To assess the use of Exomiser for reinterpretation, incorporating the latest knowledge of diseases, genes and phenotypes, a large-scale reanalysis of 24,015 unsolved cases from the 100kGP was performed: selected on the basis of not having a known diagnostic finding after the 100kGP primary pipeline run 2016–2019. The 100kGP primary pipeline largely involved the identification and interpretation of rare, segregating, de novo, predicted loss-of-function (pLoF) or predicted pathogenic missense variants in curated panels of known genes related to the patient’s disease in PanelApp4. These 24,015 cases were analysed using Exomiser 13.1.0 and the Feb 2022 database release, with default settings on single proband and family-based variant call format (VCF) files. This generates rare (<0.1% autosomal/X-linked dominant or homozygous recessive, <2% autosomal/X-linked compound heterozygous recessive; using publicly available sequencing datasets including gnomAD), protein-coding (including canonical splice acceptor/donor and splice region), segregating and most predicted pathogenic (per each gene) candidate variants for each case.

A conservative candidate selection procedure was used to identify the 725 most likely diagnoses (Fig. 1b). First of all, the Exomiser combined scores were rescaled to new 0–1 scores using the softmax function: exp(10 * score)/sum(exp(10* score)) for the top-ranked scores (up to a maximum of 1000). Only those scoring above 0.1 were retained. These were further filtered for:

having a human phenotype score >0.6 or involving a gene classified green in the latest recruited disease panel (23/2/2022) in PanelApp4 with the correct mode of inheritance for the disease-gene association;

classified as either (i) de novo by the 100kGP, (ii) pLoF by Exomiser, or (iii) P/LP by ClinVar with non-conflicting evidence and multiple sources;

not classified as tier 1 or 2 and, hence, already interpreted and rejected by the GMCs in the previous pipeline;

classified P/LP by Exomiser’s automated ACMG classifier;

variant type (missense versus LoF) consistent with previously reported variants for the disease;

hallmark phenotypic features of the disease present in the patient.

Finally, the 725 candidates were independently reviewed by the Genomics England clinical genetics team to identify 463 (2% of the 24,015 cases) to return as newly discovered diagnoses, with 153 remaining as variants of uncertain significance (VUS) and 109 rejected as false variant calls after IGV review (Fig. 1b). The Genomics England team is composed of clinical scientists and geneticists and performed an equivalent variant classification to that which would be performed in a diagnostic laboratory and confirmed 463/616 (75%) of automatically classified, correctly called variants were indeed P/LP.

251/463 of these new diagnoses were based on ClinVar P/LP variants with consistent evidence from multiple submitters: 144 were identified in the original 100kGP pipeline but overlooked as they affected genes outside the panel at the time of analysis, whilst 107 were previously filtered out and retained here due to Exomiser whitelisting feature where such variants are always retained regardless of filtering settings. 98/463 new diagnoses were made based on de novo or LoF variants in genes that are present on the latest versions of the panels associated with the patient’s disease. For 84/99 of these, the gene was not on the panel when the primary 100kGP pipeline was run, suggesting new evidence has since emerged for the disease-gene association. For example, a de novo PPP3CA:p.Asn117Lys variant in an intellectual disability patient was the top-ranked Exomiser candidate based on the association to Houge-Janssens syndrome 3 described in 20195 and therefore not highlighted in the 100kGP primary pipeline run prior to that date. Finally, Exomiser highlighting of candidates in genes that are still not present on the disease panel associated with the patient was responsible for 114/463 of new diagnoses, e.g., a de novo MORC2:p.Gly36Arg variant in a mitochondrial disorders patient was the top ranked Exomiser candidate based on the association with a newly described neurodevelopmental disorder6. Overall 330 (72%) of the 463 diagnoses involved a variant that was identified in the primary 100KGP pipeline but in a gene that was not in the relevant panel(s) at the time. 205 (62%) of these disease-gene associations were already known and overlooked by the PanelApp strategy revealing the higher sensitivity of a less targeted approach, whilst the remainder represent new discoveries identified in the reinterpretation.

Extensive manual interpretation was required for these new diagnoses; consequently, future reanalysis would ideally only highlight candidates due to new disease gene discoveries or newly assigned P/LP variants. We therefore investigated the best strategy to achieve this with the Exomiser framework on 37 solved cases from the 100kGP primary pipeline based on all those identified with a diagnosis in a disease-gene association appearing in OMIM between February 2019 and February 2022. This date range was chosen as Exomiser database releases from this time period are backwards-compatible with Exomiser 13.1.0. Ideally, a much larger cohort of solved cases would have been used in this evaluation but we were also limited by most 100kGP cases having been analysed prior to 2019. Exomiser 13.1.0 was run on these cases using all seven versions of the database from Feb 2019 till Feb 2022. We investigated in detail the combination of Exomiser variant and human phenotype scores that optimised the detection of these new diagnoses whilst reducing the number of false positive candidates to investigate (Supplementary Table 1). The selection of these two scores was made to ensure independence between the two variables while enabling the capture of both likely pathogenic variants via the variant score and newly discovered disease-gene associations through the increments in the human phenotype score. Each variant called by Exomiser was classified as a true positive (TP), false negative (FN), false positive (FP) or true negative (TN) by comparing the results obtained using the combination of Exomiser score tested and a trusted external observation (the diagnosed variants). Measures of recall and precision, as well as F and F2 scores, were derived using R/4.2.1. The F2 score, which is a weighted harmonic mean of precision and recall where recall is weighted higher than precision, is often utilised in diagnostic settings and was used for optimising the best combination of scores.

A combination of variant score >0.8 and an increase in human phenotype score of 0.2 between Exomiser runs was identified as the optimal way to detect candidates. Comparing Exomiser results based on Feb 2019 vs Feb 2022 analysis (Fig. 2), these thresholds highlight 54 new candidates in the 37 solved cases with 31 being the correct diagnosis, representing impressive recall (84%) and precision (57%). For the 6 cases not detected by these criteria, this was due to missense variants having a low predicted pathogenicity or patient Human Phenotype Ontology (HPO) terms not similar enough to the new disease-HPO annotations to increase the score by 0.2. For the former, future incorporation as P/LP in ClinVar will ensure they get flagged due to Exomiser whitelisting. On the latter, presumably, additional phenotype data was available to the recruiting clinician to make them confident of the diagnosis. Finally, Exomiser’s automated ACMG/AMP classifier converted 92% of the diagnostic variants from VUS to P/LP and including this extra condition in the reinterpretation strategy further improves precision to 88% with only a small drop in recall to 82%. On the basis of this investigation, we recommend a combination of variant score > 0.8 and an increase in human phenotype score of 0.2 to easily identify candidates from Exomiser’s programmatic output (TSV, VCF or JSON). From the analysis of the families investigated here, this reduces the number of candidates to review per case from a median of 30 (range 11-214) to only one or two variants per case. The number and complexity of variants to review after Exomiser filtering obviously varies but based on typical interpretation times per variant, this will make it possible to reinterpret a case in minutes rather than more than an hour.

Fig. 2: Exomiser analysis of 100kGP cases that were unsolved in Feb 2019 but subsequently diagnosed based on a new disease-gene discovery.

Precision (dark green bars) and recall (light green bars) are shown for each Exomiser database release when new candidates were selected for the 37 cases based on an increase in the human phenotype score of 0.2 and a variant score >0.8 and, for the final bars, when also restricting to those variants classified as pathogenic/likely pathogenic by Exomiser’s automated ACMG classifier. Each version of Exomiser (Y axis) shows increased precision and similar or better recall than previous versions. Figure generated using R/4.2.1.