Skip to content

Overview

Copy number variants (CNVs) are detected using DRAGEN CNV with self-normalisation and the Shifting Level Models (SLM) segmentation mode. High quality CNVs >10 kb in size are defined as those detected by DRAGEN CNV with filter status 'PASS'. CNVs between 2 and 10 kb in size are identified by combining the results of DRAGEN CNV and DRAGEN SV callers. CNVs in this range detected by both callers with a minimum reciprocal overlap of 50% are deemed to be high quality. The Genomics England Rare Disease Interpretation Pipeline currently annotates and reports all high quality CNVs that overlap with gene biotypes considered during tiering and are ≥ 2 kb in size. Annotations include internal allele frequencies calculated for 5,415 samples.

An overview of the CNV tiering pipeline can be seen below.

CNV tiering overview

Note

There are two separate streams of analysis applied during tiering of CNVs (both use information available in PanelApp: (1) overlap of CNV regions, and (2) overlap of genes; as indicated by different colour boxes in diagram). The tiering diagram provided aims to assist with understanding of prioritisation approaches applied to CNVs and does not account for all ossible scenarios, please see text below for more information.

A CNV is considered under both prioritisation streams independently (PanelApp genes and PanelApp regions). It is possible that a CNV is appropriately prioritised and assigned multiple tiers. In this scenario, the final tier will be the highest assigned tier (see table), and is the final tier displayed in the Interpretation Portal. All assigned tiers are also displayed in variant report events information in the Interpretation Portal.

Please note that CNVs that are classified as “Not tiered” via one prioritisation stream will only be displayed in the Interpretation Portal if they receive a higher tier via the alternative CNV prioritisation stream.

Priority Rank Tier
1 A
2 B
3 Null
- Not tiered

Examples of CNVs that receive more than one tier include, but are not limited to:

  • CNVs which impact multiple genes with appropriate biotypes, where at least one gene is Green on the applied gene panel and at least one gene is not on the applied gene panel (Tier A and Tier Null)

  • CNVs which are >100Kb and overlap a PanelApp region and do not fulfil the requirements for that region (variant type, level of overlap), but do overlap a gene with an appropriate biotype that is not included in the applied gene panel (Not tiered, Tier B and Tier Null)

Only CNV calls from the proband are annotated and displayed. CNV calls in relatives are not currently considered in tiering. However, visual assessment of CNVs for all family members can be performed using coverage profiles displayed in the IGV viewer following the links from the Interpretation Portal.

Note

Mode of inheritance is not considered in CNV tiering. In contrast to small variant tiering, a single heterozygous CNV within or impacting a gene or region (with appropriate variant type and overlap) will be tiered regardless of the expected mode of inheritance recorded in PanelApp.

Tier A

A CNV is assigned Tier A if it satisfies the following criteria:

  • The CNV must not exceed the frequency threshold for both of the CNV frequency metrics (CNV_AF, CNV_AUC). The thresholds are unique to the CNV type:

    • LOSS: 0.005
    • GAIN: 0.01

Note

A CNV can be included as Tier A if one of the CNV frequency metrics (e.g. CNV_AUC) is exceeded but the other is below the threshold (e.g. CNV_AF)

AND one or both of the following criteria:

  • The CNV overlaps with a green gene in a panel applied in the analysis. All CNVs (i.e. loss and gain) overlapping any gene are considered, without requiring a minimum overlap threshold.

  • The CNV overlaps a pathogenic region in a virtual panel applied in the analysis, the overlap is above the threshold defined in PanelApp for that region, and the variant type matches (i.e., loss or gain) that of the region in PanelApp.

Note

If a Tier A CNV impacts a gene with a biallelic mode of inheritance then the prioritisation algorithm will include assessment of compound heterozygous variants across variant types.

Tier B

A CNV is assigned Tier B if it satisfies the following criteria:

  • The CNV must not exceed the frequency threshold for both of the CNV frequency metrics (CNV_AF, CNV_AUC). The thresholds are unique to the CNV type:

    • LOSS: 0.005
    • GAIN: 0.01

  • The CNV overlaps a gene with a biotype included for consideration (see CNV biotypes table below)

  • The CNV is larger than 100Kb

Note

A CNV can be included as Tier B if one of the CNV frequency metrics (e.g. CNV_AUC) is exceeded but the other is below the threshold (e.g. CNV_AF)

Tier Null

All PASS variants that overlap with a gene with a biotype included for consideration (see table below).

Note

  • Tier A CNVs may also be classified as Tier B if they are >100kb in size
  • Tier A CNVs may also be classified as Tier Null if they also impact genes that do not fulfil the criteria for Tier A but do fulfil the criteria for Tier Null
  • All CNVs that are classified as Tier B will also have a Tier Null classification
  • The highest reported tier will be considered the final tier for the CNV

CNV biotypes considered during variant tiering

CNVs will be considered during variant tiering if they impact genes with any of the following biotypes:

Biotype Description
IG_C_gene
IG_D_gene
IG_J_gene
IG_V_gene
TR_C_gene
TR_D_gene
TR_J_gene
TR_V_gene		 Immunoglobulin (Ig) variable chain and T-cell receptor (TcR) genes imported or annotated according to the IMGT.
protein_coding Contains an open reading frame (ORF).
nonsense_mediated_decay If the coding sequence (following the appropriate reference) of a transcript finishes >50bp from a downstream splice site then it is tagged as NMD. If the variant does not cover the full reference coding sequence then it is annotated as NMD if NMD is unavoidable i.e. no matter what the exon structure of the missing portion is the transcript will be subject to NMD.
non_stop_decay Transcripts that have polyA features (including signal) without a prior stop codon in the CDS, i.e. a non-genomic polyA tail attached directly to the CDS without 3' UTR. These transcripts are subject to degradation.