Emma Clement

The SOX10 gene is essential for developing neural crest-derived tissues, including the temporal bone, peripheral and central nervous systems, and melanocytes. Pathogenic SOX10 variants are linked to a broad clinical spectrum, including Waardenburg syndrome (WS) in isolation, Kallmann syndrome (KS), as well as an entity characterised by the combination of peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, Waardenburg syndrome, and Hirschsprung disease (PCWH). This study aims to characterise the full spectrum of abnormalities in the brain, temporal bone and neck regions, and their syndromic associations. 15 pediatric patients with genetically confirmed SOX10 germline pathogenic variants were included. All underwent MRI, and 9 also had CT of the temporal bone. Imaging and clinical data were systematically analysed by two pediatric neuroradiologists. Phenotypic analysis revealed bilateral temporal bone abnormalities in all patients, mainly characterised by a specific combination of semicircular canal (SCC) dysplasia/hypoplasia (with high prevalence of severely hypoplastic or absent posterior SCC) and a very reproducible form of cochlear hypoplasia called "flattened cochlea". Olfactory bulb agenesis or hypoplasia was identified in all patients but two. Other abnormalities include white matter changes suggestive of a hypomyelination pattern or deficient myelination in four and neck findings typically characterised by parotid gland aplasia/hypoplasia (15/15, 100%) or lacrimal gland aplasia/hypoplasia (13/15, 86%). Clinical phenotypes ranged from SNHL to WS type II or IV and PCWH. These results confirm the strong correlation between pathogenic SOX10 variants and characteristic temporal bone malformations, which, in association with other radiological abnormalities, represent highly specific diagnostic markers. The constellation of findings reflects the shared neural crest origin of the affected tissues and should always be investigated to support appropriate genetic testing. Early identification of these features via MRI can aid diagnosis, especially in children without classic syndromic signs, and support the patients' management.

Background: Molecular diagnosis of rare disease plateaus at ∼50%, partly due to technical limitations of short-read sequencing and the persistent challenge of interpreting variants of uncertain significance (VUS). Splice-altering variation represents a major source of unresolved cases, yet functional assessment remains difficult in routine practice. Methods: We developed a fully modular, sample-to-answer workflow for targeted long-read RNA sequencing (lrRNA-seq) using Oxford Nanopore Technologies and applied it to six unsolved cases with suspected monogenic neurometabolic disease. Candidates were selected after WES/WGS and multidisciplinary team review (MDT) indicating ≤5 genes of interest. The workflow was designed to be diagnostically deployable, enabling near-full-length transcript assessment from accessible tissues without reliance on large control cohorts. Results: lrRNA-seq yielded actionable findings for all six probands. It confirmed pathogenic splice disruption in two cases, prompted gene exclusion in one case, and generated RNA-level evidence prioritising further DNA investigation in three cases. Across these scenarios, lrRNA-seq provided direct, mechanism-level insight that either resolved diagnosis or refined variant interpretation. The workflow provided near-full-length isoform structures with reproducible single-sample interpretation and produced informative results within two working days at <£500 per sample reagent cost. Conclusion: Targeted lrRNA-seq offers rapid, cost-effective functional evidence to resolve VUS, direct DNA follow-up, and support timely diagnosis in rare disease. The RAPID workflow demonstrates that long-read RNA sequencing can be implemented within existing diagnostic infrastructure and provides a scalable route to routine transcript-level assessment in clinical genomics.

Ubiquitin E3 ligases play crucial roles in the DNA damage response (DDR) by modulating the turnover, localization, activation, and interactions of DDR and DNA replication proteins. We performed a CRISPR-Cas9 knockout screen focused on ubiquitin E3 ligases and related proteins with the DNA topoisomerase I inhibitor camptothecin. This led us to establish that MAEA, a core subunit of the CTLH E3 ligase complex, is a critical regulator of homologous recombination and the replication stress response. In tandem, we identified eight patients with variants in MAEA who present with a neurodevelopmental disorder that we term DIADEM ( D evelopmental delay and I ntellectual disability A ssociated with DE fects in M AEA). Analysis of patient-derived cell lines and mutation modeling reveal an underlying defect in HR-dependent DNA repair and replication fork restart and protection as a likely cause of disease. Mechanistically, we find that MAEA dysfunction hinders DNA repair by reducing the efficiency of RAD51 loading at sites of DNA damage, which we propose may contribute to the presentation of DIADEM by compromising genome integrity and cell division during development.

Background: Familial exudative vitreoretinopathy (FEVR) is an inherited eye disease characterised by the incomplete development of the retinal vasculature. Over 10 genes have been associated with FEVR, but there are still a substantial number of genetically unsolved cases. The aim of this study was to analyse whole genome sequencing (WGS) data from the FEVR cases in the Genomics England (GEL) 100 000 genomes project to identify the causative variants. Methods: WGS was performed by GEL and accessed within the GEL Research Environment. FEVR cases were identified using LabKey and candidate variants were extracted using the ‘gene-variant workflow’ and ‘CNV/SV workflow’ and by using BCFtools in unfiltered VCF files. Results: Fifty-nine FEVR probands were submitted to GEL. We found six novel and eight previously reported pathogenic variants in six genes known to underlie FEVR ( TSPAN12, LRP5, FZD4, CTNNB1, KIF11 and NDP ), as well as structural variants in TSPAN12 and KIF11 . These accounted for 15/59 (25.4%) of FEVR cases. We also found candidate heterozygous variants in CTNND1 in three unsolved FEVR cases. Expanding the list of genes examined to include all genes reported to be mutated in ocular disorders likely solved a further four cases, indicating that these individuals may be misclassified as FEVR in GEL. Conclusion: By performing bespoke reanalysis of the FEVR GEL cohort, this study has highlighted additional heterozygous variants in CTNND1 in FEVR cases and increased the diagnostic yield from 20% solved by the GEL analysis pipeline to 37% (22/59), but the majority of FEVR cases remain without a molecular diagnosis.

Objective: This study aims to describe the genetic landscape of syndromic and non-syndromic hearing loss (HL) in the UK population using data from the 100,000 Genomes Project (100kGP). Design: Cohort study Setting: NHS England Participants: 2,271 families with syndromic and non-syndromic HL recruited to the 100kGP rare disease programme between 2013 and 2018. Participants with at least one Human Phenotype Ontology (HPO) term descendant of the term “Hearing impairment” (HP:0000365) were included; this equated to 5,488 individuals, comprising 2,762 affected individuals and 2,726 unaffected relatives. Main outcome measure: Diagnostic rate and prevalence of different gene diagnoses by auditory phenotype identified by whole genome sequencing. Results: The overall diagnostic yield was conservatively estimated at 27.5% (625/2271), with diagnoses identified in 273 different genes. Common causative genes included USH2A, GJB2, COL1A1 and MYO15A , accounting for approximately 20% of the diagnoses. This diagnostic rate excludes variants of uncertain significance (VUS), variants in genes where HL cannot be confidently attributed to the identified variant, or those still awaiting confirmation. The inclusion of these categories would increase the diagnostic yield to 39.6%. This work describes the 100kGP standard pipeline and supplementary analyses that include the use of Exomiser. Stratification of the cohort allowed quantification of the likelihood of genetic diagnosis with specific phenotypic combinations and identification of positive predictors for a genetic diagnosis by auditory phenotype. A statistically significant increase in diagnostic rate was reported for those with congenital (33.2%), bilateral (27%), and high-frequency (32.4%) hearing subtypes. Furthermore, in patients with HPO terms restricted to the auditory system alone, around 40% of diagnoses were attributed to genes that might have a broader syndromic phenotype (non-syndromic mimics). A high diagnostic yield (56%) was seen in patients with ear and eye abnormalities, largely driven by genes associated with Usher and Wolfram syndrome. Conclusion: In conclusion, this study offers valuable insights into the complex genomic and phenotypic architecture of both syndromic and non-syndromic HL, which has the potential to improve diagnostic pipelines and inform clinical care.

SUMMARY: With the routine use of high-resolution heavily T2-weighted sequences to evaluate patients with hearing deficits, new, subtle phenotypes of cochlear malformations are being discovered and an increasing number of genotype-phenotype correlations are being found through a reverse phenotype approach, which can help guide geneticists. In this brief report, we present subtle malformations of the apical turn of the cochlea related to 3 genetic mutations, emphasizing the importance of a careful assessment of the cochlear apex.

BACKGROUND AND PURPOSE: An “unwound” or “offset” cochlea has been described as a characteristic imaging feature in patients with branchio-oto-renal syndrome, and recently recognized to be associated in particular to those with EYA1 gene mutations. Determination of this feature has traditionally relied on subjective visual assessment. Our aim was to establish an objective assessment method for cochlear offset (the cochlear turn alignment ratio) and determine an optimal cutoff turn alignment ratio value that separates individuals with EYA1-branchio-oto-renal syndrome from those with SIX1-branchio-oto-renal syndrome and healthy controls. MATERIALS AND METHODS: Temporal bone CT or MR imaging from 40 individuals with branchio-oto-renal syndrome and 40 controls was retrospectively reviewed. Cochlear offset was determined visually by 2 independent blinded readers and then quantitatively via a standardized technique yielding the cochlear turn alignment ratio. The turn alignment ratio values were compared between cochleae qualitatively assessed as “not offset” and “offset.” Receiver operating characteristic analysis was used to determine the ability of the turn alignment ratio to differentiate between these populations and an optimal cutoff turn alignment ratio value. Cochlear offset and turn alignment ratio values were analyzed for each branchio-oto-renal syndrome genotype subpopulation and for controls. RESULTS: The turn alignment ratio can accurately differentiate between cochleae with and without an offset (P < .001). The optimal cutoff value separating these populations was 0.476 (sensitivity = 1, specificity = 0.986, J = 0.986). All except 1 cochlea among the EYA1-branchio-oto-renal syndrome subset and all with unknown genotype branchio-oto-renal syndrome had a cochlear offset and a turn alignment ratio of 0.476. CONCLUSIONS: There is a statistically significant difference in turn alignment ratios between offset and nonoffset cochleae, with an optimal cutoff of 0.476. This cutoff value allows excellent separation of EYA1-branchio-oto-renal syndrome from SIX1-branchio-oto-renal syndrome and from individuals without branchio-oto-renal syndrome or sensorineural hearing loss. The turn alignment ratio is a reliable and objective metric that can aid in the imaging evaluation of branchio-oto-renal syndrome.

BACKGROUND AND PURPOSE: Temporal bone imaging plays an important role in the work-up of branchio-oto-renal syndrome. Previous reports have suggested that the unwound or offset cochlea is a highly characteristic marker for branchio-oto-renal syndrome. Our goals were to examine the prevalence of this finding in a branchio-oto-renal syndrome cohort and analyze genetic-phenotypic associations not previously established. MATERIALS AND METHODS: This multicenter retrospective study included 38 ears in 19 unrelated individuals with clinically diagnosed branchio-oto-renal syndrome and confirmed mutations in the EYA1 or SIX1 genes. Two blinded neuroradiologists independently reviewed and documented temporal bone imaging findings in 13 categories for each ear. Imaging phenotypes were correlated with genotypes. RESULTS: There was excellent interrater agreement for all 13 phenotypic categories (κ ≥ 0.80). Of these, 9 categories showed statistically significant differences between patients with EYA1-branchio-oto-renal syndrome and SIX1-branchio-oto-renal syndrome. Cochlear offset was present in 100% of patients with EYA1-branchio-oto-renal syndrome, but in only 1 ear (12.5%) among patients with SIX1-branchio-oto-renal syndrome. A short thorny appearance of the cochlear apical turn was observed in most patients with SIX1-branchio-oto-renal syndrome. CONCLUSIONS: An offset cochlea is associated with the EYA1-branchio-oto-renal syndrome genotype. The SIX1-branchio-oto-renal syndrome genotype is associated with a different cochlear phenotype that almost always is without offset and has a short thorny tip as the apical turn. Therefore, cochlear offset is not a characteristic marker for all patients with branchio-oto-renal syndrome. The lack of a cochlear offset in a patient with clinically suspected branchio-oto-renal syndrome does not exclude the diagnosis and, in fact, may be predictive of the SIX1 genotype.

Rare diseases, particularly those with great phenotypic and genetic heterogeneity, remain a diagnostic challenge. Broadening the investigative approach through whole genome sequencing (WGS) is anticipated to improve diagnostic yield. Despite this, substantial numbers of patients remain undiagnosed through current 100,000 Genomes Project pipelines. In these cases, the causative mutation may not be prioritised due to lack of evidence associating the gene with a specific phenotype, or as a result of being inadvertently filtered out. A systematic approach to additional data analysis utilising both inheritance model filtering and ranking algorithm tools has been piloted in cases with no primary findings (NPF). Examples of diagnoses secured include a de novo TAB2mutation, causing a connective tissue phenotype with congenital heart disease and a paternally inherited COL7A1mutation, causing a variable penetrance skin blistering disorder, epidermolysis bullosa dystrophica. Identification of causative variants in WGS data remains challenging. Data led approaches to optimising additional review of cases with NPF have the prospect of improving both sensitivity and cost efficiency and may provide earlier diagnosis for individuals with rare disease, ending their diagnostic odyssey. Establishing a standardised approach to reanalysis will be particularly important as we approach the introduction of an NHS clinical sequencing service.