Overview

The Genomics England Rare Disease SNV and Indel Tiering Process is designed to aid NHS GLH evaluation of Rare Disease primary finding results by annotating variants that are plausibly pathogenic, based on their segregation in the family, frequency in control populations, predicted impact on the relevant protein(s), whether they have known pathogenic/likely pathogenic associations with disease and whether they are in a gene in a virtual panel(s) applied in the analysis incorporating the associated mode of inheritance. The process is summarised below.

Tiering can be performed in two penetrance modes: 1. Variants to be reported under complete penetrance 2. Variants to be reported under incomplete penetrance

After Tiering, variants are annotated with a tier (Tier 1, Tier 2, Tier 3) and a penetrance flag (Complete or Incomplete) to indicate the penetrance mode under which they were tiered. Incompletely penetrant variants are only reported if requested in the test order.

During the Tiering process, variants (detected and normalised by the Rare Disease Pipeline) are annotated and passed through multiple filters (population allele frequency, consequence type, segregation, quality etc.) in order to prioritise those that are potentially relevant/causal for a specific case and disease. The Genomics England Rare Disease Interpretation Pipeline annotates and reports small variants that have “PASS” filter status assigned - the current DRAGEN software implemented in the Rare Disease pipeline uses machine learning recalibration of variant quality scores, with a threshold for "PASS" filter status (using default quality score thresholds).

Simplified overview of the small variant tiering process. Note: if a variant satisfies criteria for several tiers (e.g. Tier 1 and Tier 2), multiple records are written to the interpreted genome output file, but the highest tier is assigned to the variant for analysis in the interpretation portal.