Regions | Panel name and version, region name & ID, region status, region MOI, triplosensitivity / haplosensitivity score, required % overlap | PanelApp | Static (Annotated at case ingestion. The underlying dataset used for annotation is updated with the most recent PanelApp data every hour). |
| Allele frequency (GEL internal dataset) | Internal germline allele frequency database | Genomics England dataset | Static (Annotated at the point of case ingestion. Also used within the Genomics England Rare Disease pipeline) |
| QC filter data | Indicates whether the variant passed QC filters applied during the analysis | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) | Static (Annotated at case ingestion, using the VCF file) |
STRs¶
| Annotation | Description | Source | Static / Live |
|---|---|---|---|
| Tiering results | Segregation, mode of inheritance, GMS PanelApp panels, gene and STR locus are annotated for Tiered STRs | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| STR loci and Genes | Gene and STR locus annotations | CellBase | Static (Limited by CellBase version. Annotated at case ingestion) |
| Latest PanelApp panels | For genes and STR loci - Panel name and version, gene status, gene mode of inheritance | PanelApp | Static (Annotated at case ingestion. The underlying dataset used for annotation is updated with the most recent PanelApp data every hour). |
| OMIM | Associated diseases and gene-phenotype mode of inheritance | CellBase | Static (Annotated at the point of case ingestion. The underlying data used for annotation is updated with the most recent OMIM data with every RDDSS release). |
| Normal and pathogenic thresholds | The normal and pathogenic number of repeats associated with each locus | Genomics England Rare Disease Tiering pipeline, but originate from PanelApp | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| Counts and repeat count interval | Estimation of the size of STRs for each participant, by ExpansionHunter in the pipeline. Estimated repeat count size, and an estimated range which reflects uncertainty. | Genomics England Rare Disease Tiering, Genomics England Rare Disease pipeline | Static (Annotated at case ingestion, using the VCF file) |
| Pileup plot | Visualisation plots for each STR, generated by DRAGEN, which can be used to assess the quality of the repeat size estimations computed by ExpansionHunter | Genomics England Rare Disease Tiering pipeline | Static (Annotated by the Genomics England Rare Disease Tiering pipeline) |
| QC filter data | Indicates whether the variant passed QC filters applied during the analysis | Variant VCF file (Generated by the Genomics England Rare Disease Pipeline) | Static (Annotated at case ingestion, using the VCF file) |
Data sources¶
To read more about each data source used within the product, and where it is used, please click on the below tabs.
GEL Tiering¶
Prioritisation results are the results from the Rare Disease Genomics England Tiering pipeline for the variant and the applied panels. This comprises of various metadata, including Tier, associated gene(s), segregation, mode of inheritance, and penetrance. These are displayed within the app within the Tier overlay, Tier columns in the variant grids, and the SNV details pages.
For further information on GEL Tiering, visit the Tiering section in the Genomics England Rare Disease Pipeline user guide.
GMS PanelApp¶
GMS PanelApp panels (including version, gene and green status), are annotated by the Genomics England Rare Disease Tiering pipeline. These are displayed within the app at locations including the case summary page, and the Tier overlay.
QC filter data¶
This indicates whether the variant passed QC filters applied during the analysis, and is annotated by the Genomics England Rare Disease Pipeline, where it is stored in the VCF file.
Exomiser (SNVs)¶
Exomiser is a programme that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. All rare disease cases are run through the Exomiser automated variant prioritisation framework. Exomiser results and explainability data are displayed within the app within the Exomiser column in the SNV grid, the accompanying Exomiser overlay, and within the SNV details page.
For further information on Exomiser prioritisation, visit the Exomiser page in the Genomics England Rare Disease Pipeline user guide.
Segregation, MOI, penetrance (SNVs)¶
The segregation, MOI and penetrance groupings displayed within the SNV grid in the RDDSS currently come from the GEL Tiering prioritisation results (previously known as Report Events). In future, it is planned that this data for Exomiser prioritisation results, and also for untiered variants, will be added to the annotations provided.
Zygosity (SNVs)¶
Zygosity is annotated per variant per individual in the case for SNVs, at the point of case ingestion, using the variant VCF file. The variant VCF file is generated by the Genomics England Rare Disease pipeline.
Ref / alt / total reads (SNVs)¶
Reference / alternative / total read counts are annotated per individual in the case for SNVs, at the point of case ingestion, using the variant VCF file. The variant VCF file is generated by the Genomics England Rare Disease pipeline.
DQ score (SNVs)¶
DQ scores are posterior probability scores calculated from the possible genotypes within the family and indicate the level of confidence that a variant represents a genuine de novo event. Higher scores indicate greater confidence in the supporting evidence.
DQ scores are only calculated where sufficient family data are available, such as for trios or larger family structures containing the relevant parental samples. They are not available for singleton cases. Scores may also be unavailable for cases ingested before DQ annotations were introduced, or for individual variants where no score was recorded. In these cases a warning symbol will be displayed in place of the scores, with an explanation displayed on hover.
DQ scores are displayed in the SNV grid, and where the score for a variant exceeds the pipeline thresholds (see below), a de novo label is displayed.
- SNVs: ≥0.0013
- Indels: ≥0.02
Size and Type (CNVs)¶
Normal and pathogenic thresholds (STRs)¶
The thresholds are annotated by the Genomics England Rare Disease pipeline, but originate from GMS PanelApp.
Counts and repeat count interval (STRs)¶
The counts and repeat count intervals that are displayed in the STR grid are lifted from the VCF file. For more details on these annotations, please visit the Repeat counts section in the STR grid page of the guide.
Pileup plots (STRs)¶
Pileup plots are generated by DRAGEN, and can be used to assess the quality of the repeat size estimations computed by ExpansionHunter. For more details on these annotations, please visit the Pileup plots section in the STR grid page of the guide.
Gene, transcript, exonic overlap and protein annotations (Ensembl / RefSeq)¶
Ensembl is a genome browser that provides gene annotations.
- CellBase annotates SNVs and CNVs with gene, transcript and associated annotations from Ensembl
- CellBase also annotates CNVs with exonic overlap annotations from Ensembl
- CellBase annotates STRs with gene and STR locus annotations from Ensembl
- The RDDSS displays these annotations in the variant grid and variant details page for SNVs, and in the variant grid for CNVs
- The database version of Ensembl used by CellBase may not always be the most recent. Please see the latest version of the Rare Disease Genome Analysis guide for further details.
gnomAD population frequencies (SNVs)¶
The Genome Aggregation Database (gnomAD) is a population frequency database of large-scale sequencing projects from healthy cohorts.
- CellBase annotates whether a variant is present in gnomAD (exomes, genomes and mitochondrial datasets)
- The RDDSS displays the total population germline allele frequency as well as the subpopulations
- The database version of gnomAD used by CellBase is displayed in the RDDSS and may not always be the most recent.
ClinVar (SNVs)¶
ClinVar is a public database of variant and phenotype relationships alongside supporting evidence and clinical interpretation histories.
- CellBase annotates whether a variant is present in Clinvar.
- The RDDSS displays the ClinVar ID, interpretation, review status and number of entries alongside a link to the ClinVar record in the variant grid and variant details page for germline variants.
- The database version of ClinVar used by CellBase is displayed in the RDDSS and may not always be the most recent. Please see the latest version of the Rare Disease Genome Analysis guide and CellBase for further details.
REVEL (SNVs)¶
REVEL (Rare Exome Variant Ensemble Learner) is an in-silico prediction score used to estimate the likelihood that a missense variant is disease-causing. Scores range from 0 to 1, with higher scores indicating a greater predicted likelihood that the variant is pathogenic.
REVEL scores were calculated for missense variants using GENCODE v19 transcripts on the hg19 assembly and subsequently lifted over to GRCh38. Scores are matched to each transcript using the variant and amino acid change, rather than the transcript identifier.
Because REVEL scores were calculated using legacy transcript models, scores may be unavailable where changes to the genome assembly, transcript structure, or amino acid annotation have created differences from the original REVEL source data.
REVEL is made available under the Open Database License (ODbL).
- CellBase annotates missense variants against each transcript using the variant and amino acid change, rather than using the transcript identifier
- Transcript-level scores are displayed in the transcript tables in the SNV details page and the gene overlay in the SNV grid
- Highest score for the gene where a missense consequence is displayed in the SNV grid=== "PanelApp"
Non-GMS PanelApp¶
The GEL PanelApp knowledgebase allows virtual gene panels related to human disorders to be created, stored and queried and is used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS).
- The Ensembl gene ID of each variant is used to match the variant to Panels in latest PanelApp (i.e. non-GMS PanelApp)
- The Panels (and superpanels) in which the affected gene is present are then shown on the variant grids and variant details page
- For STRs, the STR loci are also annotated from latest PanelApp
- For CNVs the regions are also annotated from latest PanelApp
CVA (SNVs)¶
The Clinical Variant Ark (CVA) is the knowledge base built from NHS Clinical Scientist interpretations of rare disease patients in the 100K Genomes Project and NHS Genomic Medicine Service. For further information, visit the CVA user guide.
OMIM¶
OMIM data is used to annotate the variants with associated diseases and gene phenotype mode of inheritance. The data is static, and is annotated at the point of ingestion, with the underlying data used for annotation being updated with each RDDSS release.
GEL population frequencies (SNVs, CNVs)¶
SNV and CNV variants are annotated with the GEL internal allele frequency dataset upon case ingestion. This is a GEL internal population frequency dataset. N.B this dataset is also used within the Genomics England Rare Disease pipeline; for further details, please see the Rare Disease Genome Analysis Guide.
Abbreviations
| Abbreviation | Definition |
|---|---|
| ACGS | Association for Clinical Genomic Science |
| ACMG | American College of Medical Genetics and Genomics |
| CDS | Coding DNA Sequence |
| CIP-API | Genomics England Clinical Interpretation API |
| CNV | Copy Number Variant |
| CVA | Clinical Variant Ark |
| EQ | Exit Questionnaire |
| RDDSS | Rare Disease Decision Support System |
| GEL | Genomics England |
| GMS | Genomic Medicine Service |
| GLH | Genomic Laboratory Hub |
| HGVS | Human Genome Variation Society |
| HTML | Hyper Text Markup Language |
| HSCN | Health and Social Care Network (N3) |
| IGV | Integrative Genomics Viewer |
| IB | Interpretation Browser |
| IP | Interpretation Portal |
| NGIS | National Genomics Informatics System |
| PID | Patient Identifiable Data |
| QC | Quality Control |
| SoF | Summary of Findings |
| SO | Sequence Ontology |
| SNV | Single Nucleotide Variant |
| SV | Structural Variant |
| TOMS | Test Order Management System |
| UAT | User Acceptance Testing |
| VCF | Variant Call Format File |
| VILs | Variant Interpretation Logs |
| WGS | Whole Genome Sequencing |