Assessing performance of pathogenicity predictors using clinically relevant variant datasets

BACKGROUND

Pathogenicity predictors are integral to genomic variant interpretation but, despite their widespread usage, an independent validation of performance using a clinically relevant dataset has not been undertaken.

METHODS

We derive two validation datasets: an 'open' dataset containing variants extracted from publicly available databases, similar to those commonly applied in previous benchmarking exercises, and a 'clinically representative' dataset containing variants identified through research/diagnostic exome and panel sequencing. Using these datasets, we evaluate the performance of three recent meta-predictors, REVEL, GAVIN and ClinPred, and compare their performance against two commonly used in silico tools, SIFT and PolyPhen-2.

RESULTS

Although the newer meta-predictors outperform the older tools, the performance of all pathogenicity predictors is substantially lower in the clinically representative dataset. Using our clinically relevant dataset, REVEL performed best with an area under the receiver operating characteristic curve of 0.82. Using a concordance-based approach based on a consensus of multiple tools reduces the performance due to both discordance between tools and false concordance where tools make common misclassification. Analysis of tool feature usage may give an insight into the tool performance and misclassification.

CONCLUSION

Our results support the adoption of meta-predictors over traditional in silico tools, but do not support a consensus-based approach as in current practice.

Diagnosis of lethal or prenatal-onset autosomal recessive disorders by parental exome sequencing

OBJECTIVE

Rare genetic disorders resulting in prenatal or neonatal death are genetically heterogeneous, but testing is often limited by the availability of fetal DNA, leaving couples without a potential prenatal test for future pregnancies. We describe our novel strategy of exome sequencing parental DNA samples to diagnose recessive monogenic disorders in an audit of the first 50 couples referred.

METHOD

Exome sequencing was carried out in a consecutive series of 50 couples who had 1 or more pregnancies affected with a lethal or prenatal-onset disorder. In all cases, there was insufficient DNA for exome sequencing of the affected fetus. Heterozygous rare variants (MAF < 0.001) in the same gene in both parents were selected for analysis. Likely, disease-causing variants were tested in fetal DNA to confirm co-segregation.

RESULTS

Parental exome analysis identified heterozygous pathogenic (or likely pathogenic) variants in 24 different genes in 26/50 couples (52%). Where 2 or more fetuses were affected, a genetic diagnosis was obtained in 18/29 cases (62%). In most cases, the clinical features were typical of the disorder, but in others, they result from a hypomorphic variant or represent the most severe form of a variable phenotypic spectrum.

CONCLUSION

We conclude that exome sequencing of parental samples is a powerful strategy with high clinical utility for the genetic diagnosis of lethal or prenatal-onset recessive disorders. © 2017 The Authors Prenatal Diagnosis published by John Wiley & Sons Ltd.

Cause of death and time of death distribution of trauma patients in a Level I trauma centre in the Netherlands

OBJECTIVE

The classical trimodal distribution of trauma deaths describes three peaks of deaths following trauma: immediate, early and late deaths. The aim of this study was to evaluate whether further maturation of the trauma centre and the improvement of survival have had an effect on the time of death distribution and resulted in a shift in causes of death.

METHODS

All trauma patients from 1999 to 2010 who died after arrival in the emergency room and prior to discharge from the hospital were included. Deaths caused by drowning, poisoning and overdose were excluded.

RESULTS

A total of 16,421 trauma patients were admitted to our hospital. 772 (4.7 %) patients died, of which 720 were included in this study. The trauma mechanism was predominantly blunt (94.7 %). 530 patients (73.6 %) had Injury Severity Score (ISS) ≥25. The most frequent causes of death were central nervous system (CNS) injury (59.9 %), exsanguinations (12.9 %) and pneumonia/respiratory insufficiency (8.5 %). The first peak of death was seen in the first hour after arrival at the emergency department; subsequently, a rapid decline was observed and no further peaks were seen. Over the years, we observed a general decrease in deaths due to exsanguination (p = 0.035) and a general increase in deaths due to CNS injury (p = 0.004).

CONCLUSION

The temporal distribution of trauma deaths in our hospital changed as maturation of the trauma centre occurred. There is one peak of trauma deaths in the first hour after admission, followed by a rapid decline; no trimodal distribution was observed. Over time, there was a decrease in exsanguinations and an increase of deaths due to CNS injury.

Mutations in PIGB Cause an Inherited GPI Biosynthesis Defect with an Axonal Neuropathy and Metabolic Abnormality in Severe Cases

Proteins anchored to the cell surface via glycosylphosphatidylinositol (GPI) play various key roles in the human body, particularly in development and neurogenesis. As such, many developmental disorders are caused by mutations in genes involved in the GPI biosynthesis and remodeling pathway. We describe ten unrelated families with bi-allelic mutations in PIGB, a gene that encodes phosphatidylinositol glycan class B, which transfers the third mannose to the GPI. Ten different PIGB variants were found in these individuals. Flow cytometric analysis of blood cells and fibroblasts from the affected individuals showed decreased cell surface presence of GPI-anchored proteins. Most of the affected individuals have global developmental and/or intellectual delay, all had seizures, two had polymicrogyria, and four had a peripheral neuropathy. Eight children passed away before four years old. Two of them had a clinical diagnosis of DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures), a condition that includes sensorineural deafness, shortened terminal phalanges with small finger and toenails, intellectual disability, and seizures; this condition overlaps with the severe phenotypes associated with inherited GPI deficiency. Most individuals tested showed elevated alkaline phosphatase, which is a characteristic of the inherited GPI deficiency but not DOORS syndrome. It is notable that two severely affected individuals showed 2-oxoglutaric aciduria, which can be seen in DOORS syndrome, suggesting that severe cases of inherited GPI deficiency and DOORS syndrome might share some molecular pathway disruptions.

p.Val804Met, the Most Frequent Pathogenic Mutation in RET, Confers a Very Low Lifetime Risk of Medullary Thyroid Cancer

CONTEXT

To date, penetrance figures for medullary thyroid cancer (MTC) for variants in rearranged during transfection (RET) have been estimated from families ascertained because of the presence of MTC.

OBJECTIVE

To gain estimates of penetrance, unbiased by ascertainment, we analyzed 61 RET mutations assigned as disease causing by the American Thyroid Association (ATA) in population whole-exome sequencing data.

DESIGN

For the 61 RET mutations, we used analyses of the observed allele frequencies in ∼51,000 individuals from the Exome Aggregation Consortium (ExAC) database that were not contributed via The Cancer Genome Atlas (TCGA; non-TCGA ExAC), assuming lifetime penetrance for MTC of 90%, 50%, and unbounded.

SETTING

Population-based.

RESULTS

Ten of 61 ATA disease-causing RET mutations were present in the non-TCGA ExAC population with observed frequency consistent with penetrance for MTC of >90%. For p.Val804Met, the lifetime penetrance for MTC, estimated from the allele frequency observed, was 4% [95% confidence interval (CI), 0.9% to 8%].

CONCLUSIONS

Based on penetrance analysis in carrier relatives of p.Val804Met-positive cases of MTC, p.Val804Met is currently understood to have high-lifetime penetrance for MTC (87% by age 70), albeit of later onset of MTC than other RET mutations. Given our unbiased estimate of penetrance for RET p.Val804Met of 4% (95% CI, 0.9% to 8%), the current recommendation by the ATA of prophylactic thyroidectomy as standard for all RET mutation carriers is likely inappropriate.

Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data.

X chromosome-linked CNVs in male infertility: discovery of overall duplication load and recurrent, patient-specific gains with potential clinical relevance

Introduction

Spermatogenesis is a highly complex process involving several thousand genes, only a minority of which have been studied in infertile men. In a previous study, we identified a number of Copy Number Variants (CNVs) by high-resolution array-Comparative Genomic Hybridization (a-CGH) analysis of the X chromosome, including 16 patient-specific X chromosome-linked gains. Of these, five gains (DUP1A, DUP5, DUP20, DUP26 and DUP40) were selected for further analysis to evaluate their clinical significance.

Materials and Methods

The copy number state of the five selected loci was analyzed by quantitative-PCR on a total of 276 idiopathic infertile patients and 327 controls in a conventional case-control setting (199 subjects belonged to the previous a-CGH study). For one interesting locus (intersecting DUP1A) additional 338 subjects were analyzed.

Results and Discussion

All gains were confirmed as patient-specific and the difference in duplication load between patients and controls is significant (p = 1.65×10⁻⁴). Two of the CNVs are private variants, whereas 3 are found recurrently in patients and none of the controls. These CNVs include, or are in close proximity to, genes with testis-specific expression. DUP1A, mapping to the PAR1, is found at the highest frequency (1.4%) that was significantly different from controls (0%) (p = 0.047 after Bonferroni correction). Two mechanisms are proposed by which DUP1A may cause spermatogenic failure: i) by affecting the correct regulation of a gene with potential role in spermatogenesis; ii) by disturbing recombination between PAR1 regions during meiosis. This study allowed the identification of novel spermatogenesis candidate genes linked to the 5 CNVs and the discovery of the first recurrent, X-linked gain with potential clinical relevance.

Health-related quality of life in trauma patients who sustained a calcaneal fracture

BACKGROUND

Calcaneal fractures are known to cause a considerable long-term disability; disability influences the public health negatively in terms of personal suffering and monetary losses. Health-related quality of life (HRQoL) in general is influenced by various patient-specific factors, and possibly trauma and fracture characteristics. Previous studies might have underestimated the impact of this injury because of several injury and patient specific exclusion criteria. In this study we provide an overview of the patient characteristics and outcome of patients with a calcaneal fracture in a Dutch level I trauma population.

METHODS

We have performed a retrospective cohort study in a trauma level 1 centre. All patients who sustained a calcaneal fracture and were 16 years or older at time of admission were included. We have retrieved the relevant patient and fracture characteristics from the medical status and evaluated current health status with a questionnaire. We have used the EQ-6D for quantification of the HRQoL. Moreover, the patient's capability to work was evaluated.

RESULTS

125 patients with 151 calcaneal fractures were identified of which 93 patients with 114 calcaneal fractures participated in this study. The median EQ-5D index value is 0.78. All dimensions of the EQ-6D are affected in particular the dimensions 'mobility', 'pain/discomfort' and 'usual activity'. 85% is capable to work. Female patients or patients with a relevant comorbidity or a psychiatric history have a significantly lower HRQoL score. In this study population no difference in HRQoL results was demonstrated among different socio-economic status, associated injuries, or severity of injury.

CONCLUSIONS

This study demonstrates that patients who sustained a calcaneal fracture have a significantly lower HRQoL than the Dutch reference population and suffer from a chronic disability. Moreover, patients that have a comorbidity, a relevant psychiatric history or are female have significantly lower HRQoL scores. Furthermore, this study shows that socio-economic status, associated injuries, or severity of injury did not influence the HRQoL in this study population.

LEVEL OF EVIDENCE

Prognostic level II.

Metallurgical analysis of failed Björk-Shiley cardiac valve prostheses

An investigation into the mechanisms of failure of current Björk-Shiley cardiac valve prostheses is reported. Two failed valves, one apparently unfailed but defective valve, and one unused valve, were examined by scanning electron microscopy and metallographic section. In the first two valves (removed 12 and 23 months after implantation) fracture was associated with the welds joining the short strut to the valve ring. The fracture surfaces in all cases were heavily faceted and showed branching cracks. Extensive wear had occurred on one fracture surface in the first case, suggesting that one leg of the short strut had failed before the other, though this had been clinically undetectable. The third valve was removed owing to failure of the suturing (24 months after implantation) but one leg of the short strut was found to be completely fractured. The other leg showed extensive cracking and porosity in the weld region. A metallographic section taken through the weld region of the fourth (unused) valve illustrated several sizable defects directly attributable to the welding process. It is suggested that the valves failed by fatigue and that these problems could be overcome if the complete valve cage were machined as a single piece.

Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes

Background

ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane-anchored protein involved in diverse processes including mitochondrial dynamics, mitochondrial DNA organization, and cholesterol metabolism. Biallelic deletions (null), recessive missense variants (hypomorph), and heterozygous missense variants or duplications (antimorph) in ATAD3A lead to neurological syndromes in humans.

Methods

To expand the mutational spectrum of ATAD3A variants and to provide functional interpretation of missense alleles in trans to deletion alleles, we performed exome sequencing for identification of single nucleotide variants (SNVs) and copy number variants (CNVs) in ATAD3A in individuals with neurological and mitochondrial phenotypes. A Drosophila Atad3a Gal4 knockin-null allele was generated using CRISPR-Cas9 genome editing technology to aid the interpretation of variants.

Results

We report 13 individuals from 8 unrelated families with biallelic ATAD3A variants. The variants included four missense variants inherited in trans to loss-of-function alleles (p.(Leu77Val), p.(Phe50Leu), p.(Arg170Trp), p.(Gly236Val)), a homozygous missense variant p.(Arg327Pro), and a heterozygous non-frameshift indel p.(Lys568del). Affected individuals exhibited findings previously associated with ATAD3A pathogenic variation, including developmental delay, hypotonia, congenital cataracts, hypertrophic cardiomyopathy, and cerebellar atrophy. Drosophila studies indicated that Phe50Leu, Gly236Val, Arg327Pro, and Lys568del are severe loss-of-function alleles leading to early developmental lethality. Further, we showed that Phe50Leu, Gly236Val, and Arg327Pro cause neurogenesis defects. On the contrary, Leu77Val and Arg170Trp are partial loss-of-function alleles that cause progressive locomotion defects and whose expression leads to an increase in autophagy and mitophagy in adult muscles.

Conclusion

Our findings expand the allelic spectrum of ATAD3A variants and exemplify the use of a functional assay in Drosophila to aid variant interpretation.

Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory

BACKGROUND

The widespread clinical application of genome-wide sequencing has resulted in many new diagnoses for rare genetic conditions, but testing regularly identifies variants of uncertain significance (VUS). The remarkable rise in the amount of genomic data has been paralleled by a rise in the number of protein structures that are now publicly available, which may have clinical utility for the interpretation of missense and in-frame insertions or deletions.

METHODS

Within a UK National Health Service genomic medicine diagnostic laboratory, we investigated the number of VUS over a 5-year period that were evaluated using protein structural analysis and how often this analysis aided variant classification.

RESULTS

We found 99 novel missense and in-frame variants across 67 genes that were initially classified as VUS by our diagnostic laboratory using standard variant classification guidelines and for which further analysis of protein structure was requested. Evidence from protein structural analysis was used in the re-assessment of 64 variants, of which 47 were subsequently reclassified as pathogenic or likely pathogenic and 17 remained as VUS. We identified several case studies where protein structural analysis aided variant interpretation by predicting disease mechanisms that were consistent with the observed phenotypes, including loss-of-function through thermodynamic destabilisation or disruption of ligand binding, and gain-of-function through de-repression or escape from proteasomal degradation.

CONCLUSIONS

We have shown that using in silico protein structural analysis can aid classification of VUS and give insights into the mechanisms of pathogenicity. Based on our experience, we propose a generic evidence-based workflow for incorporating protein structural information into diagnostic practice to facilitate variant classification.

Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1

Despite the rapid expansion in recent years of databases reporting either benign or pathogenic genetic variations, the interpretation of novel missense variants remains challenging, particularly for clinical or genetic testing laboratories where functional analysis is often unfeasible. Previous studies have shown that thermodynamic analysis of protein structure in silico can discriminate between groups of benign and pathogenic missense variants. However, although structures exist for many human disease‒associated proteins, such analysis remains largely unexploited in clinical laboratories. Here, we analyzed the predicted effect of 338 known missense variants on the structure of menin, the MEN1 gene product. Results provided strong discrimination between pathogenic and benign variants, with a threshold of >4 kcal/mol for the predicted change in stability, providing a strong indicator of pathogenicity. Subsequent analysis of seven novel missense variants identified during clinical testing of patients with MEN1 showed that all seven were predicted to destabilize menin by >4 kcal/mol. We conclude that structural analysis provides a useful tool in understanding the effect of missense variants in MEN1 and that integration of proteomic with genomic data could potentially contribute to the classification of novel variants in this disease.

Dominant mitochondrial membrane protein-associated neurodegeneration (MPAN) variants cluster within a specific C19orf12 isoform

Mitochondria membrane protein-associated neurodegeneration (MPAN) neurodegenerative disorder is typically associated with biallelic C19orf12 variants. Here we describe a new and review candidate previous monoallelic de novo C19orf12 variants to define loss of function mutations located in the putative non-membrane spanning C19orf12 isoform as the potential basis of monoallelic MPAN.

Predicting suitability of intramedullary fixation for displaced midshaft clavicle fractures

PURPOSE

Implant-related irritation is a technique-specific complication seen in a substantial number of patients treated with intramedullary nailing for clavicle fractures. The purpose of this study was to identify predictors for developing implant-related irritation in patients with displaced midshaft clavicle fractures treated with elastic stable intramedullary nailing.

METHODS

A retrospective analysis of the surgical database in two level 2 trauma centers was performed. Patients who underwent intramedullary nailing for displaced midshaft clavicle fractures between 2005 and 2012 in the first hospital were included. Age, gender, fracture comminution and fracture location were assessed as possible predictors for developing irritation using multivariate logistic regression analysis. These predictors were externally validated using data of patients treated in another hospital.

RESULTS

Eighty-one patients were included in initial analysis. In the multivariate analysis, comminuted fractures in comparison to non-comminuted fractures (72 vs. 38%, p = 0.027) and fracture location (p < 0.001) were significantly associated with the development of implant-related irritation. In particular, lateral diaphyseal fractures caused irritation compared to fractures on the medial side of the cut-off point (88 vs. 26%). External validation of these predictors in 48 additional patients treated in another hospital showed a similar predictive value of the model and a good fit.

CONCLUSION

Comminuted and lateral diaphyseal fractures were found to be statistically significant and independent predictors for developing implant-related irritation. We, therefore, believe that intramedullary nailing might not be suitable for these types of fractures. Future studies are needed to determine whether alternative surgical techniques or implants would be more suitable for these specific types of fractures.

Induced seismicity response of hydraulic fracturing: results of a multidisciplinary monitoring at the Wysin site, Poland

Shale oil and gas exploitation by hydraulic fracturing experienced a strong development worldwide over the last years, accompanied by a substantial increase of related induced seismicity, either consequence of fracturing or wastewater injection. In Europe, unconventional hydrocarbon resources remain underdeveloped and their exploitation controversial. In UK, fracturing operations were stopped after the M_w 2.3 Blackpool induced earthquake; in Poland, operations were halted in 2017 due to adverse oil market conditions. One of the last operated well at Wysin, Poland, was monitored independently in the framework of the EU project SHEER, through a multidisciplinary system including seismic, water and air quality monitoring. The hybrid seismic network combines surface mini-arrays, broadband and shallow borehole sensors. This paper summarizes the outcomes of the seismological analysis of these data. Shallow artificial seismic noise sources were detected and located at the wellhead active during the fracturing stages. Local microseismicity was also detected, located and characterised, culminating in two events of M_w 1.0 and 0.5, occurring days after the stimulation in the vicinity of the operational well, but at very shallow depths. A sharp methane peak was detected ~19 hours after the M_w 0.5 event. No correlation was observed between injected volumes, seismicity and groundwater parameters.

TECPR2-related hereditary sensory and autonomic neuropathy in two siblings from Palestine

Due to the majority of currently available genome data deriving from individuals of European ancestry, the clinical interpretation of genomic variants in individuals from diverse ethnic backgrounds remains a major diagnostic challenge. Here, we investigated the genetic cause of a complex neurodevelopmental phenotype in two Palestinian siblings. Whole exome sequencing identified a homozygous missense TECPR2 variant (Chr14(GRCh38):g.102425085G>A; NM_014844.5:c.745G>A, p.(Gly249Arg)) absent in gnomAD, segregating appropriately with the inheritance pattern in the family. Variant assessment with in silico pathogenicity prediction and protein modeling tools alongside population database frequencies led to classification as a variant of uncertain significance. As pathogenic TECPR2 variants are associated with hereditary sensory and autonomic neuropathy with intellectual disability, we reviewed previously published candidate TECPR2 missense variants to clarify clinical outcomes and variant classification using current approved guidelines, classifying a number of published variants as of uncertain significance. This work highlights genomic healthcare inequalities and the challenges in interpreting rare genetic variants in populations underrepresented in genomic databases. It also improves understanding of the clinical and genetic spectrum of TECPR2-related neuropathy and contributes to addressing genomic data disparity and inequalities of the genomic architecture in Palestinian populations.

Elucidating the clinical spectrum and molecular basis of HYAL2 deficiency

PURPOSE

We previously defined biallelic HYAL2 variants causing a novel disorder in 2 families, involving orofacial clefting, facial dysmorphism, congenital heart disease, and ocular abnormalities, with Hyal2 knockout mice displaying similar phenotypes. In this study, we better define the phenotype and pathologic disease mechanism.

METHODS

Clinical and genomic investigations were undertaken alongside molecular studies, including immunoblotting and immunofluorescence analyses of variant/wild-type human HYAL2 expressed in mouse fibroblasts, and in silico modeling of putative pathogenic variants.

RESULTS

Ten newly identified individuals with this condition were investigated, and they were associated with 9 novel pathogenic variants. Clinical studies defined genotype-phenotype correlations and confirmed a recognizable craniofacial phenotype in addition to myopia, cleft lip/palate, and congenital cardiac anomalies as the most consistent manifestations of the condition. In silico modeling of missense variants identified likely deleterious effects on protein folding. Consistent with this, functional studies indicated that these variants cause protein instability and a concomitant cell surface absence of HYAL2 protein.

CONCLUSION

These studies confirm an association between HYAL2 alterations and syndromic cleft lip/palate, provide experimental evidence for the pathogenicity of missense alleles, enable further insights into the pathomolecular basis of the disease, and delineate the core and variable clinical outcomes of the condition.

Elucidating the clinical and genetic spectrum of inositol polyphosphate phosphatase INPP4A-related neurodevelopmental disorder

PURPOSE

Biallelic INPP4A variants have recently been associated with severe neurodevelopmental disease in single-case reports. Here, we expand and elucidate the clinical-genetic spectrum and provide a pathomechanistic explanation for genotype-phenotype correlations.

METHODS

Clinical and genomic investigations of 30 individuals were undertaken alongside molecular and in silico modelling and translation reinitiation studies.

RESULTS

We characterize a clinically variable disorder with cardinal features, including global developmental delay, severe-profound intellectual disability, microcephaly, limb weakness, cerebellar signs, and short stature. A more severe presentation associated with biallelic INPP4A variants downstream of exon 4 has additional features of (ponto)cerebellar hypoplasia, reduced cerebral volume, peripheral spasticity, contractures, intractable seizures, and cortical visual impairment. Our studies identify the likely pathomechanism of this genotype-phenotype correlation entailing translational reinitiation in exon 4 resulting in an N-terminal truncated INPP4A protein retaining partial functionality, associated with less severe disease. We also identified identical reinitiation site conservation in Inpp4a-/- mouse models displaying similar genotype-phenotype correlation. Additionally, we show fibroblasts from a single affected individual exhibit disrupted endocytic trafficking pathways, indicating the potential biological basis of the condition.

CONCLUSION

Our studies comprehensively characterize INPP4A-related neurodevelopmental disorder and suggest genotype-specific clinical assessment guidelines. We propose that the potential mechanistic basis of observed genotype-phenotype correlations entails exon 4 translation reinitiation.

Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance

BACKGROUND

Genetic variants that severely alter protein products (e.g. nonsense, frameshift) are often associated with disease. For some genes, these predicted loss-of-function variants (pLoFs) are observed throughout the gene, whilst in others, they occur only at specific locations. We hypothesised that, for genes linked with monogenic diseases that display incomplete penetrance, pLoF variants present in apparently unaffected individuals may be limited to regions where pLoFs are tolerated. To test this, we investigated whether pLoF location could explain instances of incomplete penetrance of variants expected to be pathogenic for Mendelian conditions.

METHODS

We used exome sequence data in 454,773 individuals in the UK Biobank (UKB) to investigate the locations of pLoFs in a population cohort. We counted numbers of unique pLoF, missense, and synonymous variants in UKB in each quintile of the coding sequence (CDS) of all protein-coding genes and clustered the variants using Gaussian mixture models. We limited the analyses to genes with ≥ 5 variants of each type (16,473 genes). We compared the locations of pLoFs in UKB with all theoretically possible pLoFs in a transcript, and pathogenic pLoFs from ClinVar, and performed simulations to estimate the false-positive rate of non-uniformly distributed variants.

RESULTS

For most genes, all variant classes fell into clusters representing broadly uniform variant distributions, but genes in which haploinsufficiency causes developmental disorders were less likely to have uniform pLoF distribution than other genes (P < 2.2 × 10-6). We identified a number of genes, including ARID1B and GATA6, where pLoF variants in the first quarter of the CDS were rescued by the presence of an alternative translation start site and should not be reported as pathogenic. For other genes, such as ODC1, pLoFs were located approximately uniformly across the gene, but pathogenic pLoFs were clustered only at the end, consistent with a gain-of-function disease mechanism.

CONCLUSIONS

Our results suggest the potential benefits of localised constraint metrics and that the location of pLoF variants should be considered when interpreting variants.

The detection of human papillomavirus in oesophageal lesions

The polymerase chain reaction, with nested degenerate primers which amplify a specific fragment of the L1 gene of wide range of human papillomaviruses, was used to determine whether HPV DNA was present in biopsies from various oesophageal lesions. Ten out of 14 (71%) patients with oesophageal carcinoma were positive for HPV DNA either in the tumour biopsies (6/14) or in adjacent tissue (6/9). HPV DNA was detected in 6 of the 41 biopsies (15%) from patients without oesophageal malignancy. Three of these 6 positive were from biopsies with clear cell acanthosis.

Evaluation of in silico pathogenicity prediction tools for the classification of small in-frame indels

BACKGROUND

The use of in silico pathogenicity predictions as evidence when interpreting genetic variants is widely accepted as part of standard variant classification guidelines. Although numerous algorithms have been developed and evaluated for classifying missense variants, in-frame insertions/deletions (indels) have been much less well studied.

METHODS

We created a dataset of 3964 small (< 100 bp) indels predicted to result in in-frame amino acid insertions or deletions using data from gnomAD v3.1 (minor allele frequency of 1-5%), ClinVar and the Deciphering Developmental Disorders (DDD) study. We used this dataset to evaluate the performance of nine pathogenicity predictor tools: CADD, CAPICE, FATHMM-indel, MutPred-Indel, MutationTaster2021, PROVEAN, SIFT-indel, VEST-indel and VVP.

RESULTS

Our dataset consisted of 2224 benign/likely benign and 1740 pathogenic/likely pathogenic variants from gnomAD (n = 809), ClinVar (n = 2882) and, DDD (n = 273). We were able to generate scores across all tools for 91% of the variants, with areas under the ROC curve (AUC) of 0.81-0.96 based on the published recommended thresholds. To avoid biases caused by inclusion of our dataset in the tools' training data, we also evaluated just DDD variants not present in either gnomAD or ClinVar (70 pathogenic and 81 benign). Using this subset, the AUC of all tools decreased substantially to 0.64-0.87. Several of the tools performed similarly however, VEST-indel had the highest AUCs of 0.93 (full dataset) and 0.87 (DDD subset).

CONCLUSIONS

Algorithms designed for predicting the pathogenicity of in-frame indels perform well enough to aid clinical variant classification in a similar manner to missense prediction tools.