AnnotSV: an integrated tool for structural variations annotation

Mosaic deletions detected by genome sequencing in two families

Trio-based genome sequencing (GS) is useful for genetic analysis of cases in which exome sequencing failed to resolve the disease-causing variants. In this paper, we report two unrelated families with pathogenic deletions (one outside exome-covering genomic regions and the other involving a single exon) successfully identified by GS. Notably, mosaic deletions were found in both families, which were carefully evaluated in detail by analyzing GS data using Integrative Genomics Viewer, breakpoint PCR, quantitative PCR, and digital PCR. This study emphasizes the benefit of trio-based GS, enabling straightforward interpretation, further aided by other confirmatory experimental methods.

Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery

Advances in long-read sequencing have enabled routine complete assembly of human genomes, but much remains to be done to represent broader populations and show impact on disease-gene discovery. Here, we report highly accurate, near-complete and phased genomes from six Middle Eastern (ME) family trios (n = 18) with neurodevelopmental conditions, representing ancestries from Sudan, Jordan, Syria, Qatar and Afghanistan. These genomes revealed 42.2 Mb of new sequence (13.8% impacting known genes), 75 new HLA/KIR alleles and strong signals of inbreeding, with ROH covering up to one-third of chromosomes 6 and 12 in one individual. Using assembly-based variant calling, we identified 23 de novo and recessive variants as strong candidates for causing previously unresolved symptoms in the probands. The ME genomes revealed unique variation relative to existing references, showing enhanced mappability and variant calling. These results underscore the value of de novo assembly for disease variant discovery and the need for sampled ME-specific references to better characterize population-relevant variation.

Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models

Orofacial clefting (OFC) is a frequent congenital anomaly and can occur either in the context of underlying syndromes or in isolation (nonsyndromic). The two common OFC phenotypes are cleft lip with/without cleft palate (CL/P) and cleft palate only (CPO). In this study, we searched for penetrant CL/P genes, by evaluating de novo copy number variants (CNV) from an exome sequencing dataset of 50 nonsyndromic patient-parent trios. We detected a heterozygous 86 kb de novo deletion affecting exons 4-11 of ZFHX4, a gene previously associated with OFC. Genetic and phenotypic data from our in-house and the AGORA cohort (710 and 229 individuals with nonsyndromic CL/P) together with literature and database reviews demonstrate that ZFHX4 variants can lead to both nonsyndromic and syndromic forms not only of CL/P but also CPO. Expression analysis in published single-cell RNA-sequencing data (mouse embryo, zebrafish larva) at relevant time-points support an important role of Zfhx4/zfhx4 in craniofacial development. To characterize the role of zfhx4 in zebrafish craniofacial development, we knocked out/down the zebrafish orthologue. Cartilage staining of the zfhx4 CRISPR F0 knockout and morpholino knockdown at 4 days post-fertilization showed an underdeveloped and abnormally shaped ethmoid plate and cartilaginous jaw (resembling micrognathia). While there is evidence for the dominant inheritance of ZFHX4 variants in OFC, we here present a patient with a possible recessive inheritance. In conclusion, ZFHX4 has a highly heterogeneous phenotypic spectrum and variable mode of inheritance. Our data highlight that ZFHX4 should be considered in genetic testing in patients with nonsyndromic clefting.

Cerebral small vessel disease associated with COL4A1 and COL4A2 duplication: clinical and MRI features resembling CADASIL

BACKGROUND

Large duplications or triplications involving the 13q33-34 chromosomal region, which encompass the COL4A1 and COL4A2 genes, have been reported in association with cerebral small vessel disease (CSVD) in a few patients. Herein, we report an additional case of CSVD linked to a duplication of COL4A1 and COL4A2 and provide a detailed summary of the associated clinical and MRI findings.

METHODS

A patient with CSVD underwent detailed clinical and neuroimaging evaluations. Targeted next-generation sequencing (NGS) and copy number variation sequencing (CNV-seq) based on whole genome sequencing were used to identify the genetic basis of the disease.

RESULTS

The patient experienced his first ischemic stroke at age 51. Cranial MRI revealed extensive acute and chronic lacunar infarcts and white matter hyperintensities across both cerebral hemispheres, with involvement of the anterior temporal lobe and the external capsule. Bilateral thalamic microbleeds were also noted. The clinical features and MRI findings are similar to those observed in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Targeted NGS and CNV-seq analysis identified a duplication in the region of chromosome 13, which included the COL4A1 and COL4A2 genes.

CONCLUSIONS

This case provides further evidence supporting the association of CNVs in COL4A1 and COL4A2 with CSVD. When hereditary CSVD is suspected and no micro-mutations in CSVD-associated genes are identified, CNV analysis of the 13q region should be considered.

Long-Read Whole-Genome Sequencing as a Tool for Variant Detection in Inherited Retinal Dystrophies

Advances in whole-genome sequencing (WGS) have significantly enhanced our ability to detect genomic variants underlying inherited diseases. In this study, we performed long-read WGS on 24 patients with inherited retinal dystrophies (IRDs) to validate the utility of nanopore sequencing in detecting genomic variations. We confirmed the presence of all previously detected variants and demonstrated that this approach allows for the precise refinement of structural variants (SVs). Furthermore, we could perform genotype phasing by sequencing only the probands, confirming that the variants were inherited in trans. Moreover, nanopore sequencing enables the detection of complex variants, such as transposon insertions and structural rearrangements. This comprehensive assessment illustrates the power of long-read sequencing in capturing diverse forms of genomic variation and in improving diagnostic accuracy in IRDs.

Unraveling the hidden complexity of cancer through long-read sequencing

Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the genome, transcriptome, and epigenome, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long-read sequencing for both germline and somatic cancer analysis. We provide an overview of the computational methodologies tailored to long-read data and highlight key discoveries and resources within cancer genomics that were previously inaccessible with prior technologies. We also address future opportunities and persistent challenges, including the experimental and computational requirements needed to scale to larger sample sizes, the hurdles in sequencing and analyzing complex cancer genomes, and opportunities for leveraging machine learning and artificial intelligence technologies for cancer informatics. We further discuss how the telomere-to-telomere genome and the emerging human pangenome could enhance the resolution of cancer genome analysis, potentially revolutionizing early detection and disease monitoring in patients. Finally, we outline strategies for transitioning long-read sequencing from research applications to routine clinical practice.

A Hitchhiker's Guide to long-read genomic analysis

Over the past decade, long-read sequencing has evolved into a pivotal technology for uncovering the hidden and complex regions of the genome. Significant cost efficiency, scalability, and accuracy advancements have driven this evolution. Concurrently, novel analytical methods have emerged to harness the full potential of long reads. These advancements have enabled milestones such as the first fully completed human genome, enhanced identification and understanding of complex genomic variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from initial data processing to variant calling and annotation, focusing on how these methods improve our ability to interpret a wide array of genomic variants. Additionally, we discuss the current challenges, limitations, and future directions in the field, offering a detailed examination of the state-of-the-art bioinformatics methods for long-read sequencing.

Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing

Solve-RD is a pan-European rare disease (RD) research program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilized 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural variants (SVs), single-nucleotide variants (SNVs), insertion-deletions (indels), and short tandem repeat (STR) expansions in previously studied RD families without a clear molecular diagnosis. Our cohort includes 293 individuals from 114 genetically undiagnosed RD families selected by European Reference Network (ERN) experts. Of these, 21 families were affected by so-called "unsolvable" syndromes for which genetic causes remain unknown and for which prior testing was not a prerequisite. The remaining 93 families had at least one individual affected by a rare neurological, neuromuscular, or epilepsy disorder without a genetic diagnosis despite extensive prior testing. Clinical interpretation and orthogonal validation of variants in known disease genes yielded 12 novel genetic diagnoses due to de novo and rare inherited SNVs, indels, SVs, and STR expansions. In an additional five families, we identified a candidate disease-causing variant, including an MCF2/FGF13 fusion and a PSMA3 deletion. However, no common genetic cause was identified in any of the "unsolvable" syndromes. Taken together, we found (likely) disease-causing genetic variants in 11.8% of previously unsolved families and additional candidate disease-causing SVs in another 5.4% of these families. In conclusion, our results demonstrate the potential added value of HiFi long-read genome sequencing in undiagnosed rare diseases.

Heterozygous deletion of 10q24.31-q24.33- a new syndrome associated with multiple congenital anomalies: case report and literature review

BACKGROUND

Congenital anomalies and neurodevelopmental disorders are complex conditions often requiring comprehensive diagnostic approaches. Next-generation sequencing (NGS), particularly whole-exome sequencing (WES), has greatly improved the detection of pathogenic variants, including copy number variations (CNVs), which account for up to 35% of genetic causes in neurological patients. Combining CNV and single nucleotide variant (SNV) analysis through WES enhances diagnostic accuracy, especially in cases with unclassified congenital anomalies.

CASE PRESENTATION AND LITERATURE REVIEW

This study reports a 14-year-old male patient with multiple congenital anomalies, including hypospadias, complete cleft palate, and recurrent pneumonia. His clinical presentation includes significant physical and intellectual developmental delays, autism-like symptoms, and spastic diplegia. Whole-exome sequencing (WES) was performed due to these complex symptoms, revealing a novel heterozygous deletion on chromosome 10q24.31-q24.33. Laboratory findings indicated agammaglobulinemia, leading to prophylactic antibiotic therapy and immunoglobulin replacement. Additional imaging studies showed cystic malformation of the middle lobe of the right lung, sliding hiatal hernia with prolapse of the gastric mucosa, and brain anomalies consistent with Joubert syndrome.

CONCLUSIONS

This case underscores the importance of genetic analysis in understanding the etiology of congenital anomalies and neurodevelopmental disorders, providing critical insights into the molecular mechanisms driving complex phenotypes. The identified chromosomal deletion contributes to the existing literature on genomic imbalances associated with similar phenotypes.

Bi-Allelic MARVELD2 Variant Identified with Exome Sequencing in a Consanguineous Multiplex Ghanaian Family Segregating Non-Syndromic Hearing Loss

Genetic studies and phenotypic expansion of hearing loss (HL) for people living in Africa are greatly needed. We evaluated the clinical phenotypes of three affected siblings presenting non-syndromic (NS) HL and five unaffected members of a consanguineous Ghanaian family. Analysis of exome sequence data was performed for all affected and one unaffected family members. In-depth genetic and cellular characterization studies were performed to investigate biological significance of the implicated variant using bioinformatic tools and cell-based experimentation. Audiological examinations showed severe-to-profound, bilateral, symmetrical, and post-lingual onset. The whole-exome sequencing (WES) identified a homozygous frameshift variant: MARVEL domain containing 2 (MARVELD2):c.1058dup;p.(Val354Serfs*5) in all affected siblings. This frameshift variant leads to an early stop codon insertion and predicted to be targeted by nonsense medicated decay (mutant protein predicted to lack conserved C-terminal domain if translated). Cell immunofluorescence and immunocytochemistry studies exposed the functional impact of the mutant protein's expression, stability, localization, protein-protein binding, barrier function, and actin cytoskeleton architecture. The identified variant segregates with NSHL in the index Ghanaian family. The data support this nonsense variant as pathogenic, likely to impact the homeostasis of ions, solutes, and other molecules, compromising membrane barrier and signaling in the inner ear spaces.

Machine learning-predicted chromatin organization landscape across pediatric tumors

Structural variants (SVs) are increasingly recognized as important contributors to oncogenesis through their effects on 3D genome folding. Recent advances in whole-genome sequencing have enabled large-scale profiling of SVs across diverse tumors, yet experimental characterization of their individual impact on genome folding remains infeasible. Here, we leveraged a convolutional neural network, Akita, to predict disruptions in genome folding caused by somatic SVs identified in 61 tumor types from the Children's Brain Tumor Network dataset. Our analysis reveals significant variability in SV-induced disruptions across tumor types, with the most disruptive SVs coming from lymphomas and sarcomas, metastatic tumors, and germline cell tumors. Dimensionality reduction of disruption scores identified five recurrently disrupted regions enriched for high-impact SVs across multiple tumors. Some of these regions are highly disrupted despite not being highly mutated, and harbor tumor-associated genes and transcriptional regulators. To further interpret the functional relevance of high-scoring SVs, we integrated epigenetic data and developed a modified Activity-by-Contact scoring approach to prioritize SVs with disrupted genome contacts at active enhancers. This method highlighted highly disruptive SVs near key oncogenes, as well as novel candidate loci potentially implicated in tumorigenesis. These findings highlight the utility of machine learning for identifying novel SVs, loci, and genetic mechanisms contributing to pediatric cancers. This framework provides a foundation for future studies linking SV-driven regulatory changes to cancer pathogenesis.

The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease

OBJECTIVE

Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) long-read sequencing. This study aims to determine if ONT long-read sequencing can detect a second variant in other unresolved early-onset Parkinson's disease (EOPD) cases with 1 heterozygous PRKN or PINK1 variant.

METHODS

ONT long-read sequencing was performed on EOPD patients with 1 reported PRKN/PINK1 pathogenic variant, with onset age under 50. Positive controls included EOPD patients with 2 known PRKN pathogenic variants. Initial testing involved short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification for copy number variants.

RESULTS

A total of 47 patients were studied (PRKN "one-variant," n = 23; PINK1 "one-variant," n = 12; PRKN "two-variants," n = 12). ONT long-read sequencing identified a second pathogenic variant in 26% of PRKN "one-variant" patients (6/23), but none in PINK1 "one-variant" patients (0/12). Detected variants included 1 complex inversion, 2 structural variant overlaps, and 3 duplications. In the PRKN "two-variants" group, both variants were identified in all patients (100%, 12/12).

INTERPRETATION

ONT long-read sequencing effectively identifies pathogenic structural variants in the PRKN locus missed by conventional methods. It should be considered for unresolved EOPD cases when a second variant is not detected through conventional approaches. ANN NEUROL 2025;97:753-765.

Targeted Long-Read Sequencing as a Single Assay Improves the Diagnosis of Spastic-Ataxia Disorders

OBJECTIVE

The hereditary spastic-ataxia spectrum disorders are a group of disabling neurological diseases. The traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline and improve this process using long-read sequencing.

METHODS

We developed a targeted long-read sequencing strategy with the capacity to characterise the genetic variation of all types and sizes within 469 disease-associated genes, in a single assay. We applied this to a cohort of 34 individuals with unsolved spastic-ataxia. An additional five individuals with a known genetic diagnosis were included as positive controls.

RESULTS

We identified causative pathogenic variants that would be sufficient for genetic diagnosis in 14/34 (41%) unsolved participants. The success rate was 5/11 (45%) in those who were naïve to genetic testing and 9/23 (39%) in those who were undiagnosed after prior genetic testing, completed on a clinical basis. Short tandem repeat expansions in FGF14 were the most common (7/34, 21%). Two individuals (2/34, 6%) had biallelic pathogenic expansions in RFC1 and one individual had a monoallelic pathogenic expansion in ATXN8OS/ATXN8. Causative pathogenic sequence variants other than short tandem repeat expansions were found in four individuals, including in VCP, STUB1, ANO10 and SPG7. Furthermore, all five positive controls were identified.

INTERPRETATION

Our results demonstrate the utility of targeted long-read sequencing in the genetic evaluation of patients with spastic-ataxia spectrum disorders, highlighting both the capacity to increase overall diagnostic yield and to streamline the testing pathway by capturing all known genetic causes in a single assay.

SNV/Indel and CNV Analysis in Trio-WES for Intellectual and Developmental Disabilities: Diagnostic Yield & Cost-Effectiveness

Intellectual and developmental disabilities (IDD) are clinically and genetically heterogeneous disorders of global concern. While whole exome sequencing (WES) is used to identify single nucleotide variants (SNVs) and small insertions/deletions (Indels) in IDD patients, its detection rate is limited. This study evaluated the value of integrating copy number variation (CNV) analysis into traditional SNV/Indel analysis based on trio-WES. One hundred eighty seven patients with IDD in 140 families from southwest China were incorporated into the study cohort. The overall diagnostic rate was 40.11% (75/187), with 33.16% (62/187) from SNV/Indel analysis and 6.95% (13/187) from CNV analysis. SNV/Indel analysis identified 52 variants in 42 genes, including 30 novel and 22 reported variants; CNV analysis identified 11 CNVs, comprising 1 repeat and 10 deletions, with sizes ranging from 1313 to 55 184 kb. 39.29% (55/140) families benefited from this study for their clinical diagnosis, treatment, and reproduction. Furthermore, our strategy, with an incremental cost-effectiveness ratio (ICER) of $2546.22/diagnosis, had demonstrated significant advantages in terms of cost-effectiveness and detection speed compared to previous methods. In general, by incorporating SNV/Indel and CNV analysis based on trio-WES, a robust, cost-effective, and time-saving approach for diagnosing IDD has been developed.

Understanding rare variant contributions to autism: lessons from dystrophin-deficient model

Duchenne and Becker Muscular Dystrophy are dystrophinopathies with a prevalence of 1:5000-6000 males, caused by pathogenic variants in DMD. These conditions are often accompanied by neurodevelopmental disorders (NDDs) like autism (ASD; ~20%) and intellectual disability (ID; ~30%). However, their low penetrance in dystrophinopathies suggests additional contributing factors. In our study, 83 individuals with dystrophinopathies were clinically evaluated and categorized based on ASD (36 individuals), ID risk (12 individuals), or controls (35 individuals). Exome sequencing analysis revealed an enrichment of risk de novo variants (DNVs) in ASD-DMD individuals (adjusted p value = 0.0356), with the number of DNVs correlating with paternal age (p value = 0.0133). Additionally, DMD-ASD individuals showed a higher average of rare risk variants (RRVs) compared to DMD-Controls (adjusted p value = 0.0285). Gene ontology analysis revealed an enrichment of extracellular matrix-related genes, especially collagens, and Ehlers-Danlos syndrome genes in ASD-DMD and DMD-ID groups. These findings support an oligogenic model for ASD in dystrophinopathies, highlighting the importance of investigating homogenized samples to elucidate ASD's genetic architecture.

Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery

Genotype-phenotype correlations of rare diseases are complicated by low patient number, high phenotype variability, and compound heterozygosity. Mutations may cause instability of single proteins, and affect protein complex formation or overall robustness of a specific process in a given cell. Ciliopathies offer an interesting case for studying genotype-phenotype correlations as they have a spectrum of severity and include diverse phenotypes depending on different mutations in the same protein. For instance, mutations in the intraflagellar transport protein IFT140 cause a vast spectrum of ciliopathies ranging from isolated retinal dystrophy to severe skeletal abnormalities and multi-organ diseases such as Mainzer-Saldino and Jeune syndrome. Here, the quantitative effects of 23 missense mutations in IFT140, which forms part of the crucial IFT-A complex of the ciliary machinery, were analyzed using affinity purification coupled with mass spectrometry (AP-MS). A subset of 10 mutations led to a significant and domain-specific reduction in IFT140-IFT-A complex interaction indicating complex formation issues and potentially hampering its molecular function. Knockout of IFT140 led to loss of cilia, as shown before. However, phenotypically only mild effects concerning cilia assembly were observed for two out of four tested IFT140 missense mutations. Therefore, our results demonstrate the utility of AP-MS in discerning pathogenic MMs from polymorphisms, and we postulate that reduced function is tolerated by the evolutionarily highly conserved IFT-A system.

Systematic assessment of structural variant annotation tools for genomic interpretation

Structural variants (SVs) over 50 base pairs play a significant role in phenotypic diversity and are associated with various diseases, but their analysis is complex and resource-intensive. Numerous computational tools have been developed for SV prioritization, yet their effectiveness in biomedicine remains unclear. Here we benchmarked eight widely used SV prioritization tools, categorized into knowledge-driven (AnnotSV, ClassifyCNV) and data-driven (CADD-SV, dbCNV, StrVCTVRE, SVScore, TADA, XCNV) groups in accordance with the ACMG guidelines. We assessed their accuracy, robustness, and usability across diverse genomic contexts, biological mechanisms and computational efficiency using seven carefully curated independent datasets. Our results revealed that both groups of methods exhibit comparable effectiveness in predicting SV pathogenicity, although performance varies among tools, emphasizing the importance of selecting the appropriate tool based on specific research purposes. Furthermore, we pinpointed the potential improvement of expanding these tools for future applications. Our benchmarking framework provides a crucial evaluation method for SV analysis tools, offering practical guidance for biomedical research and facilitating the advancement of better genomic research tools.

Recurrent Increased Nuchal Translucency Led to the Identification of Novel NUP107 Variants

Five percent of fetuses presents increased fetal nuchal translucency. It is a well-known marker for aneuploidy (T21, Turner syndrome) and a variety of monogenic syndromes such as Noonan syndrome and certain skeletal dysplasias, as well as associated with structural malformations such as congenital heart disease. Current diagnostic algorithms for increased nuchal translucency include a rapid test for aneuploidy (fluorescence in situ hybridization, FISH, or quantitative PCR), a cytogenetic analysis (karyotype or chromosomal microarray, CMA) followed by or concurrent with targeted gene panel analysis for RASopathies/Noonan syndrome. Some centers now propose whole exome sequencing as an adjunct, but its usefulness in isolated increased nuchal translucency remains debated. We describe the recurrence of apparently isolated increased nuchal translucency in 2 euploid fetuses. Whole genome sequencing identified two compound heterozygous variants in the NUP107 gene in both fetuses. Biallelic variants in NUP107 are responsible for severe steroid-resistant nephrotic syndrome, either isolated or syndromic (Galloway-Mowat syndrome); in addition to the renal phenotype, the latter also includes intellectual deficiency and dysmorphic features. Pregnancy termination made it impossible to assess whether the NUP107 variants found would have resulted in isolated or syndromic steroid-resistant nephrotic syndrome. However, identifying the responsible gene improved the accuracy of the genetic counseling. This family is an example of the added benefit of introducing WES/WGS in standardized protocols for prenatal diagnosis of euploid fetuses in "isolated" increased nuchal translucency.

Whole-genome sequencing analysis of Japanese autism spectrum disorder trios

AIM

Autism spectrum disorder (ASD) is a genetically and phenotypically heterogeneous neurodevelopmental disorder with a strong genetic basis. Conducting the first comprehensive whole-genome sequencing (WGS) analysis of Japanese ASD trios, this study aimed to elucidate the clinical significance of pathogenic variants and enhance the understanding of ASD pathogenesis.

METHODS

WGS was performed on 57 Japanese patients with ASD and their parents, investigating variants ranging from single-nucleotide variants to structural variants (SVs), short tandem repeats (STRs), mitochondrial variants, and polygenic risk score (PRS).

RESULTS

Potentially pathogenic variants that could explain observed phenotypes were identified in 18 patients (31.6%) overall and in 10 of 23 patients (43.5%) with comorbid intellectual developmental disorder (IDD). De novo variants in PTEN, CHD7, and HNRNPH2 were identified in patients referred for genetic counseling who exhibited previously reported phenotypes, including one patient with ASD who had profound IDD and macrocephaly with PTEN L320S. Analysis of the AlphaFold3 protein structure indicated potential inhibition of intramolecular interactions within PTEN. SV analysis identified deletions in ARHGAP11B and TMLHE. A pathogenic de novo mitochondrial variant was identified in a patient with ASD who had a history of encephalitis and cognitive decline. GO enrichment analysis of genes with nonsense variants and missense variants (Missense badness, PolyPhen-2, and Constraint >1) showed associations with regulation of growth and ATP-dependent chromatin remodeler activity. No reportable results were obtained in the analysis of STR and PRS.

CONCLUSION

Characterizing the comprehensive genetic architecture and phenotypes of ASD is a fundamental step towards unraveling its complex biology.

Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping

Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications. Additionally, both methods can capture epigenetic information as they profile native, individual DNA molecules. We compared the effectiveness of the two methods in characterizing the structural, copy number and epigenetic landscape of a clear cell renal cell carcinoma tumor. Both methods provided comparable results for basic karyotyping and CNVs, but differed in their ability to detect SVs of different sizes and types. ONT outperformed OGM in detecting small SVs, while OGM excelled in detecting larger SVs, including translocations. Differences were also observed among various ONT SV callers. Additionally, both methods provided insights into the tumor's methylome and hydroxymethylome. While ONT was superior in methylation calling, hydroxymethylation reports can be further optimized. Our findings underscore the importance of carefully selecting the most appropriate platform based on specific research questions.

Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Atrial fibrillation (AF) is a prevalent and morbid abnormality of the heart rhythm with a strong genetic component. Here, we meta-analyzed genome and exome sequencing data from 36 studies that included 52,416 AF cases and 277,762 controls. In burden tests of rare coding variation, we identified novel associations between AF and the genes MYBPC3, LMNA, PKP2, FAM189A2 and KDM5B. We further identified associations between AF and rare structural variants owing to deletions in CTNNA3 and duplications of GATA4. We broadly replicated our findings in independent samples from MyCode, deCODE and UK Biobank. Finally, we found that CRISPR knockout of KDM5B in stem-cell-derived atrial cardiomyocytes led to a shortening of the action potential duration and widespread transcriptomic dysregulation of genes relevant to atrial homeostasis and conduction. Our results highlight the contribution of rare coding and structural variants to AF, including genetic links between AF and cardiomyopathies, and expand our understanding of the rare variant architecture for this common arrhythmia.

Interstitial Cystitis: a phenotype and rare variant exome sequencing study: Interstitial Cystitis: a phenotype and exome sequencing study

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a poorly understood and underdiagnosed syndrome of chronic bladder/pelvic pain with urinary frequency and urgency. Though IC/BPS can be hereditary, little is known of its genetic etiology. Using the eMERGE data, we confirmed known phenotypic associations such as gastroesophageal reflux disease and irritable bowel syndrome and detected new associations, including osteoarthrosis/osteoarthritis and Barrett's esophagus. An exome wide ultra-rare variants analysis in 348 IC/BPS and 11,981 controls extended the previously reported association with ATP2C1 and ATP2A2, implicated in Mendelian desquamating skin disorders, but did not provide evidence for other previously proposed pathogenic pathways such as bladder development, nociception or inflammation. Pathway analysis detected new associations with "anaphase-promoting complex-dependent catabolic process", the "regulation of MAPK cascade" and "integrin binding". These findings suggest perturbations in biological networks for epithelial integrity and cell cycle progression in IC/BPS pathogenesis, and provide a roadmap for its future investigation.

Unveiling the Genetic Landscape of Coronary Artery Disease Through Common and Rare Structural Variants

BACKGROUND

Genome-wide association studies have identified several hundred susceptibility single nucleotide variants for coronary artery disease (CAD). Despite single nucleotide variant-based genome-wide association studies improving our understanding of the genetics of CAD, the contribution of structural variants (SVs) to the risk of CAD remains largely unclear.

METHOD AND RESULTS

We leveraged SVs detected from high-coverage whole genome sequencing data in a diverse group of participants from the National Heart Lung and Blood Institute's Trans-Omics for Precision Medicine program. Single variant tests were performed on 58 706 SVs in a study sample of 11 556 CAD cases and 42 907 controls. Additionally, aggregate tests using sliding windows were performed to examine rare SVs. One genome-wide significant association was identified for a common biallelic intergenic duplication on chromosome 6q21 (P=1.54E-09, odds ratio=1.34). The sliding window-based aggregate tests found 1 region on chromosome 17q25.3, overlapping USP36, to be significantly associated with coronary artery disease (P=1.03E-10). USP36 is highly expressed in arterial and adipose tissues while broadly affecting several cardiometabolic traits.

CONCLUSIONS

Our results suggest that SVs, both common and rare, may influence the risk of coronary artery disease.

Multi-omics analyses reveal biological and clinical insights in recurrent stage I non-small cell lung cancer

Post-operative recurrence rates of stage I non-small cell lung cancer (NSCLC) range from 20% to 40%. Nonetheless, the molecular mechanisms underlying recurrence hitherto remain largely elusive. Here, we generate genomic, epigenomic and transcriptomic profiles of paired tumors and adjacent tissues from 122 stage I NSCLC patients, among which 57 patients develop recurrence after surgery during follow-up. Integrated analyses illustrate that the presence of predominantly solid or micropapillary histological subtypes, increased genomic instability, and APOBEC-related signature are associated with recurrence. Furthermore, TP53 missense mutation in DNA-binding domain could contribute to shorter time to recurrence. DNA hypomethylation is pronounced in recurrent NSCLC, and PRAME is the significantly hypomethylated and overexpressed gene in recurrent lung adenocarcinoma (LUAD). Mechanistically, hypomethylation at TEAD1 binding site facilitates the transcriptional activation of PRAME. Inhibition of PRAME restrains the tumor metastasis via downregulation of epithelial-mesenchymal transition-related genes. We also identify that enrichment of AT2 cells with higher copy number variation burden, exhausted CD8 + T cells and Macro_SPP1, along with the reduced interaction between AT2 and immune cells, is essential for the formation of ecosystem in recurrent LUAD. Finally, multi-omics clustering could stratify the NSCLC patients into 4 subclusters with varying recurrence risk and subcluster-specific therapeutic vulnerabilities. Collectively, this study constitutes a promising resource enabling insights into the biological mechanisms and clinical management for post-operative recurrence of stage I NSCLC.

Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

Genomic structural variants (SVs) are a major source of genetic diversity in humans. Here, through long-read sequencing of 945 Han Chinese genomes, we identify 111,288 SVs, including 24.56% unreported variants, many with predicted functional importance. By integrating human population-level phenotypic and multi-omics data as well as two humanized mouse models, we demonstrate the causal roles of two SVs: one SV that emerges at the common ancestor of modern humans, Neanderthals, and Denisovans in GSDMD for bone mineral density and one modern-human-specific SV in WWP2 impacting height, weight, fat, craniofacial phenotypes and immunity. Our results suggest that the GSDMD SV could serve as a rapid and cost-effective biomarker for assessing the risk of cisplatin-induced acute kidney injury. The functional conservation from human to mouse and widespread signals of positive natural selection suggest that both SVs likely influence local adaptation, phenotypic diversity, and disease susceptibility across diverse human populations.

Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric CNS tumors

The contribution of rare pathogenic/likely pathogenic (P/LP) germline variants to pediatric central nervous system (CNS) tumor development remains understudied. Here, we characterized the prevalence and clinical significance of germline P/LP variants in cancer predisposition genes across 830 CNS tumor patients from the Pediatric Brain Tumor Atlas (PBTA). We identified germline P/LP variants in 24.2% (201/830) of patients and the majority (154/201) lacked clinical reporting of genetic tumor syndromes. Among P/LP carriers, 30.7% had putative somatic second hits or loss of function tumor alterations. Finally, we linked pathogenic germline variation with novel somatic events and patient survival to highlight the impact of germline variation on tumorigenesis and patient outcomes.

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

More than 50% of families with suspected rare monogenic diseases remain unsolved after whole-genome analysis by short-read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessible to SRS, facilitating long-range mapping and phasing and providing haplotype-resolved methylation profiling. To evaluate LRS's additional diagnostic yield, we sequenced a rare-disease cohort of 98 samples from 41 families, using nanopore sequencing, achieving per sample ∼36× average coverage and 32-kb read N50 from a single flow cell. Our Napu pipeline generated assemblies, phased variants, and methylation calls. LRS covered, on average, coding exons in ∼280 genes and ∼5 known Mendelian disease-associated genes that were not covered by SRS. In comparison to SRS, LRS detected additional rare, functionally annotated variants, including structural variants (SVs) and tandem repeats, and completely phased 87% of protein-coding genes. LRS detected additional de novo variants and could be used to distinguish postzygotic mosaic variants from prezygotic de novos. Diagnostic variants were established by LRS in 11 probands, with diverse underlying genetic causes including de novo and compound heterozygous variants, large-scale SVs, and epigenetic modifications. Our study demonstrates LRS's potential to enhance diagnostic yield for rare monogenic diseases, implying utility in future clinical genomics workflows.

Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses

Genetic diagnosis of rare diseases requires accurate identification and interpretation of genomic variants. Clinical and molecular scientists from 37 expert centers across Europe created the Solve-Rare Diseases Consortium (Solve-RD) resource, encompassing clinical, pedigree and genomic rare-disease data (94.5% exomes, 5.5% genomes), and performed systematic reanalysis for 6,447 individuals (3,592 male, 2,855 female) with previously undiagnosed rare diseases from 6,004 families. We established a collaborative, two-level expert review infrastructure that allowed a genetic diagnosis in 506 (8.4%) families. Of 552 disease-causing variants identified, 464 (84.1%) were single-nucleotide variants or short insertions/deletions. These variants were either located in recently published novel disease genes (n = 67), recently reclassified in ClinVar (n = 187) or reclassified by consensus expert decision within Solve-RD (n = 210). Bespoke bioinformatics analyses identified the remaining 15.9% of causative variants (n = 88). Ad hoc expert review, parallel to the systematic reanalysis, diagnosed 249 (4.1%) additional families for an overall diagnostic yield of 12.6%. The infrastructure and collaborative networks set up by Solve-RD can serve as a blueprint for future further scalable international efforts. The resource is open to the global rare-disease community, allowing phenotype, variant and gene queries, as well as genome-wide discoveries.

UniVar: A variant interpretation platform enhancing rare disease diagnosis through robust filtering and unified analysis of SNV, INDEL, CNV and SV

BACKGROUND

Interpreting the pathogenicity of genetic variants associated with rare diseases is a laborious and time-consuming endeavour. To streamline the diagnostic process and lighten the burden of variant interpretation, it is crucial to automate variant annotation and prioritization. Unfortunately, currently available variant interpretation tools lack a unified and comprehensive workflow that can collectively assess the clinical significance of these types of variants together: small nucleotide variants (SNVs), small insertions/deletions (INDELs), copy number variants (CNVs) and structural variants (SVs).

RESULTS

The Unified Variant Interpretation Platform (UniVar) is a free web server tool that offers an automated and comprehensive workflow on annotation, filtering and prioritization for SNV, INDEL, CNV and SV collectively to identify disease-causing variants for rare diseases in one interface, ensuring accessibility for users even without programming expertise. To filter common CNVs/SVs, a diverse SV catalogue has been generated, that enables robust filtering of common SVs based on population allele frequency. Through benchmarking our SV catalogue, we showed that it is more complete and accurate than the state-of-the-art SV catalogues. Furthermore, to cope with those patients without detailed clinical information, we have developed a novel computational method that enables variant prioritization from gene panels. Our analysis shows that our approach could prioritize pathogenic variants as effective as using HPO terms assigned by clinicians, which adds value for cases without specific clinically assigned HPO terms. Lastly, through a practical case study of disease-causing compound heterozygous variants across SNV and SV, we demonstrated the uniqueness and effectiveness in variant interpretation of UniVar, edging over any existing interpretation tools.

CONCLUSIONS

UniVar is a unified and versatile platform that empowers researchers and clinicians to identify and interpret disease-causing variants in rare diseases efficiently through a single holistic interface and without a prerequisite for HPO terms. It is freely available without login and installation at https://univar.live/.

The Arg99Gln Substitution in HNRNPC Is Associated with a Distinctive Clinical Phenotype Characterized by Facial Dysmorphism and Ocular and Cochlear Anomalies

Background/Objectives: Heterozygous variants in the heterogeneous nuclear ribonucleoprotein C gene (HNRNPC) have recently been reported to cause intellectual developmental disorder-74 (MRD74), a neurodevelopmental disorder with no recurrent diagnostic handles. Affected individuals show variable, non-specific, and subtle dysmorphic features. The degree of developmental delay (DD)/intellectual disability (ID) is also wide, ranging from mild to severe. The mutational spectrum is relatively broad with exon deletions and splice site and frameshift variants distributed along the entire length of the gene leading to HNRNPC loss of function. Only two missense changes located within the RNA-binding motif (RBM) and adjacent linker region of the more abundant isoform (Arg64Trp and Arg99Gln) have been described. Notably, the Arg99Gln amino acid substitution was reported in a subject presenting with a more complex and unique clinical phenotype characterized by distinctive facial features, DD/ID, cochlear aplasia, and bilateral colobomatous microphthalmia, suggesting the possible occurrence of phenotypic heterogeneity. Results: Here, we report the second individual carrying the Arg99Gln change in HNRNPC and having clinical features with a significant overlap with the peculiar phenotype of the previously described subject, supporting the occurrence of a genotype-phenotype correlation. Conclusions: Due to the concomitant occurrence of ocular and cochlear involvement as recognizable diagnostic handles, we propose that the HNRNPCArg99Gln-related phenotype should be considered as a potential differential diagnosis in subjects with ID and major signs of CHARGE syndrome not fulfilling the minimum criteria for a clinical diagnosis.

A 65 kilobase deletion of the upstream TYR gene region in a family with oculocutaneous albinism type 1

Oculocutaneous albinism type 1 is caused by variants in the TYR (tyrosinase) gene. We describe a family with two affected sibs who inherited the pathogenic missense TYR variant c.1146C > A;p.(Asn382Lys) from their mother and a deletion encompassing 65 kilobase pairs of the upstream region of the gene between hg38 coordinates chr11:89110944 and chr11:89175770, from their father. The deletion likely arose by non-homologous recombination since the regions including the two deletion breakpoints share no sequence homology. The deletion contains a single enhancer element that is homologous to a 5' Tyr core regulatory element in the mouse. A luciferase reporter assay showed that this element had a positive regulatory activity. This represents to our knowledge the first deletion solely restricted to non-coding upstream sequences of the TYR gene. It is assumed that the deletion down-regulates expression of the TYR gene and is therefore pathogenic, allowing to establish the diagnosis of OCA 1 in the patients. This study underscores the need to extend the search for pathogenic variants to regulatory regions either by whole genome sequencing or by targeted next generation sequencing of a panel including entire genes (exons, introns, flanking sequences) in order to improve the diagnostic rate in patients with albinism.

Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution

Osteosarcoma is the most common primary cancer of the bone, with a peak incidence in children and young adults. Using multi-region whole-genome sequencing, we find that chromothripsis is an ongoing mutational process, occurring subclonally in 74% of osteosarcomas. Chromothripsis generates highly unstable derivative chromosomes, the ongoing evolution of which drives the acquisition of oncogenic mutations, clonal diversification, and intra-tumor heterogeneity across diverse sarcomas and carcinomas. In addition, we characterize a new mechanism, termed loss-translocation-amplification (LTA) chromothripsis, which mediates punctuated evolution in about half of pediatric and adult high-grade osteosarcomas. LTA chromothripsis occurs when a single double-strand break triggers concomitant TP53 inactivation and oncogene amplification through breakage-fusion-bridge cycles. It is particularly prevalent in osteosarcoma and is not detected in other cancers driven by TP53 mutation. Finally, we identify the level of genome-wide loss of heterozygosity as a strong prognostic indicator for high-grade osteosarcoma.

SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome

Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, the comprehensive detection and clinical annotation of genomic variants remain intricate and technically demanding. We present SUMMER, an integrated and structured workflow specifically designed to process raw Nanopore sequencing reads. SUMMER facilitates an in-depth analysis of multiple variant types, including SNV, SV, short tandem repeat and mobile element insertion. For clinical applications, SUMMER employs SvAnna to prioritize SV candidates based on phenotype relevance and utilizes Straglr to provide reference distributions of non-pathogenic unit counts for 55 known pathogenic short tandem repeats. By addressing critical challenges in variant detection and annotation, SUMMER seeks to advance the clinical utility of long-read sequencing in diagnostic genomics. SUMMER is available on the web at https://github.com/carolhuaxia/summer .

Detection of inversion with breakpoints in ARSB causing MPS VI by whole-genome sequencing: lessons learned and best practices

Introduction

Mucopolysaccharidosis type VI (MPSVI), an autosomal recessive lysosomal storage disorder caused by pathogenic variants in ARSB gene. Usually, whole exome sequencing (WES) can identify these variants, and if WES failed to detect causative variants, whole-genome sequencing (WGS) may be considered to investigate deep intronic variations and structural alterations in patients.

Methods

Whole-exome sequencing (WES) and whole genome sequencing (WGS) were performed in a Chinese family having a boy with suspected diagnosis of MPS with macrocephaly, coarse facial features, broad forehead, thick lips, frontal bossing, craniosynostosis, blue spots, frequent upper respiratory infections, inguinal hernia, and dysostosis multiplex. Lysosomal enzymatic assays for leucocytes were used to assess the activity of arylsulfatase B of the boy's leucocytes. Sanger sequencing and karyotyping analysis were used to validate the variants identified in the boy and his parents.

Results

This boy diagnosed with MPSVI based on clinical phenotypes and laboratory biochemical assays, and WES identified only a maternally inherited missense variant, c.908G>T (p.Gly303Val), in the ARSB gene. By performing WGS, we found a paracentric inversion involving chromosome 5q14.1q13.2 (78180730-138771424 inv), disrupting the ARSB gene on the proband and his father. The inversion was confirmed through karyotyping analysis, and the breakpoints were validated by agarose gel electrophoresis and Sanger sequencing.

Disscussion

This study reminds us that WGS should be done when WES failed to achieve a molecular diagonosis, and it also underscores the importance of WGS especially in cases of high clinical suspicion.

Atypical free sialic acid storage disorder associated with tissue specific mosaicism of SLC17A5

Free sialic acid storage disorder (FSASD) is a rare autosomal recessive lysosomal storage disease caused by pathogenic SLC17A5 variants with variable disease severity. We performed a multidisciplinary evaluation of an adolescent female with suspected lysosomal storage disease and conducted comprehensive studies to uncover the molecular etiology. The proband exhibited intellectual disability, a storage disease gestalt, and mildly elevated urine free sialic acid levels. Skin electron micrographs showed prominent cytoplasmic vacuolation. Clinical exome and genome sequencing identified a maternally-inherited SLC17A5 variant: c.533delC;p.Thr178Asnfs*34. RNASeq of proband skin fibroblasts revealed exon 3 skipping, which was not detected in RNA from proband blood or parental fibroblasts. Targeted deep sequencing of proband fibroblast DNA revealed a 184 bp deletion in ∼15 % of reads, encompassing the 3' end of exon 3. Illumina Complete Long Read sequencing confirmed the deletion was in the paternally-inherited allele and found in a mosaic state in proband fibroblasts and muscle but not in blood or buccal cells. Functional studies, including SLC17A5 knockout cells and transient transfections of mutated SLC17A5 demonstrated pathogenicity of the identified variants. We report an adolescent female with atypical FSASD with tissue-specific mosaicism for an intragenic deletion in SLC17A5, explaining the atypical clinical course, mild biochemical abnormalities, and long diagnostic process.

Myotilin gene duplication causing late-onset myotilinopathy

BACKGROUND

myotilinopathy is a very rare inherited muscle disease that belongs to the group of myofibrillar myopathies. These diseases share a common alteration of the sarcomere organization at the level of the Z disk resulting in pathological protein aggregation, autophagic abnormalities, and ultimately muscle degeneration. Most reported cases are due to dominant missense mutations in the MYOT gene, two of which are largely recurrent.

METHODS

We describe the clinical, radiological, pathological, and molecular analysis including long-read sequencing of a family affected by late-onset dominant proximodistal myopathy and muscle hypertrophy.

RESULTS

We identified a duplication of the entire MYOT gene as the molecular cause of late-onset-myotilinopapthy with typical clinical and pathological features.

CONCLUSIONS

This study expands the molecular spectrum of myotilinopathy and highlights the use of long-read sequencing in the diagnosis of genetic neurological diseases caused by duplications and genomic structural variants. Myotilinopathy as well as other myofibrillar and distal myopathies should be considered in the differential diagnosis of patients affected by distal muscle weakness, even when presenting at an old age.

Novel 327bp Alu element insertion in LDLR exon 17 causes alternative splicing and familial hypercholesterolemia

BACKGROUND

Homozygous familial hypercholesterolemia (HoFH) is a severe form of familial hypercholesterolemia (FH) characterized by high low-density lipoprotein cholesterol (LDL-C) levels and increased coronary artery disease risk. This study reports a novel Alu insertion in the LDLR gene in a consanguineous Indian family, causing FH.

OBJECTIVE

To identify and characterize the mutation causing HoFH in a proband and their family members.

METHODS

Clinical exome sequencing was conducted on the proband with subsequent bioinformatic analysis of single nucleotide variants, loss-of-function variants, structural variants, and mobile element insertions (MEI). Polymerase chain reaction (PCR) amplification and Sanger sequencing of exon 17 of the LDLR gene were performed to elucidate the sequence and length of the Alu insertion. Additionally, RNA analysis of the proband identified splice site events.

RESULTS

Bioinformatic analysis revealed a small sequence duplication followed by an Alu element insertion. PCR amplification and Sanger sequencing uncovered a 17 base pair (bp) duplication at the breakpoint, a "T" base insertion, followed by a 309 bp Alu Yb8 insertion. This led to a 70 bp deletion at the beginning of exon 17 due to alternative splicing, resulting in a frameshift and extended protein truncation. The proband and siblings were homozygous for the mutation, while the parents and 2 other family members were heterozygous.

CONCLUSION

Our study uncovers a novel AluYb8 element insertion in the LDLR gene, highlighting the need for MEI detection in genetic screening for FH. Reanalyzing FH cohorts for MEIs could significantly improve diagnostic accuracy and enhance our understanding of FH genetics.

Concomitant presence of a novel ARPP21 variant and CNVs in Chinese familial amyotrophic lateral sclerosis-frontotemporal dementia patients

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder marked by the degeneration of motor neurons and progressive muscle weakness. Heredity plays an important part in the pathogenesis of ALS. Recently, with the emergence of the oligogenic pathogenic mechanism in ALS and the ongoing discovery of new mutated genes and genomic variants, there is an emerging need for larger-scale and more comprehensive genetic screenings in higher resolution. In this study, we performed whole-genome sequencing (WGS) on 34 familial ALS probands lacking the most common disease-causing mutations to explore the genetic landscape of Chinese ALS patients further. Among them, we identified a novel ARPP21 c.1231G > A (p.Glu411Lys) variant and two copy number variations (CNVs) affecting the PFN1 and RBCK1 genes in a patient with ALS-frontotemporal dementia (FTD). This marks the first report of an ARPP21 variant in Chinese ALS-FTD patients, providing fresh evidence for the association between ARPP21 and ALS. Our findings also underscore the potential role of CNVs in ALS-FTD, suggesting that the cumulative effect of multiple rare variants may contribute to disease onset. Furthermore, compared to the averages in our cohort and the reported Chinese ALS population, this patient displayed a shorter survival time and more rapid disease progression, suggesting the possibility of an oligogenic mechanism in disease pathogenesis. Further research will contribute to a deeper understanding of the rare mutations and their interactions, thus advancing our understanding of the genetic mechanisms underlying ALS and ALS-FTD.

CNVizard-a lightweight streamlit application for an interactive analysis of copy number variants

BACKGROUND

Methods to call, analyze and visualize copy number variations (CNVs) from massive parallel sequencing data have been widely adopted in clinical practice and genetic research. To enable a streamlined analysis of CNV data, comprehensive annotations and good visualizations are indispensable. The ability to detect single exon CNVs is another important feature for genetic testing. Nonetheless, most available open-source tools come with limitations in at least one of these areas. One additional drawback is that available tools deliver data in an unstructured and static format which requires subsequent visualization and formatting efforts.

RESULTS

Here we present CNVizard, an interactive Streamlit app allowing a comprehensive visualization of CNVkit data. Furthermore, combining CNVizard with the CNVand pipeline allows the annotation and visualization of CNV or SV VCF files from any CNV caller.

CONCLUSION

CNVizard, in combination with CNVand, enables the comprehensive and streamlined analysis of short- and long-read sequencing data and provide an intuitive webapp-like experience enabling an interactive visualization of CNV data.

Complete genomic profiles of 1496 Taiwanese reveal curated medical insights

INTRODUCTION

The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population.

OBJECTIVES

This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population.

METHODS

We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw).

RESULTS

We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively.

CONCLUSION

Our study highlights the overall medical insights of a complete Taiwanese genomic profile.

First Case of Macrocephaly, Dysmorphic Facies, and Psychomotor Retardation Harboring Co-inherited Variants in HERC1 and PMP22 Genes from Iran: Two Novel Variants

Here, we report a case with concomitant variants: a novel homozygous HERC1 gene variant and a novel heterozygous PMP22 duplication. The 2-year-old male presented with seizures, developmental delay, macrocephaly, hypotonia, unilateral hypertrophy, thoracic scoliosis, normal brain MRI, and elevated homocysteine level which normalized after treatment. Whole exome sequencing (WES) revealed a co-occurrence of a homozygous novel likely pathogenic variant in the HERC1 gene (NM_003922.3:c.1280dup (p.ILe469Aspfs*33) and a novel heterozygous large duplication of exon 1-5 in the PMP22 gene, which has not been reported previously. The case underscores the challenges in understanding genotype-phenotype correlations and suggests a potential interplay between these genetic variants in shaping the current and future clinical phenotype of the patient. In the case of genetic diseases, this event may have important implications on family members' counseling, and concomitant variants in Charcot-Marie-Tooth (CMT) families should be considered when significant intra-familial clinical heterogeneity is observed.

Two-Compound Heterozygous Deletions Affecting TUBGCP6 in a Patient with Microcephaly and Ocular Abnormalities and in an Unborn Sibling with Abnormal Sulcation

Introduction

TUBGCP6-related disorder is a known cause of autosomal recessive microcephaly and chorioretinopathy, which was originally recognized as a new syndrome based on unique ocular findings on a phenotypic overlap of microcephalic primordial short stature. Since the elucidation of its molecular mechanism, limited families have been published in literature and the disorder remains rare worldwide.

Case Presentation

We present the first Indian family with an affected child and sibling fetus with microcephaly, dysmorphism, and agyria/pachygyria complex on brain imaging in both and short stature, intellectual disability, and visual impairment in proband. As for many patients with long diagnostic odysseys, this child also underwent multiple genomic tests. Genome sequencing through the Indian Undiagnosed Disease Program (I-UDP) confirmed the diagnosis in both proband and sibling fetus. Compound heterozygous variants were identified in TUBGCP6 including an eleven base pair deletion (inherited from father) and 405 base pair large deletion (inherited from mother). Reverse phenotyping to confirm the ocular phenotype in proband confirmed TUBGCP6-related microcephaly and chorioretinopathy. We report third trimester microcephaly with ventriculomegaly and abnormal sulcation as part of the antenatal presentation for this condition.

Conclusion

This case represents an Indian family with a seemingly obvious clinical diagnosis compounded by a long diagnostic odyssey and the first ever structural variant to be identified via whole genome sequencing in TUBGCP6 in trans with an indel variant.

Discovery and functional analysis of a novel ALPK1 variant in ROSAH syndrome

Retinal dystrophy, optic nerve oedema, splenomegaly, anhidrosis and migraine headache (ROSAH) syndrome is an autosomal dominant disorder and to date is known to be caused by either the Thr237Met or Tyr254Cys variant in the protein kinase ALPK1. Here, we identify a family in which ROSAH syndrome is caused by a novel variant in which Ser277 is changed to Phe. All six patients examined display ocular inflammation and optic nerve elevation, four have retinal degeneration and four are registered blind. In contrast to wild-type ALPK1, which is activated specifically by bacterial ADP-heptose, ALPK1[Ser277Phe] is also activated by the human metabolites UDP-mannose and ADP-ribose and more strongly than the most frequent ROSAH-causing variant (ALPK1[Thr237Met]) but, unlike ALPK1[Thr237Met], ALPK1[Ser277Phe] is also activated by GDP-mannose. These observations can explain why ALPK1 variants causing ROSAH syndrome display constitutive activity in human cells. The side chains of Ser277 and Tyr254 interact in the crystal structure of ALPK1, but mutational analysis established that it is not the loss of this hydrogen bond between Ser277 and Tyr254 that alters the specificity of the ADP-heptose-binding pocket in the Ser277Phe and Tyr254Cys variants. The characterization of ALPK1 variants that cause ROSAH syndrome suggests ways in which drugs that selectively inhibit these disease-causing variants may be developed.

Heterogeneous Group of Genetically Determined Auditory Neuropathy Spectrum Disorders

Auditory neuropathy spectrum disorder (ANSD) is often missed by standard hearing tests, accounting for up to 10% of hearing impairments (HI) and commonly linked to variants in 23 genes. We assessed 122 children with HI, including 102 with sensorineural hearing loss (SNHL) and 20 with ANSD. SNHL patients were genotyped for common GJB2 variants using qPCR, while ANSD patients underwent whole exome sequencing, with variants analyzed across 249 genes. Homozygous GJB2 variants were found in 54.9% of SNHL patients. In 60% of ANSD patients, variants were detected in OTOF (25%), CDH23, TMC1, COL11A1, PRPS1, TWNK, and HOMER2 genes, including eight novel variants. Transient evoked otoacoustic emissions testing revealed differences at 4000 Hz (p = 0.0084) between the ANSD and SNHL groups. The auditory steady-state response (ASSR) test showed significant differences at 500 Hz (p = 2.69 × 10-4) and 1000 Hz (p = 0.0255) compared to pure-tone audiometry (PTA) in ANSD patients. Our questionnaire shows that the parents of children with SNHL often report an improved quality of life with hearing aids or cochlear implants, while parents of children with ANSD frequently experience uncertainty about outcomes (p = 0.0026), leading to lower satisfaction.

A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, with little known about SV diversity in other ancestries, particularly from Asia. Here, we present a WGS catalogue of 73,035 SVs from 8392 Singaporeans of East Asian, Southeast Asian and South Asian ancestries, of which ~65% (47,770 SVs) are novel. We show that Asian populations can be stratified by their global SV patterns and identified 42,239 novel SVs that are specific to Asian populations. 52% of these novel SVs are restricted to one of the three major ancestry groups studied (Indian, Chinese or Malay). We uncovered SVs affecting major clinically actionable loci. Lastly, by identifying SVs in linkage disequilibrium with single-nucleotide variants, we demonstrate the utility of our SV catalogue in the fine-mapping of Asian GWAS variants and identification of potential causative variants. These results augment our knowledge of structural variation across human populations, thereby reducing current ancestry biases in global references of genetic variation afflicting equity, diversity and inclusion in genetic research.

Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing

BACKGROUND

Congenital malformations of the female genital tract (CM-FGT) are characterized by abnormal development of the fallopian tubes, uterus, and vagina, often accompanied by malformations in the urinary system, bones and hearing. However, no definitive pathogenic genes and molecular genetic causes have been identified.

METHODS

We present the largest whole-genome sequencing study of CM-FGT to date, analyzing 590 individuals in China: 95 patients, 442 case-controls, and 53 familial controls.

RESULTS

Among the patients, 5.3% carried known CM-FGT-related variants. Pedigree and case-control analyses in two dimensions of coding and non-coding regulatory regions revealed seven novel de novo copy number variations, 12 rare single-nucleotide variations, and 10 rare 3' untranslated region (UTR) mutations in genes related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. Single-cell sequencing data showed that the majority of CM-FGT-related risk genes are spatiotemporally specifically expressed early in uterus development.

CONCLUSIONS

In conclusion, this study identified novel variants related to CM-FGT, particularly highlighting ASH1L as a pathogenic gene. The findings provide insights into the genetic variants underlying CM-FGT, with single-cell sequencing data revealing spatiotemporal specific expression patterns of key risk genes early in uterine development. This study significantly advances the understanding of CM-FGT etiology and genetic landscape, offering new opportunities for prenatal screening.

Whole-genome sequencing identifies novel genes for autism in Chinese trios

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high genetic heritability but heterogeneity. Fully understanding its genetics requires whole-genome sequencing (WGS), but the ASD studies utilizing WGS data in Chinese population are limited. In this study, we present a WGS study for 334 individuals, including 112 ASD patients and their non-ASD parents. We identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding regions. By integrating these variants with an association model, we identified 33 potential risk genes (P<0.001) enriched in neuron and regulation related biological process. Besides the well-known ASD genes (SCN2A, NF1, SHANK3, CHD8 etc.), several high confidence genes were highlighted by a series of functional analyses, including CTNND1, DGKZ, LRP1, DDN, ZNF483, NR4A2, SMAD6, INTS1, and MRPL12, with more supported evidence from GO enrichment, expression and network analysis. We also integrated RNA-seq data to analyze the effect of the variants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased expression. We further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on phenotype. Regarding variants in non-coding regions, a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence, which were mapped to specific genes or regulatory features. The number of de novo variants found in patient was significantly associated with the parents' ages at the birth of the child, and gender with trend. We also identified small de novo structural variants in ASD trios. The results in this study provided important evidence for understanding the genetic mechanism of ASD.

Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs.

Germline testing of Iranian families suspected of Lynch syndrome: molecular characterization and current surveillance of families with pathogenic variants in MSH2, MSH6, and PMS2

Lynch syndrome accounts for 3-5% of all colorectal and endometrial cancer cases, and suboptimal management of Lynch syndrome in the Middle East resulted in the underdiagnosis of mutation carriers. Probands from 24 unrelated Iranian families with a history of cancer(s) suggestive of Lynch syndrome underwent microsatellite instability analysis or immunohistochemistry, multigene panel testing, copy number variation detection, or multiplex ligation-dependent probe amplification. Pathogenic variants were identified in five patients (21%), including three in MSH2, one in MSH6, and one in PMS2. Microsatellite instability analysis showed the lengths of the CAT25 marker in tumor and normal samples were 149 and 148 bp, respectively. Among 21 family members with Lynch syndrome in the MSH2 gene, identified from the three families who previously underwent cascade screening, colorectal and endometrial cancers were the most frequent. While 66% of patients had insurance that included coverage for mutation carrier screening, only one insurance provider extended coverage for next-generation sequencing. Special attention to probands and telematic management of at-risk relatives to organize blood sample collection at their convenience enhanced cascade testing 20-fold per proband. In conclusion, the age of onset and segregation analysis indicated that PMS1 may not be a cancer susceptibility gene, and the tumor spectrum in MSH2 pathogenic carriers is similar to Western countries. Collecting blood samples at patients' convenience is a possible strategy to reduce the cost of identifying Lynch syndrome through cascade testing. The genetic analysis of patients for inherited cancers would optimize the current management of Lynch syndrome in Iran by omitting noncarriers from surveillance programs.

Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

Introduction

Long-read sequencing (LRS) enables accurate structural variant detection and variant phasing. When a molecular diagnosis is suspected, target enrichment can reduce the cost and duration of sequencing.

Methods

LRS was conducted in five inherited retinal dystrophy (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized after clinical exome sequencing (CES). CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region, including the entire RPE65 locus. The DNA was sequenced on a MinION platform. Short-read ×30 whole-genome sequencing (WGS) was performed for five patients to validate nanopore results.

Results

The nanopore sequencing process yielded a median of 271 reads within the targeted region, with a mean depth of 109 and a median read size of 8 kb. All variants identified by CES have been detected using this approach, and no additional RPE65 gene causative variants were found. Nanopore variant detection demonstrated performance akin to short-read WGS at similar coverage levels, although exhibiting increased false positive calls at lower coverage.

Discussion

In this study, we explore the advantages of using a targeted approach together with long-read sequencing to identify variants associated with IRD. The results underscore the utility of targeted long reads for characterizing patients affected by rare diseases when first-tier diagnostic tests are non-conclusive.