Twist exome capture allows for lower average sequence coverage in clinical exome sequencing.

BACKGROUND: Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS: We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION: We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Facial asymmetry tracks genetic diversity among Gorilla subspecies.

Mountain gorillas are particularly inbred compared to other gorillas and even the most inbred human populations. As mountain gorilla skeletal material accumulated during the 1970s, researchers noted their pronounced facial asymmetry and hypothesized that it reflects a population-wide chewing side preference. However, asymmetry has also been linked to environmental and genetic stress in experimental models. Here, we examine facial asymmetry in 114 crania from three Gorilla subspecies using 3D geometric morphometrics. We measure fluctuating asymmetry (FA), defined as random deviations from perfect symmetry, and population-specific patterns of directional asymmetry (DA). Mountain gorillas, with a current population size of about 1000 individuals, have the highest degree of facial FA (explaining 17% of total facial shape variation), followed by Grauer gorillas (9%) and western lowland gorillas (6%), despite the latter experiencing the greatest ecological and dietary variability. DA, while significant in all three taxa, explains relatively less shape variation than FA does. Facial asymmetry correlates neither with tooth wear asymmetry nor increases with age in a mountain gorilla subsample, undermining the hypothesis that facial asymmetry is driven by chewing side preference. An examination of temporal trends shows that stress-induced developmental instability has increased over the last 100 years in these endangered apes.

Common and rare variants in patients with early onset drusen maculopathy.

Early onset drusen maculopathy (EODM) can lead to advanced macular degeneration at a young age, affecting quality of life. However, the genetic causes of EODM are not well studied. We performed whole genome sequencing in 49 EODM patients. Common genetic variants were analysed by calculating genetic risk scores based on 52 age-related macular generation (AMD)-associated variants, and we analysed rare variants in candidate genes to identify potential deleterious variants that might contribute to EODM development. We demonstrate that the 52 AMD-associated variants contributed to EODM, especially variants located in the complement pathway. Furthermore, we identified 26 rare genetic variants predicted to be pathogenic based on in silico prediction tools or based on reported pathogenicity in literature. These variants are located predominantly in the complement and lipid metabolism pathways. Last, evaluation of 18 genes causing inherited retinal dystrophies that can mimic AMD characteristics, revealed 11 potential deleterious variants in eight EODM patients. However, phenotypic characteristics did not point towards a retinal dystrophy in these patients. In conclusion, this study reports new insights into rare variants that are potentially involved in EODM development, and which are relevant for future studies unravelling the aetiology of EODM.

Presence of Genetic Variants Among Young Men With Severe COVID-19.

Importance: Severe coronavirus disease 2019 (COVID-19) can occur in younger, predominantly male, patients without preexisting medical conditions. Some individuals may have primary immunodeficiencies that predispose to severe infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Objective: To explore the presence of genetic variants associated with primary immunodeficiencies among young patients with COVID-19. Design, Setting, and Participants: Case series of pairs of brothers without medical history meeting the selection criteria of young (age <35 years) brother pairs admitted to the intensive care unit (ICU) due to severe COVID-19. Four men from 2 unrelated families were admitted to the ICUs of 4 hospitals in the Netherlands between March 23 and April 12, 2020. The final date of follow-up was May 16, 2020. Available family members were included for genetic variant segregation analysis and as controls for functional experiments. Exposure: Severe COVID-19. Main Outcome and Measures: Results of rapid clinical whole-exome sequencing, performed to identify a potential monogenic cause. Subsequently, basic genetic and immunological tests were performed in primary immune cells isolated from the patients and family members to characterize any immune defects. Results: The 4 male patients had a mean age of 26 years (range, 21-32), with no history of major chronic disease. They were previously well before developing respiratory insufficiency due to severe COVID-19, requiring mechanical ventilation in the ICU. The mean duration of ventilatory support was 10 days (range, 9-11); the mean duration of ICU stay was 13 days (range, 10-16). One patient died. Rapid clinical whole-exome sequencing of the patients and segregation in available family members identified loss-of-function variants of the X-chromosomal TLR7. In members of family 1, a maternally inherited 4-nucleotide deletion was identified (c.2129_2132del; p.[Gln710Argfs*18]); the affected members of family 2 carried a missense variant (c.2383G>T; p.[Val795Phe]). In primary peripheral blood mononuclear cells from the patients, downstream type I interferon (IFN) signaling was transcriptionally downregulated, as measured by significantly decreased mRNA expression of IRF7, IFNB1, and ISG15 on stimulation with the TLR7 agonist imiquimod as compared with family members and controls. The production of IFN-γ, a type II IFN, was decreased in patients in response to stimulation with imiquimod. Conclusions and Relevance: In this case series of 4 young male patients with severe COVID-19, rare putative loss-of-function variants of X-chromosomal TLR7 were identified that were associated with impaired type I and II IFN responses. These preliminary findings provide insights into the pathogenesis of COVID-19.

Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis.

Human retrocopies, that is messenger RNA transcripts benefitting from the long interspersed element 1 machinery for retrotransposition, may have specific consequences for genomic testing. Next genetration sequencing (NGS) techniques allow the detection of such mobile elements but they may be misinterpreted as genomic duplications or be totally overlooked. We report eight observations of retrocopies detected during diagnostic NGS analyses of targeted gene panels, exome, or genome sequencing. For seven cases, while an exons-only copy number gain was called, read alignment inspection revealed a depth of coverage shift at every exon-intron junction where indels were also systematically called. Moreover, aberrant chimeric read pairs spanned entire introns or were paired with another locus for terminal exons. The 8th retrocopy was present in the reference genome and thus showed a normal NGS profile. We emphasize the existence of retrocopies and strategies to accurately detect them at a glance during genetic testing and discuss pitfalls for genetic testing.

Incisor tooth wear and age determination in mountain gorillas from Volcanoes National Park, Rwanda.

OBJECTIVES: Ecological factors, but also tooth-to-tooth contact over time, have a dramatic effect on tooth wear in primates. The aim of this study is to test whether incisor tooth wear changes predictably with age and can thus be used as an age estimation method in a wild population of mountain gorillas (Gorilla beringei beringei) from Volcanoes National Park, Rwanda. MATERIALS AND METHODS: In mountain gorillas of confidently known chronological age (N = 24), we measured the crown height of all permanent maxillary and mandibular incisors (I1 , I1 , I2 , I2 ) as a proxy for incisal macrowear. Linear and quadratic regressions for each incisor were used to test whether age can be predicted by crown height. Using these models, we then predicted age at death of two individual mountain gorillas of probable identifications, based on their incisor crown height. RESULTS: Age decreased significantly with incisor height for all teeth, but the upper first incisors (I1 ) provided the best results, with the lowest Akaike's Information Criterion corrected for small sample size (AICc) and lowest Standard Error of the Estimate (SEE). When the best age equations for each sex were applied to gorillas with probable identifications, the predicted ages differed 1.58 and 3.33 years from the probable ages of these individuals. CONCLUSIONS: Our findings corroborate that incisor crown height, a proxy for incisal wear, varies predictably with age. This relationship can be used to estimate age at death of unknown gorillas in the skeletal collection, and in some cases, to corroborate the identity of individual gorillas recovered from the forest postmortem at an advanced state of decomposition. Such identifications help fill gaps in the demographic database and support research that requires individual-level data.

Dental microwear textural analysis as an analytical tool to depict individual traits and reconstruct the diet of a primate.

OBJECTIVES: Dental microwear is a promising tool to reconstruct animals' diet because it reflects the interplay between the enamel surface and the food items recently consumed. This study examines the sources of inter-individual variations in dietary habits in a free-ranging population of mandrills (Mandrillus sphinx) using a combination of feeding monitoring and in vivo dental microwear textural analysis (DMTA). METHODS: We investigated the impact of seasonality and individual traits on four DMTA parameters. In parallel, we further studied the influence of the physical properties of the food items consumed on these four parameters, using three proxies (mechanical properties, estimates of phytolith and external grit contents). RESULTS: We found that seasonality, age, and sex all impact DMTA parameters but those results differ depending on the facet analyzed (crushing vs. shearing facets). Three DMTA parameters (anisotropy, complexity, and heterogeneity of complexity) appear sensitive to seasonal variations and anisotropy also differs between the sexes while textural fill volume tends to vary with age. Moreover, the physical properties of the food items consumed vary seasonally and also differ depending on individual sex and age. CONCLUSION: Considering the interplay between the tested variables and both dental microwear and diet, we reaffirm that food physical properties play a major role in microwear variations. These results suggest that DMTA parameters may provide valuable hints for paleoecological reconstruction using fragmentary fossil dental remains.

Buccal dental microwear texture and catarrhine diets.

OBJECTIVES: Two-dimensional dental microwear analyses on occlusal and nonocclusal enamel surfaces have been widely applied to reconstruct the feeding behaviors of extant primates and to infer ecological adaptations in fossil hominins. To date, analyses of dental microwear texture, using three-dimensional, Scale-Sensitive Fractal Analysis approaches has only been applied to occlusal surfaces. Here, for the first time, we apply this 3D proxy to buccal enamel surfaces of catarrhine primates of known feeding ecologies to assess the utility of nonocclusal microwear texture variables as indicators of dietary habits. MATERIALS AND METHODS: Buccal microwear texture attributes were collected from high-resolution second molar casts in a sample of seven extant African catarrhine taxa with differing dietary behaviors. A white-light confocal microscope with a 100× objective lens was used to record six microwear texture variables that assess complexity, anisotropy, heterogeneity, and textural fill volume. RESULTS: The physical properties and variation in hardness of ingested foods is reflected by significant differences in the microwear variables on buccal enamel surfaces between species, which is in agreement with early reports using 2D microwear signatures of the same samples. Species that consume hard brittle items showed high buccal enamel complexity and low anisotropy values, while folivorous species that consume tough foods revealed high anisotropy and low complexity enamel patterns. DISCUSSION: Buccal microwear texture analysis on enamel surfaces clearly reflects diet-related variation in nonhuman primates. Our findings indicate that microwear texture attributes on nonworking enamel surfaces provide an alternative procedure for reconstructing dietary behavior when wear facets on occlusal surfaces are lacking.

Body growth and life history in wild mountain gorillas (Gorilla beringei beringei) from Volcanoes National Park, Rwanda.

OBJECTIVES: Great apes show considerable diversity in socioecology and life history, but knowledge of their physical growth in natural settings is scarce. We characterized linear body size growth in wild mountain gorillas from Volcanoes National Park, Rwanda, a population distinguished by its extreme folivory and accelerated life histories. METHODS: In 131 individuals (0.09-35.26 years), we used non-invasive parallel laser photogrammetry to measure body length, back width, arm length and two head dimensions. Nonparametric LOESS regression was used to characterize cross-sectional distance and velocity growth curves for males and females, and consider links with key life history milestones. RESULTS: Sex differences became evident between 8.5 and 10.0 years of age. Thereafter, female growth velocities declined, while males showed increased growth velocities until 10.0-14.5 years across dimensions. Body dimensions varied in growth; females and males reached 98% of maximum body length at 11.7 and 13.1 years, respectively. Females attained 95.3% of maximum body length by mean age at first birth. Neonates were 31% of maternal size, and doubled in size by mean weaning age. Males reached maximum body and arm length and back width before emigration, but experienced continued growth in head dimensions. CONCLUSIONS: While comparable data are scarce, our findings provide preliminary support for the prediction that mountain gorillas reach maximum body size at earlier ages compared to more frugivorous western gorillas. Data from other wild populations are needed to better understand comparative great ape development, and investigate links between trajectories of physical, behavioral, and reproductive maturation.

Molar shape variability in platyrrhine primates.

Recent phylogenetic analyses suggest that platyrrhines constitute a monophyletic group represented by three families: Cebidae, Atelidae, and Pitheciidae. Morphological variability between and within these three families, however, is widely discussed and debated. The aim of this study was to assess molar shape variability in platyrrhines, to explore patterns of interspecific variation among extant species, and to evaluate how molar shape can be used as a taxonomic indicator. The analyses were conducted using standard multivariate analyses of geometric morphometric data from 802 platyrrhine lower molars. The results indicated that the interspecific variation exhibited a highly homoplastic pattern related to functional adaptation of some taxa. However, phylogeny was also an important factor in shaping molar morphological traits, given that some phenotypic similarities were consistent with current phylogenetic positions. Our results show that the phylogenetic and functional signals of lower molar shape vary depending on the taxa and the tooth considered. Based on molar shape, Aotus showed closer similarities to Callicebus, as well as to some Cebidae and Ateles-Lagothrix, due to convergent evolutionary trends caused by similar dietary habits, or due to fast-evolving branches in the Aotus lineage, somewhat similar to the shape of Callicebus and Cebidae.

Phylogenetic signal in molar dental shape of extant and fossil catarrhine primates.

Morphology has been widely used for inferring the phylogenies of numerous taxonomic groups. Recent molecular studies performed on extant non-human primates, however, have cast doubt on the reliability of cranial and postcranial characters for characterizing evolutionary affinities. Because molecular evidence is often not available for fossil specimens, detecting phylogenetic signals in anatomical features is of great relevance. Here we have analyzed molar (M1 and M2) crown shape by means of geometric morphometrics in a large sample of both extant and fossil Miocene catarrhine primates to detect the phylogenetic signal in molar morphometry. Results support that molar shape carries a strong phylogenetic signal, mostly at the superfamily level but also to some extent at the family level. Dietary factors, however, appear to have less influence, especially for M2. The Miocene Pliopithecoidea, Cercopithecoidea, and Hominoidea superfamilies clearly grouped according to the expected taxonomic affinities with the extant groups, although some discrepancies were found depending on the tooth considered. Our findings suggest that although molar crown shape can be used as a reliable proxy for establishing taxonomic affinities of catarrhine fossil primates with extant groups, a significant amount of interspecific variation exists, indicative of derived adaptations at the genus or species level.

Tooth wear and feeding ecology in mountain gorillas from Volcanoes National Park, Rwanda.

OBJECTIVES: Ecological factors have a dramatic effect on tooth wear in primates, although it remains unclear how individual age contributes to functional crown morphology. The aim of this study is to determine how age and individual diet are related to tooth wear in wild mountain gorillas (Gorilla beringei beringei) from Volcanoes National Park, Rwanda. MATERIAL AND METHODS: We calculated the percent of dentine exposure (PDE) for all permanent molars (M1-M3) of known-age mountain gorillas (N = 23), to test whether PDE varied with age using regression analysis. For each molar position, we also performed stepwise multiple linear regression to test the effects of age and percentage of time spent feeding on different food categories on PDE, for individuals subject to long-term observational studies by the Dian Fossey Gorilla Fund International's Karisoke Research Center. RESULTS: PDE increased significantly with age for both sexes in all molars. Moreover, a significant effect of gritty plant root consumption on PDE was found among individuals. Our results support prior reports indicating reduced tooth wear in mountain gorillas compared to western gorillas, and compared to other known-aged samples of primate taxa from forest and savanna habitats. DISCUSSION: Our findings corroborate that mountain gorillas present very low molar wear, and support the hypothesis that age and the consumption of particular food types, namely roots, are significant determinants of tooth wear variation in mountain gorillas. Future research should characterize the mineral composition of the soil in the Virunga habitat, to test the hypothesis that the physical and abrasive properties of gritty foods such as roots influence intra- and interspecific patterns of tooth wear.

Validation of two independent photogrammetric techniques for determining body measurements of gorillas.

The ability to accurately measure morphological characteristics of wild primates in the field is challenging, yet critical for understanding fundamental aspects of their biology and behavior. Recent studies have shown that digital photogrammetry can be used to non-invasively measure morphological traits of wild primates, as it allows for the determination of geometric properties of objects remotely from photographic images. We report here on a rare opportunity to test this methodology by comparing measurements obtained directly from living great apes to those obtained from photographs. We test the accuracy and precision of two independent photogrammetric techniques, employing the use of parallel lasers and a distance meter, respectively, for obtaining measurements of static objects and captive western lowland gorillas (Gorilla gorilla gorilla) (n = 4) at Zoo Atlanta. For static objects, the mean percent error between corresponding measurements collected by the same observer directly versus using photogrammetry was 0.49-0.74% for the parallel laser method and 0.62-0.76% for the distance meter method. For gorillas, mean percent error between corresponding direct and remote measurements was 2.72-5.20% for the parallel laser method and 2.20-7.51% for the distance meter method. Correlations between direct measurements and corresponding parallel laser and distance meter measurements of gorillas were highly significant with R2 values and slopes approaching 1.0 (parallel lasers: R2 = 0.9989, P < 0.0001; distance-meter: R2 = 0.9990, P < 0.0001). Further, variation between measurements of the same targets collected repeatedly by the same observer, and between different observers, was uniformly low across methods (CV, range = 0.003-0.013). While errors are slightly higher for the distance meter technique, both methods show great promise for addressing a wide range of questions requiring the non-invasive collection of morphological data from wild primates. Am. J. Primatol. 78:418-431, 2016. © 2015 Wiley Periodicals, Inc.

Dental shape variability in cercopithecoid primates: a model for the taxonomic attribution of macaques from Roman archaeological contexts.

Morphometric variation of biological structures has been widely used to determine taxonomic affinities among taxa, and teeth are especially informative for both deep phylogenetic relationships and specific ecological signals. We report 2-dimensional geometric morphometrics (GM) analyses of occlusal crown surfaces of lower molars (M1, n = 141; M2, n = 158) of cercopithecoid primate species. A 12-landmark configuration, including cusp tips and 8 points of the molar crown contour, were used to evaluate patterns of variation in lower molar shape among cercopithecoid primates and to predict the taxonomic attribution of 2 archaeological macaques from Roman time periods. The results showed that the lower molar shape of cercopithecoid primates reflects taxonomic affinities, mostly at a subfamily level and close to a tribe level. Thus, the cusp positions and crown contour were important elements of the pattern related to interspecific variation. Additionally, the archaeological specimens, attributed to Macaca sylvanus based on osteological information, were classified using the GM molar shape variability of the cercopithecoid primates studied. The results suggest that their molar shape resembled both M. sylvanus and M. nemestrina, and species attribution varied depending on the comparative sample used.

Savanna chimpanzee (Pan troglodytes) crop feeding at Dindefelo, Senegal: challenges and implications for conservation.

Chimpanzees (Pan troglodytes) are categorized as Endangered by the International Union for Conservation of Nature, and habitat loss due to conversion of land for agriculture is one of the major threats to wild populations of this species. This challenging scenario can lead to negative human-chimpanzee interactions, including crop feeding. Chimpanzees consume crops across their geographical range, although little is known about this behavior in savanna habitats. Here we provide new evidence of crop feeding by savanna chimpanzees. We conducted our observations at Dindefelo, a community nature reserve in southeastern Senegal. The chimpanzees were observed to feed on mango (Mangifera indica) and also on baobab (Adansonia digitata), a wild species considered a crop by local people when found in and around villages. Although local people use the fruits of these species for food and income, they tolerated crop-feeding events until recently. In 2023, a case of harassment of a crop-feeding chimpanzee in a mango orchard was witnessed, and four days later a chimpanzee corpse was found at the same place. We conclude that habitat conversion into agricultural fields, uncontrolled bush fires and extraction of wild fruits are the important factors influencing crop-feeding events at Dindefelo. Our findings highlight the need to better understand human-chimpanzee interactions in the anthropogenic landscape of Dindefelo to help mitigate negative attitudes and behaviors towards chimpanzees.

Genome sequencing as a generic diagnostic strategy for rare disease.

BACKGROUND: To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline genetic diagnosis for rare disease. METHODS: We performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across different workflows, representative of our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide variants and indels < 50 bp), large variants (copy number variants and short tandem repeats) and other variants (structural variants and aneuploidies). Variant calling format files were queried per variant, from which workflow-specific true positive rates (TPRs) for detection were determined. A TPR of ≥ 98% was considered the threshold for transition to GS. A GS-first scenario was generated for our laboratory, using diagnostic efficacy and predicted false negative as primary outcome measures. As input, we modeled the diagnostic path for all 24,570 individuals referred in 2022, combining the clinical referral, the transition of the underlying workflow(s) to GS, and the variant type(s) to be detected. RESULTS: Overall, 95% (1206/1271) of variants were detected. Detection rates differed per variant category: small variants in 96% (826/860), large variants in 93% (341/366), and other variants in 87% (39/45). TPRs varied between workflows (79-100%), with 7/10 being replaceable by GS. Models for our laboratory indicate that a GS-first strategy would be feasible for 84.9% of clinical referrals (750/883), translating to 71% of all individuals (17,444/24,570) receiving GS as their primary test. An estimated false negative rate of 0.3% could be expected. CONCLUSIONS: GS can capture clinically relevant germline variants in a 'GS-first strategy' for the majority of clinical indications in a genetics diagnostic lab.

Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples.

Mobile element insertions (MEIs) are a known cause of genetic disease but have been underexplored due to technical limitations of genetic testing methods. Various bioinformatic tools have been developed to identify MEIs in Next Generation Sequencing data. However, most tools have been developed specifically for genome sequencing (GS) data rather than exome sequencing (ES) data, which remains more widely used for routine diagnostic testing. In this study, we benchmarked six MEI detection tools (ERVcaller, MELT, Mobster, SCRAMble, TEMP2 and xTea) on ES data and on GS data from publicly available genomic samples (HG002, NA12878). For all the tools we evaluated sensitivity and precision of different filtering strategies. Results show that there were substantial differences in tool performance between ES and GS data. MELT performed best with ES data and its combination with SCRAMble increased substantially the detection rate of MEIs. By applying both tools to 10,890 ES samples from Solve-RD and 52,624 samples from Radboudumc we were able to diagnose 10 patients who had remained undiagnosed by conventional ES analysis until now. Our study shows that MELT and SCRAMble can be used reliably to identify clinically relevant MEIs in ES data. This may lead to an additional diagnosis for 1 in 3000 to 4000 patients in routine clinical ES.

The performance of genome sequencing as a first-tier test for neurodevelopmental disorders.

Genome sequencing (GS) can identify novel diagnoses for patients who remain undiagnosed after routine diagnostic procedures. We tested whether GS is a better first-tier genetic diagnostic test than current standard of care (SOC) by assessing the technical and clinical validity of GS for patients with neurodevelopmental disorders (NDD). We performed both GS and exome sequencing in 150 consecutive NDD patient-parent trios. The primary outcome was diagnostic yield, calculated from disease-causing variants affecting exonic sequence of known NDD genes. GS (30%, n = 45) and SOC (28.7%, n = 43) had similar diagnostic yield. All 43 conclusive diagnoses obtained with SOC testing were also identified by GS. SOC, however, required integration of multiple test results to obtain these diagnoses. GS yielded two more conclusive diagnoses, and four more possible diagnoses than ES-based SOC (35 vs. 31). Interestingly, these six variants detected only by GS were copy number variants (CNVs). Our data demonstrate the technical and clinical validity of GS to serve as routine first-tier genetic test for patients with NDD. Although the additional diagnostic yield from GS is limited, GS comprehensively identified all variants in a single experiment, suggesting that GS constitutes a more efficient genetic diagnostic workflow.

Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction.

A significant number of individuals with a rare disorder such as Usher syndrome (USH) and (non-)syndromic autosomal recessive retinitis pigmentosa (arRP) remain genetically unexplained. Therefore, we assessed subjects suspected of USH2A-associated disease and no or mono-allelic USH2A variants using whole genome sequencing (WGS) followed by an improved pipeline for variant interpretation to provide a conclusive diagnosis. One hundred subjects were screened using WGS to identify causative variants in USH2A or other USH/arRP-associated genes. In addition to the existing variant interpretation pipeline, a particular focus was put on assessing splice-affecting properties of variants, both in silico and in vitro. Also structural variants were extensively addressed. For variants resulting in pseudoexon inclusion, we designed and evaluated antisense oligonucleotides (AONs) using minigene splice assays and patient-derived photoreceptor precursor cells. Biallelic variants were identified in 49 of 100 subjects, including novel splice-affecting variants and structural variants, in USH2A or arRP/USH-associated genes. Thirteen variants were shown to affect USH2A pre-mRNA splicing, including four deep-intronic USH2A variants resulting in pseudoexon inclusion, which could be corrected upon AON treatment. We have shown that WGS, combined with a thorough variant interpretation pipeline focused on assessing pre-mRNA splicing defects and structural variants, is a powerful method to provide subjects with a rare genetic condition, a (likely) conclusive genetic diagnosis. This is essential for the development of future personalized treatments and for patients to be eligible for such treatments.