InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines

Integrated analysis of oral rinse-derived and plasma circulating tumour DNA for mutation profiling and outcome prediction with oral squamous cell carcinoma

This study evaluates the potential of oral rinse-derived and plasma circulating tumour DNA (ctDNA) in HPV-negative oral squamous cell carcinoma (OSCC), where early recurrence occurs in a significant proportion of patients, contributing to poor prognosis. Analysis of paired tissue, oral rinse, and plasma samples from 123 patients revealed ctDNA detection rates of 94.3% in oral rinse and 80.5% in plasma samples. Combined testing improved mutation detection sensitivity to 48.6%. A machine learning model integrating seven mutated genes (TP53, TERT, IKZF1, EP300, MYC, EGFR, PIK3CA) and clinical factors demonstrated robust prediction of recurrence (validation AUC: 0.854) and survival outcomes. Integration of pretreatment plasma ctDNA status further enhanced predictive performance. In longitudinal analysis, ctDNA detected recurrence approximately four months before clinical manifestation. These findings suggest that integrated ctDNA analysis offers improved mutation profiling and outcome prediction, potentially enabling earlier interventions in OSCC.

SCN9A should not be considered an epilepsy gene; Refuting a gene-disease association

OBJECTIVE

The SCN9A gene is primarily expressed in nociceptive pathways within the peripheral nervous system, and pathogenic variants are associated with human pain disorders. In recent years, several studies have proposed SCN9A as a monogenic cause of epilepsy. Our objective was to critically appraise the SCN9A-epilepsy gene-disease relationship.

METHODS

We assessed "epilepsy-associated" SCN9A variants from four sources: (1) the literature up to December 2023 (n = 27), (2) epilepsy patients referred for genetic testing at a regional service in Glasgow, UK over a 5-year period (n = 30), (3) the Human Genetics Mutation Database (n = 25), and (4) ClinVar (n = 1546). The latter two are genome-wide variant databases, accepting submissions from genetic laboratories and research groups. We checked whether each SCN9A variant is present in the Genome Aggregation Database (gnomAD) V4 (a reference population database for variant interpretation), and classified its pathogenicity based on the American College of Molecular Genetics and Genomics/Association of Molecular Pathologists guidelines.

RESULTS

Only three SCN9A variants were classified as "likely pathogenic," of which two were identified in healthy individuals in gnomAD. A total of 1540 of the 1546 SCN9A variants in ClinVar labeled as being associated with epilepsy were also reported in association with hereditary sensory and autonomic neuropathy. No further clinical data were provided in 1482 of these submissions.

SIGNIFICANCE

There is no convincing genetic evidence to support SCN9A as a causative epilepsy gene. As such, the inclusion of SCN9A in epilepsy genetic testing panels should be reassessed. Research centers and genetic testing laboratories should be rigorous and consistent in their submissions to variant databases.

Gain-of-function PPM1D mutations attenuate ischemic stroke

Identification of genetic aberrations in stroke, the second leading cause of death worldwide, is of paramount importance for understanding the disease pathogenesis and generating new therapies. Whole-genome sequencing from 10,241 ischemic stroke patients identified eight patients carrying gain-of-function mutations on coding variants in the protein phosphatase magnesium-dependent 1 δ (PPM1D) gene. Patients carrying PPM1D mutations exhibit better stroke-related clinical phenotypes, including improvements in peripheral inflammation, fibrinogen, low-density lipoprotein, cholesterol and plateletcrit level. Experimental brain ischemia in Ppm1d-deficient (Ppm1d-/-) mice resulted in enlarged lesions and pronounced neurological impairments. Spatial transcriptomics revealed a distinct Ppm1d-associated gene expression pattern, indicating disrupted endothelial homeostasis during ischemic brain injury. Proteomic analysis demonstrated that differentially expressed proteins in primary brain endothelial cells from Ppm1d-/- mice were significantly enriched in the peroxisome proliferator-activated receptors (PPARs)-mediated metabolic signaling. Mechanistically, Ppm1d deficiency promoted aberrant fatty acid β-oxidation and increased oxidative stress, which impaired endothelial cell function through the PPARα pathway. A small molecule, T2755, was identified to engage Trp427 and stabilize PPM1D, thereby mitigating ischemic brain injury in mice. Collectively, we find that PPM1D protects against ischemic brain injury and validates its pharmacological stabilizer T2755 as a promising therapy for ischemic stroke. Gain-of-function PPM1D mutations attenuate ischemic cerebral injury. Whole-genome sequencing data of 10,241 ischemic stroke patients from the Third Chinese National Stroke Registry (CNSR-III) identified eight patients with gain-of-function mutations in the protein phosphatase magnesium-dependent 1 δ (PPM1D) gene (17q23.2). These mutation carriers displayed improved peripheral inflammation, decreased fibrinogen, low-density lipoprotein, cholesterol and plateletcrit level. Ppm1d-deficient (Ppm1d-/-) mice exhibited exacerbated stroke outcomes, characterized by enlarged infarct volumes, disrupted cerebrovascular architecture, and enhanced neuro-inflammation. Mechanistically, Ppm1d deficiency induced the disturbance of endothelial fatty acid metabolism involving the PPARα pathway. Through integrated computational modeling, virtual screening, and in vitro validation, T2755 was identified as a small molecule PPM1D stabilizer. Pharmacological PPM1D stabilization with T2755 significantly attenuated ischemic brain injury in murine models.

Reproductive and cognitive phenotypes in carriers of recessive pathogenic variants

The genetic landscape of human Mendelian diseases is shaped by mutation and selection. Although selection on heterozygotes is well-established in autosomal-dominant disorders, convincing evidence for selection in carriers of pathogenic variants associated with recessive conditions is limited. Here, we studied heterozygous pathogenic variants in 1,929 genes, which cause recessive diseases when bi-allelic, in n = 378,751 unrelated European individuals from the UK Biobank. We find evidence suggesting fitness effects in heterozygous carriers for recessive genes, especially for variants in constrained genes across a broad range of diseases. Our data suggest reproductive effects at the population level, and hence natural selection, for autosomal-recessive disease variants. Further, variants in genes that underlie intellectual disability are associated with lower educational attainment in carriers, and we observe an altered genetic landscape, characterized by a threefold reduction in the calculated frequency of bi-allelic intellectual disability in the population relative to other recessive disorders.

Investigating the dual role of mitochondrial and nuclear genome variants in pediatric cardiomyopathies

Mitochondrial defects can lead to cardiomyopathies, which can be particularly severe in children. However, many cases of pediatric cardiomyopathy have no known etiology. To address this, we sought to explore if mitochondrial genome defects might be a contributor, as this could offer insights into disease mechanisms and guide targeted interventions. We first sequenced cardiomyopathy-related genes in twenty-seven pediatric patients diagnosed with primary non-syndromic cardiomyopathy and performed whole mtDNA sequencing in both patients and thirty-one healthy controls. The initial sequencing identified pathogenic variants in seven patients but subsequent mtDNA sequencing revealed additional insights. Specifically, a variant in FOXRED1, encoding FAD-dependent oxidoreductase domain-containing protein-1 which functions in mitochondrial complex I stability, and another variant in cytochrome c oxidase-I, MT-CO1, crucial for aerobic metabolism, were identified in two siblings with hypertrophic cardiomyopathy. In another case with hypertrophic cardiomyopathy, a variant in cytochrome b, MT-CYB, is likely a key factor in the abnormal contraction of cardiac muscle contraction. Furthermore, a novel 12 S rRNA variant was found in a patient with left ventricular non-compaction, and this offers a promising explanation for the pathogenesis, given the gene's high expression in the left ventricle. Taken together, mtDNA variants act synergistically with others, potentially disrupting myocardial bioenergetics.

Comprehensive molecular profiling of FH-deficient renal cell carcinoma identifies molecular subtypes and potential therapeutic targets

Fumarate hydratase-deficient renal cell carcinoma (FH-deficient RCC) is a rare yet highly lethal kidney cancer. To deepen our understanding of FH-deficient RCC, we conduct a comprehensive integrated genomic study. We analyze the association of FH alteration patterns with tumor heterogeneity and develop a CpG site-specific methylation signature for precise identification of FH-deficient RCC. Transcriptomic analysis unveils three distinctive molecular subtypes characterized by enrichment of immune/Angiogenic/Stromal (C1), WNT/Notch/MAPK (C2), and proliferation/stemness (C3) pathways, respectively. Tumors in C1 derive the most substantial survival benefit from a combination of immune checkpoint blockade (ICB) and anti-angiogenic therapy. Tumors in C2 display moderate response to this therapeutic approach. In contrast, tumors in C3 exhibit an unfavorable response to anti-angiogenic monotherapy and its combination with ICB. These findings contribute to a profound understanding of the aggressive nature of FH-deficient RCC, offering insights into potential precision medicine approaches for disease management.

The usefulness of comprehensive genome profiling test in screening of Lynch syndrome independent of the conventional clinical screening or microsatellite instability tests

Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline pathogenic variants of DNA mismatch repair (MMR) genes. To diagnose LS, the microsatellite instability (MSI) test or immunohistochemistry of MMR enzymes is used as a conventional clinical screening method for all patients with colorectal and endometrial cancers. Recently, patients with advanced-stage cancers have undergone comprehensive genomic profiling (CGP), which is useful not only for the detection of molecularly targeted personalized therapies, but also for the screening of hereditary cancer syndromes by determining presumed germline pathogenic variants (PGPVs). Between January 2020 and April 2024, 1583 patients underwent CGP at our institute. PGPVs in MMR genes were detected in 19 patients. Although one patient died prior to the disclosure of the results and eight patients declined confirmatory genetic testing, the remaining ten patients underwent confirmatory genetic tests, of whom six were found to have a hereditary origin. Two additional patients were diagnosed with LS using tumor-normal paired CGP. Eventually, a total of eight patients were diagnosed with LS. Herein, we describe two patients with microsatellite-stable cancer who could not be diagnosed using conventional clinical screening or MSI testing. Furthermore, we showed that pathogenic variants of MMR genes do not always correlate with high MSI prediction scores in several cancer types in The Cancer Genome Atlas (TCGA) dataset analysis. These findings highlight the usefulness of CGP as a screening tool to identify individuals with possible LS, especially when conventional criteria and MSI/MMR testing fail.

Evaluating variant pathogenicity prediction tools to establish African inclusive guidelines for germline genetic testing

BACKGROUND

Genetic germline testing is restricted for African patients. Lack of ancestrally relevant genomic data perpetuated by African diversity has resulted in European-biased curated clinical variant databases and pathogenic prediction guidelines. While numerous variant pathogenicity prediction tools (VPPTs) exist, their performance has yet to be established within the context of African diversity.

METHODS

To address this limitation, we assessed 54 VPPTs for predictive performance (sensitivity, specificity, false positive and negative rates) across 145,291 known pathogenic or benign variants derived from 50 Southern African and 50 European men matched for advanced prostate cancer. Prioritising VPPTs for optimal ancestral performance, we screened 5.3 million variants of unknown significance for predicted functional and oncogenic potential.

RESULTS

We observe a 2.1- and 4.1-fold increase in the number of known and predicted rare pathogenic or benign variants, respectively, against a 1.6-fold decrease in the number of available interrogated variants in our European over African data. Although sensitivity was significantly lower for our African data overall (0.66 vs 0.71, p = 9.86E-06), MetaSVM, CADD, Eigen-raw, BayesDel-noAF, phyloP100way-vertebrate and MVP outperformed irrespective of ancestry. Conversely, MutationTaster, DANN, LRT and GERP-RS were African-specific top performers, while MutationAssessor, PROVEAN, LIST-S2 and REVEL are European-specific. Using these pathogenic prediction workflows, we narrow the ancestral gap for potentially deleterious and oncogenic variant prediction in favour of our African data by 1.15- and 1.1-fold, respectively.

CONCLUSION

Although VPPT sensitivity favours European data, our findings provide guidelines for VPPT selection to maximise rare pathogenic variant prediction for African disease studies.

Genetic Contributions to Alzheimer's Disease and Frontotemporal Dementia in Admixed Latin American Populations

Latin America's diverse genetic landscape provides a unique opportunity to study Alzheimer's disease (AD) and frontotemporal dementia (FTD). The Multi-Partner Consortium to Expand Dementia Research in Latin America (ReDLat) recruited 2,162 participants with AD, FTD, or as healthy controls from six countries: Argentina, Brazil, Chile, Colombia, Mexico, and Peru. Participants underwent genomic sequencing and population structure analyses were conducted using Principal Component Analysis and ADMIXTURE. The study revealed a predominant mix of American, African, and European ancestries, with an additional East Asian component in Brazil. Variant curation identified 17 pathogenic variants, pathogenic C9orf72 expansion, and 44 variants of uncertain significance. Seventy families showed autosomal dominant inheritance, with 48 affected by AD and 22 by FTD. This represents the first large-scale genetic study of AD and FTD in Latin America, highlighting the need to consider diverse ancestries, social determinants of health, and cultural factors when assessing genetic risk for neurodegenerative diseases.

Genomics and integrative clinical data machine learning scoring model to ascertain likely Lynch syndrome patients

BACKGROUND

Lynch syndrome (LS) screening methods include multistep molecular somatic tumor testing to distinguish likely-LS patients from sporadic cases, which can be costly and complex. Also, direct germline testing for LS for every diagnosed solid cancer patient is a challenge in resource limited settings. We developed a unique machine learning scoring model to ascertain likely-LS cases from a cohort of colorectal cancer (CRC) patients.

METHODS

We used CRC patients from the cBioPortal database (TCGA studies) with complete clinicopathologic and somatic genomics data. We determined the rate of pathogenic/likely pathogenic variants in five (5) LS genes (MLH1, MSH2, MSH6, PMS2, EPCAM), and the BRAF mutations using a pre-designed bioinformatic annotation pipeline. Annovar, Intervar, Variant Effect Predictor (VEP), and OncoKB software tools were used to functionally annotate and interpret somatic variants detected. The OncoKB precision oncology knowledge base was used to provide information on the effects of the identified variants. We scored the clinicopathologic and somatic genomics data automatically using a machine learning model to discriminate between likely-LS and sporadic CRC cases. The training and testing datasets comprised of 80% and 20% of the total CRC patients, respectively. Group regularisation methods in combination with 10-fold cross-validation were performed for feature selection on the training data.

RESULTS

Out of 4800 CRC patients frorm the TCGA datasets with clinicopathological and somatic genomics data, we ascertained 524 patients with complete data. The scoring model using both clinicopathological and genetic characteristics for likely-LS showed a sensitivity and specificity of 100%, and both had the maximum accuracy, area under the curve (AUC) and AUC for precision-recall (AUCPR) of 1. In a similar analysis, the training and testing models that only relied on clinical or pathological characteristics had a sensitivity of 0.88 and 0.50, specificity of 0.55 and 0.51, accuracy of 0.58 and 0.51, AUC of 0.74 and 0.61, and AUCPR of 0.21 and 0.19, respectively.

CONCLUSIONS

Simultaneous scoring of LS clinicopathological and somatic genomics data can improve prediction and ascertainment for likely-LS from all CRC cases. This approach can increase accuracy while reducing the reliance on expensive direct germline testing for all CRC patients, making LS screening more accessible and cost-effective, especially in resource-limited settings.

Clinical presentation of congenital hypogonadotropic hypogonadism in males with delayed puberty according to genetic etiology: a systematic review and meta-analysis after reclassification of gene variants

STUDY QUESTION

Which phenotypes can be confidently linked to a genetic etiology in males with congenital hypogonadotropic hypogonadism (CHH) resulting in absent or arrested puberty?

SUMMARY ANSWER

In this systematic review and reclassification of the disease-causing potential of gene variants using the recommendations of the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP), we found that absent or arrested puberty in males with CHH was linked to 93 genes, of which 29 were unequivocally disease-causing.

WHAT IS KNOWN ALREADY

The number of genes and phenotype characterizations associated with CHH in males has rapidly increased since the advent of next-generation sequencing technologies; however, the quality of the evidence for the interpretation of the causal relationship of gene variants is limited due to the lack of systematic criteria applied to the assessment of the pathogenic potential of the variants.

STUDY DESIGN, SIZE, DURATION

We performed a systematic review of original articles indexed in PubMed until 5 October 2022 and using the search terms '(('hypogonadotropic hypogonadism' OR Kallmann) AND (sequencing OR mutation OR variant))' limited to 'Humans' and 'English'.

PARTICIPANTS/MATERIALS, SETTING, METHODS

After two investigators undertook the literature search independently, titles and abstracts of all records were reviewed by four of the authors to identify those articles to be included in the full-text review. Clinical data and the association with gene variants were extracted from males with delayed or arrested puberty due to CHH according to the article authors' criteria. Raw sequence variant information was used to reevaluate their pathogenic potential applying the ACMG/AMP guidelines for variant classification with InterVar. Subsequently, we considered the phenotype specificity criteria for sequence variant pathogenicity classification, based on curated genes associated with CHH, and classified patients into three categories: with monogenic disease-causing variants in genes associated with CHH, with variants in genes whose causality is unclear, and with variants that are not disease-causing.

MAIN RESULTS AND THE ROLE OF CHANCE

From a total of 1083 records, we included 245 publications with 775 male patients with CHH resulting in absent or arrested puberty, carrying 1001 variants in 93 genes. Gene variants were detected by Sanger sequencing in 61.8% of the cases and by next-generation sequencing (NGS) technologies in the rest. After variant reclassification of causality, 278 individuals were not considered to have a bona fide disease-causing gene variant, and 497 patients were reclassified as carrying at least one disease-causing variant associated with CHH. They carried 503 different disease-causing variants in 29 genes. Spontaneous puberty was absent in 85.5% and arrested in 14.5% of the 497 individuals with CHH carrying bona fide disease-causing variants. In males with absent puberty (complete hypogonadotrophic hypogonadism), FGFR1 and ANOS1 were the most frequently affected genes, accounting for 53.5% of the disease-causing variants. In males with incomplete spontaneous puberty (partial hypogonadotrophic hypogonadism), variants in FGFR1, NR0B1, and GNRHR were found in 70.3% of the cases. Micropenis, cryptorchidism and/or low testicular volume, considered 'red flags' for the diagnosis of CHH, were found in less than 30% of males, with cryptorchidism being more frequently observed in association with variants in FGFR1, ANOS1, KISS1R, SOX10, and GNRH1, and micropenis being more prevalent in patients with variants in TACR3, KISS1R, or GNRH1. Clinical manifestations in non-reproductive organs were found in 39.8% of the patients with bona fide disease-causing variants.

LIMITATIONS, REASONS FOR CAUTION

Because we included studies going back to the initial genetic reports of patients with CHH, results obtained by Sanger sequencing represent a significant proportion of the whole sample, which may be biased by the use of a candidate gene strategy. A subanalysis of cases studied by NGS modified the results only slightly.

WIDER IMPLICATIONS OF THE FINDINGS

This comprehensive synthesis will help clinicians in the guidance of reverse phenotyping once the precise genetic diagnosis is established, and researchers in the design of functional studies to clarify the role of specific sequence variants in the etiology of male CHH. A genetic etiology of CHH in males with absent or arrested puberty should be considered even in the absence of micropenis, cryptorchidism, and/or low testicular volume.

STUDY FUNDING/COMPETING INTEREST(S)

This work was partially funded by grants PICT I-A-2018-02972 of Fondo de Promoción Científica y Técnica (FONCYT), PICT A-CAT III2021-73 of Fondo Argentino Sectorial (FONARSEC) and Proyectos de Redes Federales de Alto Impacto 2023 #3 of Ministerio de Ciencia, Tecnología e Innovación, Argentina. Competing interests: None declared.

REGISTRATION NUMBER

None declared.

Synchronous bilateral Wilms tumors are prone to develop independently and respond differently to preoperative chemotherapy

Wilms tumor (WT) is the most common kidney cancer in infants and young children. The determination of the clonality of bilateral WTs is critical to the treatment, because lineage-independent and metastatic tumors may require different treatment strategies. Here we found synchronous bilateral WT (n = 24 tumors from 12 patients) responded differently to preoperative chemotherapy. Transcriptome, whole-exome and whole-genome analysis (n = 12 tumors from 6 patients) demonstrated that each side of bilateral WT was clonally independent in terms of somatic driver mutations, copy number variations and transcriptomic profile. Molecular timing analysis revealed distinct timing and patterns of chromosomal evolution and mutational processes between the two sides of WT. Mutations in WT1, CTNNB1 and copy-neutral loss of heterozygosity of 11p15.5 provide possible genetic predisposition for the early initiation of bilateral WT. Our results provide comprehensive evidence and new insights regarding the separate initiation and early embryonic development of bilateral WT, which may benefit clinical practices in treating metastatic or refractory bilateral WT.

Celeste: A cloud-based genomics infrastructure with variant-calling pipeline suited for population-scale sequencing projects

Background

The All of Us Research Program (All of Us) is one of the world's largest sequencing efforts that will generate genetic data for over one million individuals from diverse backgrounds. This historic megaproject will create novel research platforms that integrate an unprecedented amount of genetic data with longitudinal health information. Here, we describe the design of Celeste, a resilient, open-source cloud architecture for implementing genomics workflows that has successfully analyzed petabytes of participant genomic information for All of Us - thereby enabling other large-scale sequencing efforts with a comprehensive set of tools to power analysis. The Celeste infrastructure is tremendously scalable and has routinely processed fluctuating workloads of up to 9,000 whole-genome sequencing (WGS) samples for All of Us, monthly. It also lends itself to multiple projects. Serverless technology and container orchestration form the basis of Celeste's system for managing this volume of data.

Results

In 12 months of production (within a single Amazon Web Services (AWS) Region), around 200 million serverless functions and over 20 million messages coordinated the analysis of 1.8 million bioinformatics, quality control, and clinical reporting jobs. Adapting WGS analysis to clinical projects requires adaptation of variant-calling methods to enrich the reliable detection of variants with known clinical importance. Thus, we also share the process by which we tuned the variant-calling pipeline in use by the multiple genome centers supporting All of Us to maximize precision and accuracy for low fraction variant calls with clinical significance.

Conclusions

When combined with hardware-accelerated implementations for genomic analysis, Celeste had far-reaching, positive implications for turn-around time, dynamic scalability, security, and storage of analysis for one hundred-thousand whole-genome samples and counting. Other groups may align their sequencing workflows to this harmonized pipeline standard, included within the Celeste framework, to meet clinical requisites for population-scale sequencing efforts. Celeste is available as an Amazon Web Services (AWS) deployment in GitHub, and includes command-line parameters and software containers.

The genetic landscape of sporadic adult-onset degenerative ataxia: a multi-modal genetic study of 377 consecutive patients from the longitudinal multi-centre SPORTAX cohort

BACKGROUND

While most sporadic adult-onset neurodegenerative diseases have only a minor monogenic component, given several recently identified late adult-onset ataxia genes, the genetic burden may be substantial in sporadic adult-onset ataxias. We report systematic mapping of the genetic landscape of sporadic adult-onset ataxia in a well-characterised, multi-centre cohort, combining several multi-modal genetic screening techniques, plus longitudinal natural history data.

METHODS

Systematic clinico-genetic analysis of a prospective longitudinal multi-centre cohort of 377 consecutive patients with sporadic adult-onset ataxia (SPORTAX cohort), including clinically defined sporadic adult-onset ataxia of unknown aetiology (SAOA) (n = 229) and 'clinically probable multiple system atrophy of cerebellar type' (MSA-Ccp) (n = 148). Combined GAA-FGF14 (SCA27B) and RFC1 repeat expansion screening with next-generation sequencing (NGS) was complemented by natural history and plasma neurofilament light chain analysis in key subgroups.

FINDINGS

85 out of 377 (22.5%) patients with sporadic adult-onset ataxia carried a pathogenic or likely pathogenic variant, thereof 67/229 (29.3%) patients with SAOA and 18/148 (12.2%) patients meeting the MSA-Ccp criteria. This included: 45/377 (11.9%) patients with GAA-FGF14≥250 repeat expansions (nine with MSA-Ccp), 17/377 (4.5%) patients with RFC1 repeat expansions (three with MSA-Ccp), and 24/377 (6.4%) patients with single nucleotide variants (SNVs) identified by NGS (six with MSA-Ccp). Five patients (1.3%) were found to have two relevant genetic variants simultaneously (dual diagnosis).

INTERPRETATION

In this cohort of sporadic adult-onset ataxia, a cohort less likely to have a monogenic cause, a substantial burden of monogenic variants was identified, particularly GAA-FGF14 and RFC1 repeat expansions. This included a substantial share of patients meeting the MSA-Ccp criteria, suggesting a reduced specificity of this clinical diagnosis and potential co-occurrence of MSA-C plus a second, independent genetic condition. These findings have important implications for the genetic work-up and counselling of patients with sporadic ataxia, even when presenting with MSA-like features. With targeted treatments for genetic ataxias now on the horizon, these findings highlight their potential utility for these patients.

FUNDING

This work was supported by the Clinician Scientist programme "PRECISE.net" funded by the Else Kröner-Fresenius-Stiftung (to DM, AT, CW, OR, and MS), by the Deutsche Forschungsgemeinschaft (as part of the PROSPAX project), and by the Canadian Institutes of Health Research and the Fondation Groupe Monaco. Support was also provided by Humboldt Research Fellowship for Postdocs and the Hertie-Network of Excellence in Clinical Neuroscience and a Fellowship award from the Canadian Institutes of Health Research.

Biallelic MED16 variants disrupt neural development and lead to an intellectual disability syndrome

Mediator Complex Subunit 16 (MED16, MIM: 604062) is a member of the Mediator complex which controls many aspects of transcriptional activity in all eukaryotes. Here, we report two individuals from a non-consanguineous family with biallelic variants in MED16 identified by exome sequencing. The affected individuals present with global developmental delay, intellectual disability, and dysmorphisms. To assess the pathogenicity of the variants, functional studies were performed in Drosophila and patient-derived cells. The fly ortholog med16 is expressed in neurons and some glia of the developing central nervous system (CNS). Loss of med16 leads to a reduction in eclosion and lifespan, as well as impaired synaptic transmission. In neurons differentiated from the patient-derived induced pluripotent stem cells (iPSCs), the neurite outgrowth is impaired and rescued by expression of exogenous MED16. The patient-associated variants behave as loss-of-function (LoF) alleles in flies and iPSCs. Additionally, the transcription of genes related to neuronal maturation and function is preferentially altered in patient cells relative to differentiated H9 controls. In summary, our findings support that MED16 is important for appropriate development and function, and that biallelic MED16 variants cause a neurodevelopmental disease.

An integrative scoring approach for prioritization of rare autism spectrum disorder candidate variants from whole exome sequencing data

Discerning clinically relevant autism spectrum disorder (ASD) candidate variants from whole-exome sequencing (WES) data is complex, time-consuming, and labor-intensive. To this end, we developed AutScore, an integrative prioritization algorithm of ASD candidate variants from WES data and assessed its performance to detect clinically relevant variants. We studied WES data from 581 ASD probands, and their parents registered in the Azrieli National Center database for Autism and Neurodevelopment Research. We focused on rare allele frequency (< 1%) and high-quality proband-specific variants affecting genes associated with ASD or other neurodevelopmental disorders (NDDs). We developed AutScore and AutScore.r and assigned each variant based on their pathogenicity, clinical relevance, gene-disease association, and inheritance patterns. Finally, we compared the performance of both AutScore versions with the rating of clinical experts and the NDD variant prioritization algorithm, AutoCaSc. Overall, 1161 rare variants distributed in 687 genes in 441 ASD probands were evaluated by AutScore with scores ranging from - 4 to 25, with a mean ± SD of 5.89 ± 4.18. AutScore.r cut-off of ≥ 0.335 performs better than AutoCaSc and AutScore in detecting clinically relevant ASD variants, with a detection accuracy rate of 85% and an overall diagnostic yield of 10.3%. Five variants with AutScore.r of ≥ 0.335 were distributed in five novel ASD candidate genes. AutScore.r is an effective automated ranking system for ASD candidate variants that could be implemented in ASD clinical genetics pipelines.

The prevalence of pathogenic variants in the BMPR2 gene in patients with the idiopathic pulmonary arterial hypertension in the Russian population: sequencing data and meta-analysis

BACKGROUND

Idiopathic pulmonary arterial hypertension (IPAH) is a rare and severe form of pulmonary hypertension, with a genetic basis most commonly associated with mutations in the BMPR2 gene. However, no genetic testing has been reported for IPAH patients in the Russian population, nor have systematic studies been conducted to assess the frequency of pathogenic variants in this group.

METHODS

The study cohort included 105 IPAH patients, consisting of 23 males and 82 females, who were managed at the PH care center in Moscow, Russia, from 2014 to 2024. Genetic testing was performed using whole-genome sequencing. Variant identification and annotation were conducted using GATK, DeepVariant, VEP, sv-callers and AnnotSV. A meta-analysis, performed with MOOSE, included 24 studies involving 3124 IPAH patients and 470 P/LP variants. Pathogenicity reassessment was carried out using InterVar, which incorporates ACMG criteria.

RESULTS

Analysis of 105 adult IPAH patients in Russia revealed 11 patients (10.48%) as carriers of pathogenic or likely pathogenetic (P/LP) BMPR2 variants. As the result of reassessment, the number of P/LP BMPR2 variants raised from 394 (59%) to 445 (67%) with 80 pathogenic variants became of uncertain significance, and 152 unclassified variants became P/LP. The meta-analysis of these reevaluated pathogenic variants showed that while the frequency of P/LP variants in our cohort (10.48%) is lower than the overall average of 17.75% from the meta-analysis, the difference is not statistically significant (p = 0.062). Additionally, we report three P/LP BMPR2 variants, not reported in literature, with one being structural, and four P/LP variants in TBX4, ATP13A3 and AQP1 genes from 27 IPAH genes in 3 patients.

CONCLUSIONS

For the first time, we present the results of genetic testing in IPAH patients from the Russian population. Despite the considerable heterogeneity in the world-wide data, the prevalence of pathogenic BMPR2 mutations in IPAH patients from the Russian population does not significantly differ from the overall average in the meta-analysis. It is crucial to periodically reassess the pathogenicity of published variants, as half of the pathogenic BMPR2 IPAH variants were reclassified as LP or of uncertain significance.

Germline Pathogenic DROSHA Variants Are Linked to Pineoblastoma and Wilms Tumor Predisposition

PURPOSE

DROSHA, DGCR8, and DICER1 regulate miRNA biogenesis and are commonly mutated in cancer. Although DGCR8 and DICER1 germline pathogenic variants (GPV) cause autosomal dominant tumor predisposition, no association between DROSHA GPVs and clinical phenotypes has been reported.

EXPERIMENTAL DESIGN

After obtaining informed consent, sequencing was performed on germline and tumor samples from all patients. The occurrence of germline DROSHA GPVs was investigated in large pediatric and adult cancer datasets. The population prevalence of DROSHA GPVs was investigated in the UK Biobank and Geisinger DiscovEHR cohorts.

RESULTS

We describe nine children from eight families with heterozygous DROSHA GPVs and a diagnosis of pineoblastoma (n = 8) or Wilms tumor (n = 1). A somatic second hit in DROSHA was detected in all eight tumors analyzed. All pineoblastoma tumors analyzed were classified as miRNA processing-altered 1 subtype. We estimate the population prevalence of germline DROSHA loss-of-function variants to be 1:3,875 to 1:4,843 but find no evidence for increased adult cancer risk.

CONCLUSIONS

This is the first report of DROSHA-related tumor predisposition. As pineoblastoma and Wilms tumor are also associated with DICER1 GPVs, our results suggest that the tissues of origin for these tumors are uniquely tolerant of general miRNA loss. The miRNA processing-altered 1 pineoblastoma subtype is associated with older age of diagnosis and better outcomes than other subtypes, suggesting DROSHA GPV status may have important clinical and prognostic significance. We suggest that genetic testing for DROSHA GPVs be considered for patients with pineoblastoma, Wilms tumor, or other DICER1-/DGCR8-related conditions and propose surveillance recommendations through research studies for individuals with DROSHA GPVs.

Frequency of variants in Mendelian Alzheimer's disease genes within the Alzheimer's Disease Sequencing Project

BackgroundPrior studies examined variants within presenilin-2 (PSEN2), presenilin-1 (PSEN1), and amyloid precursor protein (APP) genes. However, previously-reported clinically-relevant variants and other predicted damaging missense (DM) variants have not been characterized in a newer release of the Alzheimer's Disease Sequencing Project (ADSP).ObjectiveTo characterize previously-reported clinically-relevant variants and DM variants in PSEN2, PSEN1, APP within the participants from the ADSP.MethodsWe identified rare variants (MAF < 1%) in PSEN2, PSEN1, and APP in 14,641 individuals with whole genome sequencing and 16,849 individuals with whole exome sequencing available (Ntotal = 31,490). We additionally curated variants from ClinVar, OMIM, and Alzforum and report carriers of variants in clinical databases as well as predicted DM variants in these genes.ResultsWe detected 31 previously-reported clinically-relevant variants with alternate alleles observed within the ADSP: 4 variants in PSEN2, 25 in PSEN1, and 2 in APP. The overall variant carrier rate for the 31 clinically-relevant variants in the ADSP was 0.3%. We observed that 79.5% of the variant carriers were cases compared to 3.9% were controls. In those with AD, the mean age of onset of AD among carriers of these clinically-relevant variants was 19.6 ± 1.4 years earlier compared with noncarriers (p = 7.8 × 10-57). Additionally, we identified 197 rare variants (MAF < 1%) within ADSP participants not reported in known clinical databases.ConclusionsA small proportion of individuals in the ADSP are carriers of a previously-reported clinically-relevant variant allele for AD and these participants have significantly earlier age of AD onset compared to noncarriers.

Clinical Characteristics and Visual Prognostic Biomarkers in Pericentral Retinitis Pigmentosa: A Study in a South Korean Cohort

PURPOSE

To investigate the clinical characteristics of South Korean patients with pericentral retinitis pigmentosa (RP) and to identify clinical biomarkers associated with rapid visual acuity decline based on baseline factors.

METHODS

This retrospective study included 59 eyes of 31 patients diagnosed with pericentral RP. Comprehensive ophthalmological examinations and genetic sequencing were conducted to assess the baseline characteristics. For biomarker analysis, eyes were categorized into two groups based on the annual rate of change in visual acuity. The clinical findings of the two groups were evaluated to identify the biomarkers associated with rapid loss of visual acuity.

RESULTS

Patients with pericentral RP in this study exhibited a mean best-corrected visual acuity of 0.17 ± 0.23 in logarithm of the minimum angle of resolution. The visual field test showed annular or semicircular scotoma with relatively preserved periphery and 27 eyes (45.8%) exhibited no macular complications in optical coherence tomography. Genetic analysis identified genes associated with previous typical and pericentral RP studies but also highlighted that many genetic causes of pericentral RP remain unidentified. Of the 55 eyes for which the rate of visual acuity change could be estimated, 18 exhibited an annual decline of ≥10%, whereas 37 showed an annual decline of <10%. Male sex and prolonged b-wave latency on dark-adapted 0.01 electroretinogram correlated with rapid visual acuity decline in the multivariate analysis.

CONCLUSIONS

South Korean patients with pericentral RP exhibited a milder phenotype compared to typical RP patients reported in previous studies. Genetic analysis revealed heterogeneity, with mutations in some genes commonly associated with milder forms of RP. Male sex and prolonged b-wave latency on dark-adapted 0.01 electroretinogram were significant biomarkers for predicting rapid visual acuity decline. Monitoring initial b-wave latency is important for predicting visual decline, particularly in male patients with pericentral RP.

Variable Ophthalmologic Phenotypes Associated with Biallelic Loss-of-Function Variants in POMGNT1

O-mannosylation is a post-translational modification required for the proper function of various proteins and critical for development and growth. POMGNT1 encodes the enzyme O-linked-mannose β-1,2-N-acetylglucosaminyltransferase 1, which catalyzes the second step in the synthesis of α-dystroglycan O-mannosyl glycans. Among POMGNT1-related α-dystroglycanopathies, muscle-eye-brain (MEB) disease presents with congenital muscular dystrophy, structural brain abnormalities, and retinal dystrophy. Defects in protein O-mannosylation due to biallelic loss-of-function POMGNT1 mutations produce disturbances in assembling and organizing the basal membrane in the neuroretinal system, involving both the central and peripheral nervous systems. In the retina, POMGNT1 is expressed in photoreceptors and is localized near the photoreceptor cilium basal body, a structure critical for protein transport. Recent studies have reported an isolated degenerative ocular phenotype without any involvement of muscular or neuronal tissues. Here, we report on a family with three siblings affected by an apparently isolated clinically variable retinal disease and sharing biallelic inactivating POMGNT1 variants. Notably, the rod-cone dystrophy phenotype in the three siblings varied significantly in onset, presentation, and severity. These findings provide further evidence of the clinical variability associated with defective POMGNT1 function.

Functional profiling of KCNE1 variants informs population carrier frequency of Jervell and Lange-Nielsen syndrome type 2

Congenital long-QT syndrome (LQTS) is most often associated with pathogenic variants in KCNQ1 encoding the pore-forming voltage-gated potassium channel subunit of the slow delayed rectifier current ( I Ks ). Generation of I Ks requires assembly of KCNQ1 with an auxiliary subunit encoded by KCNE1 , which is also associated with LQTS but causality of autosomal dominant disease is disputed. By contrast, KCNE1 is an accepted cause of recessive type 2 Jervell and Lange-Nielson syndrome (JLN2). The functional consequences of most KCNE1 variants have not been determined and the population prevalence of JLN2 is unknown. Methods : We determined the functional properties of 95 KCNE1 variants co-expressed with KCNQ1 in heterologous cells using high-throughput voltage-clamp recording. Experiments were conducted with each KCNE1 variant expressed in the homozygous state and then a subset was studied in the heterozygous state. The carrier frequency of JLN2 was estimated by considering the population prevalence of dysfunctional variants. Results : There is substantial overlap between disease-associated and population KCNE1 variants. When examined in the homozygous state, 68 KCNE1 variants exhibited significant differences in at least one functional property compared to WT KCNE1, whereas 27 variants did not significantly affect function. Most dysfunctional variants exhibited loss-of-function properties. We observed no evidence of dominant-negative effects. Most variants were scored as variants of uncertain significance (VUS) and inclusion of functional data resulted in revised classifications for only 14 variants. The population carrier frequency of JLN2 was calculated as 1 in 1034. Peak current density and activation voltage-dependence but no other biophysical properties were correlated with findings from a mutational scan of KCNE1. Conclusions : Among 95 disease-associated or population KCNE1 variants, many exhibit abnormal functional properties but there was no evidence of dominant-negative behaviors. Using functional data, we inferred a population carrier frequency for recessive JLN2. This work helps clarify the pathogenicity of KCNE1 variants.

Genomic analysis of small renal masses reveals mutations linked with renal cell carcinoma and fast-growing tumors

PURPOSE

Small renal masses (SRMs) SRMs are a heterogeneous group of small kidney lesions. Currently, the genomic landscape of SRMs is understudied, and clinically relevant tools for malignancy detection and fast tumor growth prediction are lacking. The aim of the study was to evaluate whether mutations in SRMs are associated with increased risk of renal cell carcinoma (RCC) or aggressive tumors.

METHODS

In this pilot study, 52 patients with SRMs were divided based on tumor histology into RCC and benign tumors, while RCC cases were divided into fast-growing and slow-growing tumor groups. Tissue biopsy samples evaluated for mutations in 51 cancer hotspot genes using next generation sequencing and qPCR. Non-benign mutations were tested for associations with RCC and clinical features. Receiver operating curve analysis used for evaluation of mutation biomarker models prediction of RCC and fast-growing tumors.

RESULTS

75% of SRMs harbored non-synonymous alterations in 16/51 genes. 38.5% of detected mutations were listed in ClinVar and correlated with smaller SRM volume (p = 0.023). KRAS, VHL, HNF1A, TP53, and ATM mutations were predominantly detected in RCC rather than benign SRMs (p = 0.046). SRMs with pathogenic mutations were at three times higher risk of being RCC and four times higher risk of fast growth.

CONCLUSION

Genomic biomarkers may improve risk stratification and management of patients with SRMs, however a more extensive genomic analysis of SRMs is still needed.

Truncated Variants in FAM20A and WDR72 Genes Underlie Autosomal Recessive Amelogenesis Imperfecta in Four Pakistani Families

Amelogenesis Imperfecta (AI) is a set of hereditary diseases affecting enamel development, leading to various types of enamel defects, potentially impacting oral health unassociated with other generalized defects. AI manifests in syndromic and non-syndromic forms and can be inherited through autosomal recessive, autosomal dominant, or X-linked inheritance patterns. Genetic studies have identified sequence variants in a number of genes (≥ 70) linked to both syndromic and non-syndromic AI, highlighting the genetic diversity underlying the condition. The current study involved clinical evaluation and exome sequencing, aimed at identifying the causative variants in four unrelated consanguineous Pakistani families presenting AI phenotypes. The exome sequencing results revealed a novel homozygous frameshift variant FAM20A: NM_017565.4, c.188dupA; p.(Asp63Glufs*17) in families A, B, and C while a nonsense homozygous variant WDR72: NM_182758.4, c.2686C > T; p. (Arg896*) in family D. The segregation of both variants was confirmed by Sanger sequencing. Bioinformatics analysis predicted the pathogenicity of these genetic variants. These alterations suggest functional consequences, potentially impairing the FAM20A and WDR72 proteins and causing dental anomalies. This investigation significantly broadens our understanding of FAM20A and WDR72's involvement in AI. Furthermore, this study highlights the genetic heterogeneity of AI (involving FAM20A and WDR72 in this study) within the Pakistani population.

Neoadjuvant fuzuloparib combined with abiraterone for localized high-risk prostate cancer (FAST-PC): A single-arm phase 2 study

Preclinical studies suggest synergistic effects between androgen receptor inhibitors and poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors. This phase 2 trial (NCT05223582) evaluates neoadjuvant fuzuloparib plus abiraterone in 35 treatment-naive men with localized high-risk prostate cancer. Patients receive six cycles of therapy followed by radical prostatectomy. Primary endpoints are pathological complete response (pCR) and minimal residual disease (MRD, ≤5 mm). The combined pCR/MRD rate is 46% (95% confidence interval [CI]: 29%-63%), with a 53% 2-year biochemical progression-free survival rate. Grade ≥3 adverse events occur in 23% of patients. Biallelic homologous recombination repair/BRCA2 alterations correlate with faster prostate-specific antigen decline. Post-treatment genomic analyses reveal reduced MYC amplification and proliferation markers, alongside activated epithelial-mesenchymal transition/activator protein 1 (AP-1) pathways. The trial meets its primary endpoint, demonstrating feasibility and preliminary efficacy, while exploratory biomarkers may guide future studies.

Deciphering the Genetic Basis of Degenerative and Developmental Eye Disorders in 50 Pakistani Consanguineous Families Using Whole-Exome Sequencing

Degenerative and developmental eye disorders, including inherited retinal dystrophies (IRDs), anophthalmia, and congenital cataracts arise from genetic mutations, causing progressive vision loss or congenital structural abnormalities. IRDs include a group of rare, genetically, and clinically heterogeneous retinal diseases. It is caused by variations in at least 324 genes, affecting numerous retinal regions. In addition to IRDs, other developmental eye disorders such as anophthalmia and congenital cataracts also have a strong genetic basis. Autosomal recessive IRDs, anophthalmia, and congenital cataracts are common in consanguineous populations. In many endogamous populations, including those in Pakistan, a significant proportion of IRD and anophthalmia cases remain genetically undiagnosed. The present study investigated the variations in IRDs, anophthalmia, and congenital cataracts genes in 50 affected families. These unrelated consanguineous families were recruited from the different provinces of Pakistan including Punjab, Khyber Pakhtoon Khwa, Sindh, Gilgit Baltistan, and Azad Kashmir. Whole exome sequencing (WES) was conducted for the proband of each family. An in-house customized pipeline examined the data, and bioinformatics analysis predicted the pathogenic effects of identified variants. The relevant identified DNA variants of selected families were assessed in parents and healthy siblings via Sanger sequencing. WES identified 12 novel variants across 10 known IRD-associated genes. The four most frequently implicated genes were CRB1 (14.3%), GUCY2D (9.5%), AIPL1 (9.5%), and CERKL (7.1%) that together accounted for 40.4% of all molecularly diagnosed cases. Additionally, 25 reported variants in 19 known IRDs, anophthalmia, and congenital cataracts-associated genes were found. Among the identified variants, p. Trp278X, a stop-gain mutation in the AIPL1 (NM_014336) gene, was the most common causative variant detected. The most frequently observed phenotype was retinitis pigmentosa (46.5%) followed by Leber congenital amaurosis (18.6%). Furthermore, 98% of pedigrees (49 out of 50) were affected by autosomal recessive IRDs, anophthalmia and congenital cataracts. The discovery of 12 novel likely pathogenic variants in 10 IRD genes, 25 reported variants in 19 known IRDs, anophthalmia and congenital cataracts genes, atypical phenotypes, and inter and intra-familial variability underscores the genetic and phenotypic heterogeneity of developmental and degenerative eye disorders in the Pakistani population and further expands the mutational spectrum of genes associated with these ocular disorders.

Distinguishing Genetic Alterations Versus (Epi)Mutations in Silver-Russell Syndrome and Focus on the IGF1R Gene

CONTEXT

Silver-Russell Syndrome (SRS) is a growth retardation disorder characterized by pre- and postnatal growth failure, relative macrocephaly at birth, prominent forehead, body asymmetry, and feeding difficulties. The main molecular mechanisms are imprinting alterations at multiple loci, though a small number of pathogenic variants have been reported in the SRS genes IGF2-PLAG1-HMGA2 and CDKN1C. However, around 40% of clinically suspected SRS cases do not achieve a molecular diagnosis, highlighting the necessity to uncover the underlying mechanism in unsolved cases.

OBJECTIVE

Evaluate the frequency of genetic variants in undiagnosed SRS patients [Netchine-Harbison Clinical Scoring System (NH-CSS) ≥ 4], and investigate whether (epi)genetic patients may be distinguished from genetic patients.

METHODS

One hundred thirty-two clinically SRS patients without (epi)genetic deregulations were investigated by whole-exome (n = 15) and targeted (n = 117) Sequencing. Clinical data from our cohort and from an extensive revision of the literature were compared.

RESULTS

Pathogenic variants were identified in 9.1% of this cohort: 3% in IGF2, PLAG1, and HMGA2 genes and 3% in the IGF1R gene, associated with IGF-1 resistance (IGF1RES), an SRS differential diagnosis. Overall, IGF2-PLAG1-HMGA2 and IGF1R account for 3.6% of SRS with NH-CSS score ≥ 4. A clinical cross-comparison of (epi)genetic vs genetic SRS underlined (epi)genotype-phenotype correlation highlighted the prevalence of body asymmetry and relative macrocephaly in mosaic (epi)genetic SRS and recurrence of genetic familial cases. Furthermore, overlapping features were evidenced in (epi)genetic SRS and IGF1RES patients.

CONCLUSION

Our study explores the frequency of genetic SRS, underscores body asymmetry as a distinctive phenotype in (epi)genetic SRS and suggests IGF1R sequencing in a SRS diagnostic flowchart.

Genetic and protein structure prediction analyses identify a rare pathogenic PKD1 variant causing autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common monogenic kidney disorders. The diagnosis of ADPKD requires imaging findings showing multiple kidney cysts or genetic testing, in cases where a family history is unknown. We report a patient diagnosed with ADPKD based on the identification of a rare PKD1 variant. The patient was a 41-year-old female in whom cysts and calcification in the kidneys were incidentally detected. Whole-exome sequencing identified a rare PKD1 variant (NM_001009944.3: c.11557G > A/p.E3853K). Protein structure prediction of the PKD1-PKD2 complex showed that the variant may be pathogenic, leading to the diagnosis of autosomal dominant polycystic kidney disease. A detailed family history revealed that her relatives also had ADPKD, further supporting the diagnosis of ADPKD. Comprehensive genetic analysis and protein structure prediction led to the diagnosis of ADPKD and the identification of rare causative genes. These methods are useful for diagnosing hereditary kidney diseases of unknown etiologies.

Pathogenic germline variants in Chinese pancreatic adenocarcinoma patients

Putting pancreatic adenocarcinoma (PAAD) screening into perspective for high-risk individuals could significantly reduce cancer morbidity and mortality. Previous studies have profiled somatic mutations in PAAD. In contrast, the prevalence of mutations in PAAD predisposition genes has not been defined, especially in the Asian population. Using a multi-tier cohort design and whole genome/exome sequencing, we create a comprehensive germline mutation map of PAAD in 1,123 Chinese cancer patients in comparison with 11 pan-ethnic studies. For well-known pathogenic/likely pathogenic germline variants, Chinese patients exhibit overlapping but distinct germline mutation patterns comparing with Western cohorts, highlighted by lower mutation rates in known PAAD genes including BRCA1, BRCA2, ATM, CDKN2A, and CHEK2, and distinct mutations in CFTR, RAD51D, FANCA, ERCC2, and GNAS exclusive to Chinese patients. CFTR emerges as a top candidate gene following loss of heterozygosity analysis. Using an integrative multi-omics and functional validation paradigm, we discover that deleterious variants of uncertain significance may compromise CFTR's tumor suppressor function, and demonstrate the clinical relevance by using patient derived organoids for drug screen. Our multifaceted approach not only deepens the knowledge of population differences in PAAD germline mutations but also unveils potential avenues for targeted therapeutic interventions.

Genome-wide functional annotation of variants: a systematic review of state-of-the-art tools, techniques and resources

The recent advancement of sequencing technologies marks a significant shift in the character and complexity of the digital genomic data universe, encompassing diverse types of molecular data, screened through manifold technological platforms. As a result, a plethora of fully assembled genomes are generated that span vertically the evolutionary scale. Notwithstanding the tsunami of thriving innovations that accomplish unprecedented, nucleotide-level, structural and functional annotation, an exhaustive, systemic, massive genome-wide functional annotation remains elusive, particularly when the criterion is automation and efficiency in data-agnostic interpretation. The latter is of paramount importance for the elaboration of strategies for sophisticated, data-driven genome-wide annotation, which aim to impart a sustainable and comprehensive systemic approach to addressing whole genome variation. Therefore, it is essential to develop methods and tools that promote systematic functional genomic annotation, with emphasis on mechanistic information exceeding the limits of coding regions, and exploiting the chunks of pertinent information residing in non-coding regions, including promoter and enhancer sequences, non-coding RNAs, DNA methylation sites, transcription factor binding sites, transposable elements and more. This review provides an overview of the current state-of-the-art in genome-wide functional annotation of genetic variation, including existing bioinformatic tools, resources, databases and platforms currently available or reported in the literature. Particular emphasis is placed on the functional annotation of variants that lie outside protein-coding genomic regions (intronic or intergenic), their potential co-localization with regulatory element areas, such as putative non-coding RNA regions, and the assessment of their functional impact on the investigated phenotype. In addition, state-of-the-art tools that leverage data obtained from WGS and GWAS-based analyses are discussed, along with future bioinformatics directions and developments. These future directions emphasize efficient, comprehensive, and largely automated functional annotation of both coding and non-coding genomic variants, as well as their optimal evaluation.

CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)

The Genetics of Neurodevelopmental Disorders Lab in Padua provided a new intellectual disability (ID) Panel challenge for computational methods to predict patient phenotypes and their causal variants in the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6). Eight research teams submitted a total of 30 models to predict phenotypes based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. Here, we assess the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and their causal variants. We also evaluated predictions for possible genetic causes in patients without a clear genetic diagnosis. Like the previous ID Panel challenge in CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (Pathogenic/Likely Pathogenic, Variants of Uncertain Significance and Risk Factors) were provided. The phenotypic traits and variant data of 150 patients from the CAGI5 ID Panel Challenge were provided as training set for predictors. The CAGI6 challenge confirms CAGI5 results that predicting phenotypes from gene panel data is highly challenging, with AUC values close to random, and no method able to predict relevant variants with both high accuracy and precision. However, a significant improvement is noted for the best method, with recall increasing from 66% to 82%. Several groups also successfully predicted difficult-to-detect variants, emphasizing the importance of variants initially excluded by the Padua NDD Lab.

Approaches to Evaluate Whole Exome Sequencing Data That Incorporate Genetic Intolerance Scores for Congenital Anomalies, Including Intronic Regions Adjacent to Exons

BACKGROUND

Whole exome sequencing (WES) aids in diagnosing monogenic diseases, yet > 50% of all cases remain undiagnosed. We aimed to improve diagnostic precision by developing an effective WES-based strategy for detecting congenital anomalies.

METHODS

Initially, 128 probands with congenital anomalies were assessed using trio-WES and copy number variation analysis-variant interpretation was for exons and splice sites. Thereafter, we reanalyzed the sequence data for undiagnosed cases using the following methods. First, we performed trio-WES analysis, adding genetic intolerance scores annotation. Second, we analyzed all exons, splicing sites, and intron variants for cases with phenotypes suggestive of specific causative genes using SpliceAI. Lastly, using SpliceAI, we analyzed all exons, splicing sites, and intron variants in genetically constrained genes filtered with genetic intolerance scores.

RESULTS

Initial analysis diagnosed 51 of 128 cases (39.8%). In the reanalysis, first, we identified novel likely pathogenic variants in MED12 and CCDC22 associated with X-linked diseases. Second, a novel TMEM67 intron variant associated with Meckel syndrome was detected. Finally, a de novo hemizygous pathogenic intronic variant in CASK was identified in a case of intrauterine fetal death.

CONCLUSIONS

WES analysis, including intronic regions and utilizing genetic intolerance scores, has the potential to efficiently improve diagnostic yield.

An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases

Identifying disease-causing variants in Rare Disease patients' genome is a challenging problem. To accomplish this task, we describe a machine learning framework, that we called "Suggested Diagnosis", whose aim is to prioritize genetic variants in an exome/genome based on the probability of being disease-causing. To do so, our method leverages standard guidelines for germline variant interpretation as defined by the American College of Human Genomics (ACMG) and the Association for Molecular Pathology (AMP), inheritance information, phenotypic similarity, and variant quality. Starting from (1) the VCF file containing proband's variants, (2) the list of proband's phenotypes encoded in Human Phenotype Ontology terms, and optionally (3) the information about family members (if available), the "Suggested Diagnosis" ranks all the variants according to their machine learning prediction. This method significantly reduces the number of variants that need to be evaluated by geneticists by pinpointing causative variants in the very first positions of the prioritized list. Most importantly, our approach proved to be among the top performers within the CAGI6 Rare Genome Project Challenge, where it was able to rank the true causative variant among the first positions and, uniquely among all the challenge participants, increased the diagnostic yield of 12.5% by solving 2 undiagnosed cases.

Whole Exome Sequencing in Drug-Induced Angioedema Caused by Angiotensin-Converting Enzyme Inhibitors: A Pilot Study in Five Patients

Background and Objectives: One of the most common causes of drug-induced angioedema (AE-DI) is related to reduced bradykinin breakdown after the use of certain medications. This is the case for forms of AE-DI due to the use of angiotensin-converting enzyme inhibitors (ACEi), which are used for the treatment of cardiovascular conditions. The causes of AE are not clear in these patients. Given the limited number of AE-ACEi genetic loci identified by genome-wide association studies, we opted to assess the utility of NGS of a panel of relevant genes to identify candidate genetic risk factors in severely affected patients. Methods: Five hypertensive patients from unrelated families with clinical AE-ACEi were included in the study. Whole-exome sequencing, variant calling, and annotation techniques were used. ANNOVAR v18.04.16 was used to annotate the variant calls. The resulting variants for each patient were assessed using the Hereditary Angioedema Database Annotation tool and Franklin genomic platform for variant prioritization and clinical impact interpretation. Results: The genetic variant rs6025 in the F5 gene was identified in all recruited samples, which has been associated with an increase in blood clotting in AE-ACEi patients. In two patients, a common synonymous genetic variant of the ACE gene was found (rs4343). Finally, we identified the ACE genetic variant rs142947404 in only one patient. This variant has not been assessed in AE-ACEi. Conclusions: More studies will be needed to clarify the genetics involved in AE-DI. In this way, we will be able to try to predict future episodes of angioedema due to the use of ACEi.

Digenic impairments of haploinsufficient genes in patients with craniosynostosis

Craniosynostosis (CRS) is characterized by the development of abnormal cranial suture ossification and premature fusion. Despite the identification of several associated genetic disorders, the genetic determinants of CRS remain poorly understood. In this study, we conducted integrative analyses on 225 exomes, comprising 121 CRS probands and 104 parental exomes (52 trios). These analyses encompassed de novo and pathogenic variants, and digenic combinations within haploinsufficient genes harboring rare variants. Our analysis unveils a shared molecular network between genes associated with CRS and those linked to skeletal and neurodevelopmental disorders, with a notable enrichment of deleterious variants within haploinsufficient genes. Additionally, we identified a unique digenic pair (IL6ST and TRPS1) within haploinsufficient genes that was present in 2 patients with nonsyndromic CRS but absent in parents or 1,048 population controls. In vitro experiments provided evidence that the identified missense variants were hypomorphs, and accelerated bone mineralization could result from the additive effects of diminished IL6ST and TRPS1 activities in osteoblasts. Overall, our study underscores the important role of rare variations in haploinsufficient genes and suggests that in a subset of undiagnosed patients, the CRS phenotype may arise from multiple genetic variations.

[New pathogenic mutation in LMNA gene: Clinical case of familial cardiomyopathy]

We present a clinical case of familial LMNA-associated cardiomyopathy, confirmed by whole genome sequencing. The typical for lamin-associated cardiomyopathy indicates pathogenic nature of the mutation in the first exon of LMNA gene, previously considered a mutation of unknown clinical significance. The presented clinical case demonstrates a radical change in patient treatment strategies in the context of the widespread introduction of molecular genetic research methods into practice.

Subclinical parents assist in the detection of genetic variants in keratoconus by trio-based whole-exome sequencing

Purpose

To explore the genetic variants of 14 keratoconus trios containing subclinical parents.

Methods

Trio-based whole-exome sequencing was performed in 14 keratoconus trios containing subclinical parents. The variants identified in candidate genes of keratoconus were analyzed by multiple bioinformatics tools.

Results

We identified 12 variants in 10 candidate genes of keratoconus (COL5A1, TGFBI, CAST, MPDZ, WNT10A, MYOF, ERMP1, MAP3K19, COL1A1, and WNT16). All variants were novel, not previously reported, and defined as uncertain significance according to the American College of Medical Genetics and Genomics guidelines. All variants were heterozygous and autosomal dominant cosegregated in keratoconus families.

Conclusions

We found that the candidate variants identified in clinically diagnosed patients and their subclinical parents may cause keratoconus through an autosomal dominant inheritance pattern, with different variable expressivity. This study indicates that genetic testing may play an important role in identifying patients with latent keratoconus and high-risk individuals for corneal ectasia after refractive surgery.

Candidate Genetic Modifiers in Alport Syndrome: A Case Series

BACKGROUND

Alport syndrome (AS) is one of the most common monogenic kidney disorders. Recent studies have highlighted the modifier effect of variants involving podocyte and non-collagenous extracellular matrix (ECM) proteins in AS.

METHODS

We report a case series of eight patients with genetically proven AS and simultaneous variants involving podocyte and non-collagenous ECM proteins. Our aim is to describe the influence of such variants on the phenotype of patients with AS.

RESULTS

We identified 10 different type IV collagen variants. Patients were diagnosed with autosomal dominant (3/8), autosomal recessive (2/8), digenic (2/8) and X-linked AS (1/8). There were eight different variants involving podocyte and non-collagenous ECM proteins. The genes involved were CRB2, LAMA5, LAMB2, NUP107, MYO1E and PLCE1. Four patients (LAMB2, LAMA5 and PLCE1 variants) presented with nephrotic syndrome or nephrotic range proteinuria. Two patients had hearing loss. Most patients (7/8) had a family history of kidney disease. Two patients (LAMB2 and LAMA5 variants) were diagnosed with focal segmental glomerulosclerosis. Two patients developed end-stage kidney disease (LAMA5, MYO1E and NUP107 variants).

CONCLUSIONS

Although mutations of podocyte and ECM proteins do not have phenotypic expression in monoallelic form, the presence of such variants could explain the phenotypic variability of AS.

Host genetic and immune factors drive evasion of HIV-1 pathogenesis in viremic non-progressors

BACKGROUND

Viremic non-progressors (VNPs) represent an exceptional and uncommon subset of people with HIV-1, characterized by the remarkable preservation of normal CD4+ T cell counts despite uncontrolled viral replication-a trait reminiscent of natural hosts of simian immunodeficiency virus. The mechanisms orchestrating evasion from HIV-1 pathogenesis in human VNPs remain elusive, primarily due to the absence of integrative studies.

METHODS

We implemented a novel single-cell and multiomics approach to comprehensively characterize viral, genomic, transcriptomic, and metabolomic factors driving this exceedingly rare disease phenotype in 16 VNPs and 29 HIV+ progressors.

FINDINGS

Genetic predisposition to the VNP phenotype was evidenced by a higher prevalence of CCR5Δ32 heterozygosity, which was associated with lower levels of CCR5 expression and a lower frequency of infected cells in peripheral circulation. We also observed reduced levels of plasma markers of intestinal disruption and attenuated interferon responses in VNPs. These factors potentially drive the other phenotypic traits of immune preservation in this population, including the unaltered tryptophan metabolic profile, reduced activation of cytotoxic lymphocytes, and reduced bystander CD4+ T cell apoptosis.

CONCLUSIONS

In summary, our comprehensive analysis identified intricate factors collectively associated with the unique immunovirological equilibrium in VNPs, shedding light on potential avenues for therapeutic exploration in managing HIV pathogenesis.

FUNDING

The work was supported by funding from the Spanish Ministry of Science and Innovation and the National Institutes of Health (NIH).

Rare variants in cardiomyopathy genes predispose to cardiac injury in severe COVID-19 patients of African or Hispanic ancestry

In one of the earliest reports from China during COVID-19, it was noted that over 20% of patients hospitalized with the disease had significant elevations of troponin, a marker of myocardial tissue damage, that put them at a higher risk. In a hypothesis-independent whole exome sequencing (WES) study in hospitalized COVID-19 patients of diverse ancestry, we observed putative enrichment in pathogenic variants in genes known to be involved in the pathogenesis of cardiomyopathy. This observation led us to hypothesize that the observed high morbidity and mortality in these patients might be due to the presence of rare genetic factors that had previously been silent but became relevant as a consequence of the severe stress inflicted by an infection with SARS-CoV-2. To test this hypothesis, we analyzed our WES data generated from a cohort of 325 patients sequentially admitted for COVID-19 infection. In this predominantly minority population (53.9% African ancestry and 37.9% Hispanic/Latin ancestry), our initial analysis screen identified 263 variants that were identified as highly deleterious (HD) from a total of 26,661 variants of interest that represented 215 genes. Of those, we identified 46 genes (in 58 patients) harboring rare HD coding variants that were previously implicated in dilated cardiomyopathy and were considered as disease initiators for the severe COVID-19 in this study. These findings offer valuable insights into the molecular mechanisms and genetic susceptibility to heart injury in severe COVID-19. KEY MESSAGES: COVID-19 may cause cardiac damage in some affected patients without a plausible biological explanation. Our study reveals an enrichment of highly deleterious variants linked to cardiomyopathy in severe COVID-19 patients. Genetic profiling unveils the molecular basis of severe COVID-19-related heart injury, potentially aiding in patient stratification.

Comprehensive study of gene fusions in sarcomas

Sarcomas, including bone sarcomas and soft tissue sarcomas (STSs), are a heterogeneous group of mesenchymal malignancies. Recent advancements in next-generation sequencing (NGS) have enabled the identification of novel chromosomal translocations and fusion genes, which play a critical role in sarcoma subtypes. Our study focuses on gene fusions in sarcomas among Chinese patients, comparing their genomic profiles to those of Western populations. We analyzed 1048 sarcoma samples from Chinese patients using a panel of over 500 genes, identifying 481 gene fusions in 329 patients. The most common fusions included EWSR1, HMGA2, and SS18, with notable subtype-specific fusions such as EWSR1-FLI1 in Ewing sarcoma and NAB2-STAT6 in solitary fibrous tumors. In comparison to Chinese and Western populations, variations in fusion spectrum exist, potentially necessitating distinct treatment strategies; however, further validation of these fusions is warranted. Our findings highlight the importance of gene fusions as diagnostic markers and potential therapeutic targets. Actionable fusions, including kinase-related fusions like ALK, NTRK3, and BRAF, were detected in 67 patients (6.4%) and may guide precision therapies. Additionally, we observed the frequent co-occurrence of genomic alterations, particularly in cell cycle regulators such as CDK4 and MDM2. Genomic profiling of sarcomas offers valuable insights into their molecular drivers and can support personalized therapeutic approaches. Further research is needed to validate these findings and optimize treatment strategies for sarcoma patients.

Identification of regulatory genes associated with POAG by integrating expression and sequencing data

BACKGROUND

Primary open-angle glaucoma (POAG) is a subtype of glaucoma that accounts for 60%~70% of all cases. Its pathogenic mechanism is intricate and its pathogenic process is concealed. Numerous significant biological processes associated with POAG continue to be elucidated.

METHODS

In this study, by exploring the expression data of POAG tissues and normal tissues, we mined the regulatory lncRNAs and mRNAs closely associated with the pathogenesis and progression of POAG by exploring a regulatory network of competing endogenous RNA (ceRNA), established by integrating gene expression data with the known lncRNA-miRNA and miRNA-mRNA-regulatory interactions. The key regulatory pathways and regulatory elements of POAG were identified by topological analysis. Simultaneously, the exome data of 28 cases with POAG and healthy controls were analyzed to identify high-frequency mutations and genes.

RESULTS

A total of 2712 differentially expressed genes were identified, including 1828 mRNAs and 884 lncRNAs. Network analysis suggested that lncRNAs such as HAGLR, HOTAIR and MIR29B2CHG, and mRNAs such as PPP6R3, BMPR2 and CFL2, may be involved in the onset and progression of POAG. In addition, 55 mutations with potential pathogenicity were identified.

CONCLUSION

These genes and mutations provide novel potential genetic heterogeneity and genetic susceptibility of POAG, as well as fresh suggestions for elucidating the molecular mechanism underlying the pathogenesis of POAG.

Study of the impact of ClinGen Revisions on ACMG/AMP variant semi-automatic classification for Rare Diseases diagnosis

With the rapid development of massive sequencing technologies, the analysis of genetic variants for clinical diagnosis has exponentially escalated, particularly in the context of Rare Diseases (RDs). Diagnosing them involves identifying the genetic variants responsible for the underlying pathology development. In 2015, the American College of Medical Genetics (ACMG) established a set of recommendations to assess the evidence associated with each variant, aiming to achieve a standardized five tier classification. Over the past 5 years, ClinGen, the NIH-funded Clinical Genome Resource, has reviewed these criteria in order to make variant classification a more reproducible and rigorous process. This paper examines the impact of ClinGen-Rev modifications on variant classification, comparing them with the ACMG-2015 original recommendations. After analyzing sets of genetic variants, extracted from VCFs samples, using both criteria, we observed a change in 8.0 % of the clinical verdicts for these variants. ClinGen-Rev modifications correctly categorized 89.2 % of the curated variants, representing a significant improvement compared to the 65.6 % achieved by ACMG-2015. We also analyzed the modifications impact in a real like clinical setting, showing a significant overall reduction of VUS variants and thus potential reduction in analysis time. Finally, we discuss the underlying reasons for the most relevant changes in terms of specific labels and present their implications on the prioritization and selection process of variants, identifying some recommendations of key significant importance.

Deciphering the role of IL17RA in psoriasis and chronic mucocutaneous candidiasis: shared pathways and distinct manifestations

Introduction

Psoriasis and chronic mucocutaneous candidiasis (CMC), although distinct in their clinical manifestations, often coexist within specific patient cohorts. Despite this intriguing clinical observation, their genetic etiologies have been studied separately, neglecting the shared inflammatory mediator, interleukin 17A-F (IL17A-F). Consequently, the immunogenetic foundations underlying these conditions have remained enigmatic.

Methods

In this study, we analyzed the case of a 5-year-old female born to consanguineous parents who presented with concomitant psoriasis and CMC phenotypes. Utilizing whole exome and transcriptomic sequencing, we meticulously investigated the genetic underpinnings and molecular pathways underlying these complex pathologies. RNA sequencing was performed on a skin biopsy to confirm transcriptomic profiles associated with these conditions.

Results

We identified a novel bi-allelic variant (NM_014339.6, c.1173C>G A) within the interleukin 17 receptor type A (IL17RA) gene, resulting in a premature stop codon (p. Tyr391Ter). Despite the truncation, our investigations revealed that this variant produces a fully functional IL17RA protein. This was evident from the presence of IL17RA in the patient's peripheral blood mononuclear cells (PBMCs) and the ability of the mutant IL17RA to dimerize with both wild-type protein and its partners IL17RC and IL17RD. Transcriptomic analysis of the skin biopsy showed a distinct psoriasis-associated signature intertwined with inflammatory pathways, including responses to fungal infections.

Discussion

This report unveils an unprecedented genetic link serving as a common denominator for psoriasis and CMC. The novel IL17RA variant highlights the pivotal role of this receptor in the shared inflammatory pathways underlying these conditions. Our findings bridge a critical knowledge gap and provide insights into the molecular mechanisms connecting these diseases. This discovery not only advances our understanding of their pathophysiology but also lays the groundwork for personalized therapeutic strategies, heralding a new era of precision medicine for patients with intertwined psoriasis and CMC.

The natural history of CDKL5 deficiency disorder into adulthood

Knowledge of the natural history of CDKL5 deficiency disorder (CDD) is limited to the results of cross-sectional analysis of largely pediatric cohorts. Assessment of outcomes in adulthood is critical for clinical decision-making and future precision medicine approaches but is challenging because of the diagnostic gap and duration of follow-up that would be required for prospective studies. We aimed to delineate the natural history retrospectively from adulthood. We analyzed clinical data about an international cohort of 67 adults with CDD. We analyzed demographic, phenotypic, CDKL5 Developmental Score (CDS), and treatment data, and tested associations with genetic factors, sex, and a positive or negative history of neonatal seizures, as an early predictor of prognosis. All but one of 67 adults (55 females, median age of 24 years at last follow-up) had epilepsy, typically beginning with epileptic spasms or tonic seizures before 4 months of age. Focal-onset and non-motor seizures emerged later. Fewer than a third had been documented as having bilateral tonic-clonic seizures or status epilepticus. Seizures often improved with age, but 73% had never experienced more than 6 months of seizure-freedom. Clobazam, sodium valproate, and lamotrigine were the most frequently prescribed antiseizure medications, but no specific treatment demonstrated superiority. Common comorbidities included movement disorders, visual impairment, sleep disorders, constipation, and scoliosis. All participants had intellectual disability, 75% had not acquired speech and 45% had regressed developmentally. 16% never achieved any CDS skill, but most attained at least three, and 28% attained six or all seven. By adulthood, half of those who had achieved any CDS skill retained all their CDS skills. The skills most frequently lost were independent walking and standing. Those with a history of neonatal seizures tended to attain fewer CDS skills and were more likely to have abnormal muscle tone in adulthood, atrioventricular conduction delay, and potential complications of their illness and treatment. Individuals carrying missense variants attained more CDS skills than those with other variants and were more likely to lose skills in adulthood and develop anxiety, possibly reflecting the limited neurodevelopment of those with non-missense variants, who manifested a more multisystemic disorder. In summary, retrospective data from adulthood elucidates the evolution of symptoms, variation in developmental outcomes, and the treatment landscape in CDKL5 deficiency disorder. Presence a non-missense variants or a history of neonatal seizures indicates a more complex disorder and lower developmental trajectory. Our findings will inform management decisions, prognostication, and the design of clinical trials in CDKL5 Deficiency Disorder.

GoFCards: an integrated database and analytic platform for gain of function variants in humans

Gain-of-function (GOF) variants, which introduce new or amplify protein functions, are essential for understanding disease mechanisms. Despite advances in genomics and functional research, identifying and analyzing pathogenic GOF variants remains challenging owing to fragmented data and database limitations, underscoring the difficulty in accessing critical genetic information. To address this challenge, we manually reviewed the literature, pinpointing 3089 single-nucleotide variants and 72 insertions and deletions in 579 genes associated with 1299 diseases from 2069 studies, and integrated these with the 3.5 million predicted GOF variants. Our approach is complemented by a proprietary scoring system that prioritizes GOF variants on the basis of the evidence supporting their GOF effects and provides predictive scores for variants that lack existing documentation. We then developed a database named GoFCards for general geneticists and clinicians to easily obtain GOF variants in humans (http://www.genemed.tech/gofcards). This database also contains data from >150 sources and offers comprehensive variant-level and gene-level annotations, with the aim of providing users with convenient access to detailed and relevant genetic information. Furthermore, GoFCards empowers users with limited bioinformatic skills to analyze and annotate genetic data, and prioritize GOF variants. GoFCards offers an efficient platform for interpreting GOF variants and thereby advancing genetic research.

Whole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population

BACKGROUND

Keratoconus (KC) is a prevalent corneal condition with a modest genetic basis. Recent studies have reported significant genetic associations in multi-ethnic cohorts. However, the situation in the Chinese population remains unknown. This study was conducted to identify novel genetic variants linked to KC and to evaluate the potential applicability of a polygenic risk model in the Han Chinese population.

METHODS

A total of 830 individuals diagnosed with KC and 779 controls from a Chinese cohort were enrolled and genotyped by whole-genome sequencing (WGS). Common and rare variants were respectively subjected to single variant association analysis and gene-based burden analysis. Polygenic risk score (PRS) models were developed using top single-nucleotide polymorphisms (SNPs) identified from a multi-ethnic meta-analysis and then evaluated in the Chinese cohort.

RESULTS

The characterization of germline variants entailed correction for population stratification and validation of the East Asian ancestry of the included samples via principal component analysis. For rare protein-truncating variants (PTVs) with minor allele frequency (MAF) < 5%, ZC3H11B emerged as the top prioritized gene, albeit failing to reach the significance threshold. We detected three common variants reaching genome-wide significance (P ≤ 5 × 10-8), all of which are novel to KC. Our study validated three well known predisposition loci, COL5A1, EIF3A and FNDC3B. Additionally, a significant correlation of allelic effects was observed for suggestive SNPs between the largest multi-ethnic meta-genome-wide association study (GWAS) and our study. The PRS model, generated using top SNPs from the meta-GWAS, stratified individuals in the upper quartile, revealing up to a 2.16-fold increased risk for KC.

CONCLUSIONS

Our comprehensive WGS-based GWAS in a large Chinese cohort enhances the efficiency of array-based genetic studies, revealing novel genetic associations for KC and highlighting the potential for refining clinical decision-making and early prevention strategies.

Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling

A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a significant challenge in genome analysis due to their high sequence similarity to the parent genes and their frequent absence in the reference genome. This homology can lead to errors in variant identification, as sequences derived from processed pseudogenes can be incorrectly assigned to parental genes, complicating correct variant calling. In this study, we quantified the occurrence of variant calling errors associated with pseudogenes, generated by the most popular germline variant callers, namely GATK-HC, DRAGEN, and DeepVariant, when analysing 30x human whole-genome sequencing data (n = 13,307). The results show that the presence of pseudogenes can interfere with variant calling, leading to false positive identifications of potentially clinically relevant variants. Compared to other approaches, DeepVariant was the most effective in correcting these errors.

Interpreting Variants of Uncertain Significance in PCD: Abnormal Splicing Caused by a Missense Variant of DNAAF3

BACKGROUND

Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder characterized by dysfunction of motile cilia. While approximately 50 genes have been identified, around 25% of PCD patients remain genetically unexplained; elucidating the pathogenicity of specific variants remains a challenge.

METHODS

Whole exome sequencing (WES) and Sanger sequencing were conducted to identify potential pathogenic variants of PCD. Minigene assays were performed to evaluate the pathogenicity of variants. Transmission electron microscopy (TEM) and high-speed video analysis (HSVA) were conducted to analyze the function of cilia in respiratory epithelial cells.

RESULTS

We identified two variants of DNAAF3: c.557G>A, p.G186E in exon 5, and c.1364G>A, p.G455D at the terminal nucleotide of exon 10 in a 16-year-old male patient. Through a minigene assay, we demonstrated that the c.1364G>A variant led to a four-nucleotide skipping. The cilia in epithelial ciliary cells of the proband were almost immotile. The absence of outer dynein arms and inner dynein arms was also observed.

CONCLUSIONS

Our study identified two compound heterozygous variants of DNAAF3, a pathogenic gene for PCD, and proved that a novel missense variant c.1364G>A affects splicing. Our findings not only expanded the spectrum of mutations in the DNAAF3 gene but also highlighted the importance of investigating variants of uncertain significance (VUS) for comprehensive genetic diagnoses.

Nephrocalcinosis, distal renal tubular acidosis and skeletal abnormality in two siblings with ROGDI -related Kohlschütter-Tönz syndrome

INTRODUCTION

Kohlschütter-Tönz (KTS) is a rare autosomal recessive, genetically heterogeneous disorder characterized by a triad of early-onset seizures, global developmental delay or regression, and amelogenesis imperfecta of both temporary and permanent teeth. To date, 66 cases have been reported in the literature, of which 44 with genetic confirmation.

CASE REPORT

Here we report the observation of sibling pairs in a family from a small village in India who presented with nephrocalcinosis, distal renal tubular acidosis, and skeletal abnormality. Nephrocalcinosis has only been reported once before in an individual affected with KTS.

RESULTS

Trio exome sequencing revealed a novel, homozygous, likely pathogenic variant, c.646-2_649del, in exon 9 of the ROGDI gene (NM_024589.3) in the first child. Sanger sequencing confirmed homozygosity in both children. Both parents are heterozygous carriers of the same variant.

CONCLUSION

Further research needs to be done to identify the exact mechanism by which ROGDI -encoded protein deficiency leads to nephrocalcinosis and distal renal tubular acidosis.