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Bridges Y, de Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JO. Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598672. [PMID: 38915571 PMCID: PMC11195176 DOI: 10.1101/2024.06.13.598672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to measure and is impacted by many factors, for example, ontology structure, annotation completeness or changes to the underlying algorithm. Assertions of the capabilities of VGPAs are often not reproducible, in part because there is no standardised, empirical framework and openly available patient data to assess the efficacy of VGPAs - ultimately hindering the development of effective prioritisation tools. Results In this paper, we present our benchmarking tool, PhEval, which aims to provide a standardised and empirical framework to evaluate phenotype-driven VGPAs. The inclusion of standardised test corpora and test corpus generation tools in the PhEval suite of tools allows open benchmarking and comparison of methods on standardised data sets. Conclusions PhEval and the standardised test corpora solve the issues of patient data availability and experimental tooling configuration when benchmarking and comparing rare disease VGPAs. By providing standardised data on patient cohorts from real-world case-reports and controlling the configuration of evaluated VGPAs, PhEval enables transparent, portable, comparable and reproducible benchmarking of VGPAs. As these tools are often a key component of many rare disease diagnostic pipelines, a thorough and standardised method of assessment is essential for improving patient diagnosis and care.
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Affiliation(s)
- Yasemin Bridges
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Katherina G Cortes
- School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Melissa Haendel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel R Korn
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | | | - James A McLaughlin
- Samples, Phenotypes, and Ontologies (SPOT), European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Peter N Robinson
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Julius Ob Jacobsen
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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Mone F, Abu Subieh H, Doyle S, Hamilton S, Mcmullan DJ, Allen S, Marton T, Williams D, Kilby MD. Evolving fetal phenotypes and clinical impact of progressive prenatal exome sequencing pathways: cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:723-730. [PMID: 34940998 DOI: 10.1002/uog.24842] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVES To determine (1) the diagnostic yield and turnaround time (TAT) of two consecutive prenatal exome sequencing (ES) pathways, (2) the evolution of the fetal phenotype and (3) the clinical impact of detecting causative pathogenic variants and incidental findings. METHODS This was a retrospective cohort analysis of prospectively collected fetal cases that underwent trio ES in the presence of a structural anomaly and normal chromosomal microarray testing in the West Midlands Regional Genetics Laboratory, Birmingham, UK. The study included two phases: (1) between July 2018 and October 2020, the clinical pathway from the Prenatal Assessment of Genomes and Exomes (PAGE) study was adopted and involved prenatal trio ES based on a panel of 1542 development disorder genes and case selection by a multidisciplinary team; (2) between October 2020 and July 2021, prenatal trio ES investigation was based on the National Health Service (NHS) England R21 pathway, with definitive inclusion criteria and a panel of 1205 prenatally relevant genes. Deep phenotyping was performed throughout pregnancy and postnatally. RESULTS A total of 54 cases were included. The diagnostic yield before vs after R21 pathway implementation was 28.0% (7/25) and 55.2% (16/29), respectively (P = 0.04). The respective values for mean TAT were 54.0 days (range, 14-213 days) and 14.2 days (range, 3-29 days). In cases in which a causative pathogenic variant was identified and in which the pregnancy reached the third trimester, additional anomalies were detected between the second and third trimesters in 73.3% (11/15) of cases, predominantly secondary to progressive hydropic features (3/11 (27.3%)), arthrogryposis (3/11 (27.3%)) or brain anomaly (2/11 (18.2%)). In three cases, a variant of uncertain significance was reclassified to likely pathogenic based on postnatal information. Detection of a causative pathogenic variant had a significant clinical impact in 78.3% (18/23) of cases, most frequently affecting decision-making regarding the course of the pregnancy and neonatal management (7/18 (38.9%)). CONCLUSIONS Prenatal ES using the NHS England R21 pathway showed great promise when applied to this cohort, allowing a genetic diagnosis to be made in over half of preselected cases with a fetal structural anomaly on ultrasound. Monitoring and real-time updating of fetal phenotype and reclassification of variants based on postnatal findings is vital to increase the clinical impact that is already evident from this emerging genomic technology. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - H Abu Subieh
- Department of Maternal & Fetal Medicine, Kanad Hospital, Al Ain, Abu Dhabi, United Arab Emirates
| | - S Doyle
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - S Hamilton
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - D J Mcmullan
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - S Allen
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - T Marton
- West Midland's Perinatal Pathology Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - D Williams
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Edgbaston, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, UK
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4
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Umlai UKI, Bangarusamy DK, Estivill X, Jithesh PV. Genome sequencing data analysis for rare disease gene discovery. Brief Bioinform 2021; 23:6366880. [PMID: 34498682 DOI: 10.1093/bib/bbab363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/24/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
Rare diseases occur in a smaller proportion of the general population, which is variedly defined as less than 200 000 individuals (US) or in less than 1 in 2000 individuals (Europe). Although rare, they collectively make up to approximately 7000 different disorders, with majority having a genetic origin, and affect roughly 300 million people globally. Most of the patients and their families undergo a long and frustrating diagnostic odyssey. However, advances in the field of genomics have started to facilitate the process of diagnosis, though it is hindered by the difficulty in genome data analysis and interpretation. A major impediment in diagnosis is in the understanding of the diverse approaches, tools and datasets available for variant prioritization, the most important step in the analysis of millions of variants to select a few potential variants. Here we present a review of the latest methodological developments and spectrum of tools available for rare disease genetic variant discovery and recommend appropriate data interpretation methods for variant prioritization. We have categorized the resources based on various steps of the variant interpretation workflow, starting from data processing, variant calling, annotation, filtration and finally prioritization, with a special emphasis on the last two steps. The methods discussed here pertain to elucidating the genetic basis of disease in individual patient cases via trio- or family-based analysis of the genome data. We advocate the use of a combination of tools and datasets and to follow multiple iterative approaches to elucidate the potential causative variant.
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Affiliation(s)
- Umm-Kulthum Ismail Umlai
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Dhinoth Kumar Bangarusamy
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qGenomics), Barcelona, Catalonia, Spain
| | - Puthen Veettil Jithesh
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
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Zhu F, Zhang F, Hu L, Liu H, Li Y. Integrated Genome and Transcriptome Sequencing to Solve a Neuromuscular Puzzle: Miyoshi Muscular Dystrophy and Early Onset Primary Dystonia in Siblings of the Same Family. Front Genet 2021; 12:672906. [PMID: 34276779 PMCID: PMC8283672 DOI: 10.3389/fgene.2021.672906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Neuromuscular disorders (NMD), many of which are hereditary, affect muscular function. Due to advances in high-throughput sequencing technologies, the diagnosis of hereditary NMDs has dramatically improved in recent years. METHODS AND RESULTS In this study, we report an family with two siblings exhibiting two different NMD, Miyoshi muscular dystrophy (MMD) and early onset primary dystonia (EOPD). Whole exome sequencing (WES) identified a novel monoallelic frameshift deletion mutation (dysferlin: c.4404delC/p.I1469Sfs∗17) in the Dysferlin gene in the index patient who suffered from MMD. This deletion was inherited from his unaffected father and was carried by his younger sister with EOPD. However, immunostaining staining revealed an absence of dysferlin expression in the proband's muscle tissue and thus suggested the presence of the second underlying mutant allele in dysferlin. Using integrated RNA sequencing (RNA-seq) and whole genome sequencing (WGS) of muscle tissue, a novel deep intronic mutation in dysferlin (dysferlin: c.5341-415A > G) was discovered in the index patient. This mutation caused aberrant mRNA splicing and inclusion of an additional pseudoexon (PE) which we termed PE48.1. This PE was inherited from his unaffected mother. PE48.1 inclusion altered the Dysferlin sequence, causing premature termination of translation. CONCLUSION Using integrated genome and transcriptome sequencing, we discovered hereditary MMD and EOPD affecting two siblings of same family. Our results added further weight to the combined use of RNA-seq and WGS as an important method for detection of deep intronic gene mutations, and suggest that integrated sequencing assays are an effective strategy for the diagnosis of hereditary NMDs.
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Affiliation(s)
- Feng Zhu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengxiao Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lizhi Hu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haowen Liu
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yahua Li
- Department of Respiratory Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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6
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Amanat S, Gallego-Martinez A, Lopez-Escamez JA. Genetic Inheritance and Its Contribution to Tinnitus. Curr Top Behav Neurosci 2021; 51:29-47. [PMID: 32705497 DOI: 10.1007/7854_2020_155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tinnitus is the abnormal perception of sound that affects more than 15% of adult population around the globe. Severe tinnitus is considered a complex disorder that arises as result of the interaction of genetic and environmental factors, and it is associated with several comorbidities such as hearing loss, anxiety, and insomnia. We begin this review with an introduction to human molecular genetics and the role of genetic variation on the inheritance. There are some genetic reports on tinnitus heritability including concordance studies in twins and adoptees or aggregation in families providing some evidence for familial aggregation in patients with severe tinnitus and high concordance in monozygotic twins with bilateral tinnitus. So, sex differences in familial aggregation and heritability of bilateral tinnitus suggest a potential sexual dimorphism in tinnitus inheritance.Molecular genetic studies have been demonstrated to be a useful tool to understand the role of genetic variation in rare diseases and complex disorders. The reported associations in common variants in neurotrophic factors such as GDNF, BDNF, or potassium channels genes were underpowered, and the lack of replication questions these findings. Although candidate gene approaches have failed in replicating these genetic associations, the development of high throughput sequencing technology and the selection of extreme phenotypes are strategies that will allow the clinicians and researchers to combine genetic information with clinical data to implement a personalized diagnosis and therapy in patients with tinnitus.
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Affiliation(s)
- Sana Amanat
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain.
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, Granada, Spain.
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, Granada, Spain.
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Gallego-Martinez A, Lopez-Escamez JA. Genetic architecture of Meniere’s disease. Hear Res 2020; 397:107872. [DOI: 10.1016/j.heares.2019.107872] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/12/2019] [Accepted: 12/09/2019] [Indexed: 01/26/2023]
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Oh EH, Shin JH, Cho JW, Choi SY, Choi KD, Choi JH. TRPM7 as a Candidate Gene for Vestibular Migraine. Front Neurol 2020; 11:595042. [PMID: 33193064 PMCID: PMC7649787 DOI: 10.3389/fneur.2020.595042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Objectives: Vestibular migraine (VM) is a common vestibular disorder, and familial aggregation of VM with autosomal-dominant inheritance has been described, which supports a genetic background. This study aimed to describe the clinical phenotype of a family with VM, and identify a candidate gene for VM. Methods: We recruited six individuals (four affected and two unaffected) from three consecutive generations of a Korean family with VM, and performed whole-exome sequencing to search for candidate genes. Results: All affected individuals presented with recurrent vertigo, headache, and nausea/vomiting that fulfilled the diagnostic criteria of VM. Two individuals also experienced transient hemiparesis or dysarthria during the episodes. The symptoms were triggered by physical or emotional stress. Interictal examinations showed uni- or bi-directional horizontal gaze-evoked nystagmus in three of the individuals. They had no causative mutations in genes causing familial hemiplegic migraine or episodic ataxia. Through whole-exome sequencing from three affected individuals, we identified a nonsense mutation c.3526C>T in TRPM7 that encodes a cation channel selective to Ca2+ and Mg2+. Conclusions: Alterations in intracellular Ca2+ and Mg2+ homeostasis by TRPM7 mutation may contribute to the development of the VM phenotype. Our result suggest that TRPM7 is a novel candidate gene for VM.
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Affiliation(s)
- Eun Hye Oh
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jin-Hong Shin
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Jae Wook Cho
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Seo-Young Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Kwang-Dong Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Jae-Hwan Choi
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
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Episodic Vestibular Syndrome with Hyperventilation-Induced Downbeat Nystagmus. THE CEREBELLUM 2020; 20:796-803. [PMID: 33083962 DOI: 10.1007/s12311-020-01204-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Hyperventilation-induced downbeat nystagmus (HV-DBN) has been reported in cerebellar disorders and explained by a loss of the inhibitory cerebellar output via a metabolic effect on cerebellar Ca2+ channels. The aim of this study was to determine the clinical characteristics and underlying pathogenesis of episodic vestibular syndrome (EVS) with HV-DBN. Of 667 patients with EVS, we recruited 22 with HV-DBN and assessed their clinical characteristics, video-oculographic findings, and the results of molecular genetic analyses. The age at symptom onset was 47.5 ± 13.0 years (mean ± SD), and there was a female preponderance (n = 15, 68%). The duration of vertigo/dizziness attacks ranged from minutes to a few days, and 11 patients (50%) fulfilled the diagnostic criteria for vestibular migraine. HV-induced new-onset DBN in 8 patients, while the remaining 14 showed augmentation of spontaneous DBN by HV. The maximum slow-phase velocity of HV-DBN ranged from 2.2 to 11.9°/s, which showed a statistical difference with that of spontaneous DBN (median = 4.95, IQR = 3.68-6.55 vs. median = 1.25, IQR = 0.20-2.15, p < 0.001). HV-DBN was either purely downbeat (n = 11) or accompanied with small horizontal components (n = 11). Other neuro-otologic findings included perverted head-shaking nystagmus (n = 11), central positional nystagmus (n = 7), saccadic pursuit (n = 3), and horizontal gaze-evoked nystagmus (n = 1). Gene expression profiling with a bioinformatics analysis identified 43 upregulated and 49 downregulated differentially expressed genes (DEGs) in patients with EVS and HV-DBN and revealed that the downregulated DEGs were significantly enriched in terms related to the ribosome pathway. Our results suggest that the underlying cerebellar dysfunction would be responsible for paroxysmal attacks of vertigo in patients with EVS and HV-DBN.
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Tomar S, Sethi R, Lai PS. Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing. Eur J Hum Genet 2019; 27:1389-1397. [PMID: 31053788 DOI: 10.1038/s41431-019-0412-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022] Open
Abstract
Selection and prioritization of phenotype-centric variants remains a challenging part of variant analysis and interpretation in clinical exome sequencing. Phenotype-driven shortlisting of patient-specific gene lists can avoid missed diagnosis. Here, we analyzed the relevance of using primary Human Phenotype Ontology identifiers (HPO IDs) in prioritizing Mendelian disease genes across 30 in-house, 10 previously reported, and 10 recently published cases using three popular web-based gene prioritization tools (OMIMExplorer, VarElect & Phenolyzer). We assessed partial HPO-based gene prioritization using randomly chosen and top 10%, 30%, and 50% HPO IDs based on information content and found high variance within rank ratios across the former vs the latter. This signified that randomly selected less-specific HPO IDs for a given disease phenotype performed poorly by ranking probe gene farther away from the top rank. In contrast, the use of top 10%, 30%, and 50% HPO IDs individually could rank the probe gene among the top 1% in the ranked list of genes that was equivalent to the results when the full list of HPO IDs were used. Hence, we conclude that use of just the top 10% of HPO IDs chosen based on information content is sufficient for ranking the probe gene at top position. Our findings provide practical guidance for utilizing structured phenotype semantics and web-based gene-ranking tools to aid in identifying known as well unknown candidate gene associations in Mendelian disorders.
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Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System (NUHS), 1E Kent Ridge Road, 119228, Singapore.
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Zhu Z, Han X, Wang Y, Liu W, Lu Y, Xu C, Wang X, Hao L, Song Y, Huang S, Rizak JD, Li Y, Han C. Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans. Front Genet 2019; 10:28. [PMID: 30778368 PMCID: PMC6369210 DOI: 10.3389/fgene.2019.00028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
Previous studies have found that fecundity is a multigenic trait regulated, in part, by mitochondrial-nuclear (mit-n) genetic interactions. However, the identification of specific nuclear genetic loci or genes interacting with the mitochondrial genome and contributing to the quantitative trait fecundity is an unsolved issue. Here, a panel of recombinant inbred advanced intercrossed lines (RIAILs), established from a cross between the N2 and CB4856 strains of C. elegans, were used to characterize the underlying genetic basis of mit-n genetic interactions related to fecundity. Sixty-seven single nucleotide polymorphisms (SNPs) were identified by association mapping to be linked with fecundity among 115 SNPs linked to mitotype. This indicated significant epistatic effects between nuclear and mitochondria genetics on fecundity. In addition, two specific nuclear genetic loci interacting with the mitochondrial genome and contributing to fecundity were identified. A significant reduction in fecundity was observed in the RIAILs that carried CB4856 mitochondria and a N2 genotype at locus 1 or a CB4856 genotype at locus 2 relative to the wild-type strains. Then, a hybrid strain (CNC10) was established, which was bred as homoplasmic for the CB4856 mtDNA genome and N2 genotype at locus 1 in the CB4856 nuclear background. The mean fecundity of CNC10 was half the fecundity of the control strain. Several functional characteristics of the mitochondria in CNC10 were also influenced by mit-n interactions. Overall, experimental evidence was presented that specific nuclear genetic loci or genes have interactions with the mitochondrial genome and are associated with fecundity. In total, 18 genes were identified using integrative approaches to have interactions with the mitochondrial genome and to contribute to fecundity.
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Affiliation(s)
- Zuobin Zhu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xiaoxiao Han
- Center of Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuechen Wang
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Wei Liu
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Yue Lu
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Chang Xu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xitao Wang
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yuanjian Song
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Shi Huang
- School of Life Sciences, Xiangya Medical School, Central South University, Changsha, China
| | | | - Ying Li
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Conghui Han
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, China
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Ahmad H, Requena T, Frejo L, Cobo M, Gallego-Martinez A, Martin F, Lopez-Escamez JA, Bronstein AM. Clinical and Functional Characterization of a Missense ELF2 Variant in a CANVAS Family. Front Genet 2018; 9:85. [PMID: 29628936 PMCID: PMC5876245 DOI: 10.3389/fgene.2018.00085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/28/2018] [Indexed: 12/30/2022] Open
Abstract
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is a rare disorder with an unknown etiology. We present a British family with presumed autosomal dominant CANVAS with incomplete penetrance and variable expressivity. Exome sequencing identified a rare missense variant in the ELF2 gene at chr4:g.140058846 C > T, c.10G > A, p.A4T which segregated in all affected patients. By using transduced BE (2)-M17 cells, we found that the mutated ELF2 (mt-ELF2) gene increased ATXN2 and reduced ELOVL5 gene expression, the causal genes of type 2 and type 38 spinocerebellar ataxias. Both, western blot and confocal microscopy confirmed an increase of ataxin-2 in BE(2)-M17 cells transduced with lentivirus expressing mt-ELF2 (CEE-mt-ELF2), which was not observed in cells transduced with lentivirus expressing wt-ELF2 (CEE-wt-ELF2). Moreover, we observed a significant decrease in the number and size of lipid droplets in the CEE-mt-ELF2-transduced BE (2)-M17 cells, but not in the CEE-wt-ELF2-transduced BE (2)-M17. Furthermore, changes in the expression of ELOVL5 could be related with the reduction of lipid droplets in BE (2)-M17 cells. This work supports that ELF2 gene regulates the expression of ATXN2 and ELOVL5 genes, and defines new molecular links in the pathophysiology of cerebellar ataxias.
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Affiliation(s)
- Hena Ahmad
- Division of Brain Sciences, Imperial College, Charing Cross Hospital, London, United Kingdom.,National Hospital for Neurology & Neurosurgery, London, United Kingdom
| | - Teresa Requena
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Lidia Frejo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Marien Cobo
- Gene and Cell Therapy Group, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Francisco Martin
- Gene and Cell Therapy Group, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Universidad de Granada, Granada, Spain
| | - Adolfo M Bronstein
- Division of Brain Sciences, Imperial College, Charing Cross Hospital, London, United Kingdom.,National Hospital for Neurology & Neurosurgery, London, United Kingdom
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