Next-generation diagnostics and disease-gene discovery with the Exomiser

Smedley, Damian; Jacobsen, Julius O. B.; Jäger, Marten; Köhler, Sebastian; Holtgrewe, Manuel; Schubach, Max; Siragusa, Enrico; Żemojtel, Tomasz; Buske, Orion J.; Washington, Nicole; Bone, William P.; Haendel, Melissa; Robinson, Peter N.

doi:10.1038/nprot.2015.124

Cited by 311 publications

(280 citation statements)

References 79 publications

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“…First, the diagnostic service is provisioned for worldwide referral institutions on a singleton basis and there are no prespecified criteria for the clinical phenotyping of referred individuals. Detailed clinical phenotyping in complement to genomic analysis has been shown to discover and accelerate diagnoses in the clinic 24 25. Second, the 105 gene enrichment does not include all genes that are now known as a cause of IRD, and application of whole exome sequencing (WES) or whole genome sequencing (WGS) techniques to individuals without a molecular diagnosis has identified variants in other genes as a cause of disease, for example, mutations in IQCB1 identified through WES 26.…”

Section: Discussionmentioning

confidence: 99%

Molecular findings from 537 individuals with inherited retinal disease

et al. 2016

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Background Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. Methods We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). Results Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. Conclusions Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.

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Section: Discussionmentioning

confidence: 99%

Molecular findings from 537 individuals with inherited retinal disease

et al. 2016

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“…The strong clinical suspicion of a mitochondrial etiology in Case 3 allowed elimination of variants of uncertain significance from the ES report, and drove ES reanalysis for plausible new gene candidates. An emerging alternative to requesting reanalysis through the clinical laboratory is to use publicly available software (e.g., AMELIE (Birgmeier et al, ), Exomiser (Smedly et al, )) that uses sequencing files, variant call files, candidate gene lists, or candidate variant lists and patient phenotype terms (e.g., HPO terms) to rank patient variants by suspicion for disease/diagnosis. Due to advances in knowledge and publicly available large genetic databases, reassessment of variants and genetic data can identify candidates for additional analysis.…”

Section: Discussionmentioning

confidence: 99%

A toolkit for genetics providers in follow‐up of patients with non‐diagnostic exome sequencing

Zastrow

Kohler

Bonner

et al. 2019

Journal of Genetic Counseling

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There are approximately 7,000 rare diseases affecting 25–30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up‐to‐date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%–41% of the patients receive a molecular diagnosis. The remaining three‐fifths to three‐quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non‐diagnostic ES results, but strategic follow‐up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow‐up of cases where ES is non‐diagnostic. Solved case examples illustrate different types of non‐diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype‐disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.

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“…We chose to use VCF files as input to our algorithm, since VCF files with variants called from exome or genome sequencing data are commonly used as a standard format for interpretive software such as Exomiser [24–26]. We, therefore, developed an algorithm to postprocess VCF files from WGS to identify REF-HAP and ALT-HAP genotypes and to flag ASDP-associated variant calls.…”

Section: Resultsmentioning

confidence: 99%

Alternate-locus aware variant calling in whole genome sequencing

et al. 2016

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BackgroundThe last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. The new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS).MethodsWe developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions. We investigate 121 in-house WGS datasets that have been aligned to the GRCh37 and GRCh38 assemblies.ResultsWe show that stretches of sequences that are largely but not entirely identical between the primary assembly and an alternate locus can result in multiple variant calls against regions of the primary assembly. In WGS analysis, this results in characteristic and recognizable patterns of variant calls at positions that we term alignable scaffold-discrepant positions (ASDPs). In 121 in-house genomes, on average 51.8±3.8 of the 178 regions were found to correspond best to an alternate locus rather than the primary assembly sequence, and filtering these genomes with our algorithm led to the identification of 7863 variant calls per genome that colocalized with ASDPs. Additionally, we found that 437 of 791 genome-wide association study hits located within one of the regions corresponded to ASDPs.ConclusionsOur algorithm uses the information contained in the 178 structurally variable regions of the GRCh38 genome assembly to avoid spurious variant calls in cases where samples contain an alternate locus rather than the corresponding segment of the primary assembly. These results suggest the great potential of fully incorporating the resources of graph-like genome assemblies into variant calling, but also underscore the importance of developing computational resources that will allow a full reconstruction of the genotype in personal genomes. Our algorithm is freely available at https://github.com/charite/asdpex.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-016-0383-z) contains supplementary material, which is available to authorized users.

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Next-generation diagnostics and disease-gene discovery with the Exomiser

Cited by 311 publications

References 79 publications

Molecular findings from 537 individuals with inherited retinal disease

Molecular findings from 537 individuals with inherited retinal disease

A toolkit for genetics providers in follow‐up of patients with non‐diagnostic exome sequencing

Alternate-locus aware variant calling in whole genome sequencing

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