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Gul I, Khan TA, Akbar NU, Gul N, Ali R, Khan SN. Novel mutations in CYBB Gene Cause X-linked chronic Granulomatous Disease in Pakistani patients. Ital J Pediatr 2023; 49:95. [PMID: 37533075 PMCID: PMC10399011 DOI: 10.1186/s13052-023-01496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/10/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Chronic Granulomatous Disease (CGD) is a primary immunodeficiency that causes susceptibility to recurrent fungal and bacterial infections. The CYBB gene encodes gp91phox component of the Phagocytic Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and specifically, X-linked CGD is caused by mutations in the CYBB gene, located on the X chromosome. The aim of the study was to characterize functional and genetic mutations in X-linked CGD. METHODS Functional analysis was conducted on the whole blood of seventeen male individuals who were suspected to have X-linked chronic granulomatous disease (CGD). Flow cytometry was employed to assess the capacity of NADPH oxidase, measuring both H2O2 production and gp91phox protein expression in neutrophils. Additionally, DNA Sanger sequencing was performed for genetic analysis. The pathogenicity of novel mutations was assessed by pathogenicity prediction tools. RESULT Among the seventeen patients evaluated, five patients (P1, P2, P3, P4, and P5) displayed impaired H2O2 production by their neutrophils upon stimulation with Phorbol myristate acetate (PMA), accompanied by abnormal gp91phox expression. DNA sequencing of the CYBB gene identified specific mutations in each patient. In P1 and P2 (previously reported cases), a hemizygous missense mutation, c.925G > A/p.E309K was identified. In P3 and P4 (novel cases), hemizygous nonsense mutations, c.216T > A/p.C72X were found. Lastly, in P5 (also a novel case), a hemizygous missense mutation, c.732T > G/p.C244W was detected. These mutations reside in exons 9,3 and 7 of the CYBB gene, respectively. CONCLUSIONS The current study contributes to the understanding of the clinical and genetic spectrum associated with X-linked chronic granulomatous disease (CGD). It highlights the significance of early diagnosis in CGD and emphasizes the importance of lifelong prophylaxis to prevent severe infections.
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Affiliation(s)
- Irum Gul
- Department of Zoology, Kohat University of Science and Technology, 26000, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, 25160, Peshawar, Pakistan.
| | - Noor Ul Akbar
- Department of Zoology, Kohat University of Science and Technology, 26000, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Naila Gul
- Department of Zoology, Kohat University of Science and Technology, 26000, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Rehman Ali
- Department of Zoology, Kohat University of Science and Technology, 26000, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, 26000, Kohat, Khyber Pakhtunkhwa, Pakistan.
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Feng W, Lopez JR, Antrobus S, Zheng J, Uryash A, Dong Y, Beqollari D, Bannister RA, Hopkins PM, Beam KG, Allen PD, Pessah IN. Putative malignant hyperthermia mutation Ca V1.1-R174W is insufficient to trigger a fulminant response to halothane or confer heat stress intolerance. J Biol Chem 2023; 299:104992. [PMID: 37392848 PMCID: PMC10413282 DOI: 10.1016/j.jbc.2023.104992] [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: 04/04/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023] Open
Abstract
Malignant hyperthermia susceptibility (MHS) is an autosomal dominant pharmacogenetic disorder that manifests as a hypermetabolic state when carriers are exposed to halogenated volatile anesthetics or depolarizing muscle relaxants. In animals, heat stress intolerance is also observed. MHS is linked to over 40 variants in RYR1 that are classified as pathogenic for diagnostic purposes. More recently, a few rare variants linked to the MHS phenotype have been reported in CACNA1S, which encodes the voltage-activated Ca2+ channel CaV1.1 that conformationally couples to RyR1 in skeletal muscle. Here, we describe a knock-in mouse line that expresses one of these putative variants, CaV1.1-R174W. Heterozygous (HET) and homozygous (HOM) CaV1.1-R174W mice survive to adulthood without overt phenotype but fail to trigger with fulminant malignant hyperthermia when exposed to halothane or moderate heat stress. All three genotypes (WT, HET, and HOM) express similar levels of CaV1.1 by quantitative PCR, Western blot, [3H]PN200-110 receptor binding and immobilization-resistant charge movement densities in flexor digitorum brevis fibers. Although HOM fibers have negligible CaV1.1 current amplitudes, HET fibers have similar amplitudes to WT, suggesting a preferential accumulation of the CaV1.1-WT protein at triad junctions in HET animals. Never-the-less both HET and HOM have slightly elevated resting free Ca2+ and Na+ measured with double barreled microelectrode in vastus lateralis that is disproportional to upregulation of transient receptor potential canonical (TRPC) 3 and TRPC6 in skeletal muscle. CaV1.1-R174W and upregulation of TRPC3/6 alone are insufficient to trigger fulminant malignant hyperthermia response to halothane and/or heat stress in HET and HOM mice.
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Affiliation(s)
- Wei Feng
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA
| | - Jose R Lopez
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA; Department of Research, Mount Sinai Medical Center, Miami Beach, Florida, USA
| | - Shane Antrobus
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA
| | - Jing Zheng
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA
| | - Arkady Uryash
- Department of Research, Mount Sinai Medical Center, Miami Beach, Florida, USA
| | - Yao Dong
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA
| | - Donald Beqollari
- Department of Medicine-Cardiology Division, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Roger A Bannister
- Department of Medicine-Cardiology Division, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Philip M Hopkins
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Kurt G Beam
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Paul D Allen
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA; Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Isaac N Pessah
- Department of Molecular Biosciences, University of California Davis, Davis, California, USA.
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Ding X, Singh P, Schimenti K, Tran TN, Fragoza R, Hardy J, Orwig KE, Olszewska M, Kurpisz MK, Yatsenko AN, Conrad DF, Yu H, Schimenti JC. In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes. Proc Natl Acad Sci U S A 2023; 120:e2219925120. [PMID: 37459509 PMCID: PMC10372637 DOI: 10.1073/pnas.2219925120] [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: 11/22/2022] [Accepted: 05/25/2023] [Indexed: 07/20/2023] Open
Abstract
Infertility is a heterogeneous condition, with genetic causes thought to underlie a substantial fraction of cases. Genome sequencing is becoming increasingly important for genetic diagnosis of diseases including idiopathic infertility; however, most rare or minor alleles identified in patients are variants of uncertain significance (VUS). Interpreting the functional impacts of VUS is challenging but profoundly important for clinical management and genetic counseling. To determine the consequences of these variants in key fertility genes, we functionally evaluated 11 missense variants in the genes ANKRD31, BRDT, DMC1, EXO1, FKBP6, MCM9, M1AP, MEI1, MSH4 and SEPT12 by generating genome-edited mouse models. Nine variants were classified as deleterious by most functional prediction algorithms, and two disrupted a protein-protein interaction (PPI) in the yeast two hybrid (Y2H) assay. Though these genes are essential for normal meiosis or spermiogenesis in mice, only one variant, observed in the MCM9 gene of a male infertility patient, compromised fertility or gametogenesis in the mouse models. To explore the disconnect between predictions and outcomes, we compared pathogenicity calls of missense variants made by ten widely used algorithms to 1) those annotated in ClinVar and 2) those evaluated in mice. All the algorithms performed poorly in terms of predicting the effects of human missense variants modeled in mice. These studies emphasize caution in the genetic diagnoses of infertile patients based primarily on pathogenicity prediction algorithms and emphasize the need for alternative and efficient in vitro or in vivo functional validation models for more effective and accurate VUS description to either pathogenic or benign categories.
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Affiliation(s)
- Xinbao Ding
- College of Veterinary Medicine, Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Priti Singh
- College of Veterinary Medicine, Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Kerry Schimenti
- College of Veterinary Medicine, Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Tina N. Tran
- College of Veterinary Medicine, Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - Jimmaline Hardy
- School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA15213
| | - Kyle E. Orwig
- School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA15213
| | - Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan60-479, Poland
| | - Maciej K. Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan60-479, Poland
| | - Alexander N. Yatsenko
- School of Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA15213
| | - Donald F. Conrad
- Oregon Health & Science University, Division of Genetics, Oregon National Primate Research Center, Beaverton, OR97006
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - John C. Schimenti
- College of Veterinary Medicine, Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
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Parada-Márquez JF, Maldonado-Rodriguez ND, Triana-Fonseca P, Contreras-Bravo NC, Calderón-Ospina CA, Restrepo CM, Morel A, Ortega-Recalde OJ, Silgado-Guzmán DF, Angulo-Aguado M, Fonseca-Mendoza DJ. Pharmacogenomic profile of actionable molecular variants related to drugs commonly used in anesthesia: WES analysis reveals new mutations. Front Pharmacol 2023; 14:1047854. [PMID: 37021041 PMCID: PMC10069477 DOI: 10.3389/fphar.2023.1047854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Genetic interindividual variability is associated with adverse drug reactions (ADRs) and affects the response to common drugs used in anesthesia. Despite their importance, these variants remain largely underexplored in Latin-American countries. This study describes rare and common variants found in genes related to metabolism of analgesic and anaesthetic drug in the Colombian population. Methods: We conducted a study that included 625 Colombian healthy individuals. We generated a subset of 14 genes implicated in metabolic pathways of common medications used in anesthesia and assessed them by whole-exome sequencing (WES). Variants were filtered using two pipelines: A) novel or rare (minor allele frequency-MAF <1%) variants including missense, loss-of-function (LoF, e.g., frameshift, nonsense), and splice site variants with potential deleterious effect and B) clinically validated variants described in the PharmGKB (categories 1, 2 and 3) and/or ClinVar databases. For rare and novel missense variants, we applied an optimized prediction framework (OPF) to assess the functional impact of pharmacogenetic variants. Allelic, genotypic frequencies and Hardy-Weinberg equilibrium were calculated. We compare our allelic frequencies with these from populations described in the gnomAD database. Results: Our study identified 148 molecular variants potentially related to variability in the therapeutic response to 14 drugs commonly used in anesthesiology. 83.1% of them correspond to rare and novel missense variants classified as pathogenic according to the pharmacogenetic optimized prediction framework, 5.4% were loss-of-function (LoF), 2.7% led to potential splicing alterations and 8.8% were assigned as actionable or informative pharmacogenetic variants. Novel variants were confirmed by Sanger sequencing. Allelic frequency comparison showed that the Colombian population has a unique pharmacogenomic profile for anesthesia drugs with some allele frequencies different from other populations. Conclusion: Our results demonstrated high allelic heterogeneity among the analyzed sampled, enriched by rare (91.2%) variants in pharmacogenes related to common drugs used in anesthesia. The clinical implications of these results highlight the importance of implementation of next-generation sequencing data into pharmacogenomic approaches and personalized medicine.
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Affiliation(s)
| | | | - Paula Triana-Fonseca
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Carlos Alberto Calderón-Ospina
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Carlos M. Restrepo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Oscar Javier Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | | | - Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Mariana Angulo-Aguado, ; Dora Janeth Fonseca-Mendoza,
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Mariana Angulo-Aguado, ; Dora Janeth Fonseca-Mendoza,
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Liu Y, Yeung WSB, Chiu PCN, Cao D. Computational approaches for predicting variant impact: An overview from resources, principles to applications. Front Genet 2022; 13:981005. [PMID: 36246661 PMCID: PMC9559863 DOI: 10.3389/fgene.2022.981005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
One objective of human genetics is to unveil the variants that contribute to human diseases. With the rapid development and wide use of next-generation sequencing (NGS), massive genomic sequence data have been created, making personal genetic information available. Conventional experimental evidence is critical in establishing the relationship between sequence variants and phenotype but with low efficiency. Due to the lack of comprehensive databases and resources which present clinical and experimental evidence on genotype-phenotype relationship, as well as accumulating variants found from NGS, different computational tools that can predict the impact of the variants on phenotype have been greatly developed to bridge the gap. In this review, we present a brief introduction and discussion about the computational approaches for variant impact prediction. Following an innovative manner, we mainly focus on approaches for non-synonymous variants (nsSNVs) impact prediction and categorize them into six classes. Their underlying rationale and constraints, together with the concerns and remedies raised from comparative studies are discussed. We also present how the predictive approaches employed in different research. Although diverse constraints exist, the computational predictive approaches are indispensable in exploring genotype-phenotype relationship.
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Affiliation(s)
- Ye Liu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S. B. Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Philip C. N. Chiu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- *Correspondence: Philip C. N. Chiu, ; Dandan Cao,
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- *Correspondence: Philip C. N. Chiu, ; Dandan Cao,
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6
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Referral indications for malignant hyperthermia susceptibility diagnostics in patients without adverse anesthetic events in the era of next-generation sequencing. Anesthesiology 2022; 136:940-953. [PMID: 35285867 DOI: 10.1097/aln.0000000000004199] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The introduction of next-generation sequencing into the diagnosis of neuromuscular disorders has resulted in an increased number of newly identified RYR1 variants. We hypothesize that there is an increased referral of patients to Malignant Hyperthermia (MH)-units without a personal/family history of adverse anesthetic events suspected for MH. This retrospective multicenter cohort study evaluates patient referral indications and outcomes for those without a history of an adverse anesthetic event. METHODS Patients referred between 2010-2019 to the MH-units in Antwerp, Lund, Nijmegen and Toronto were included. Previously tested patients and relatives of previously tested patients were excluded. Data collection included demographics, referral details, muscle contracture and genetic testing results including REVEL scores. Referral indications were categorized into those with a personal/family history of adverse anesthetic event and other indications including exertional and/or recurrent rhabdomyolysis, RYR1 variant(s) detected in diagnostic testing in the neuromuscular clinic without a specific diagnosis (in a family member), diagnosed RYR1-related myopathy (in a family member), idiopathically elevated resting creatine kinase values, exertional heat stroke and other. RESULTS A total of 520 medical records were included, with the three most frequent referral indications; personal history of an adverse anesthetic event (211/520; 40.6%), family history of an adverse anesthetic event (115/520; 22.1%), and exertional and/or recurrent rhabdomyolysis (46/520; 8.8%). The proportion of patients referred without a personal/family history of an adverse anesthetic event increased to 43.6% (133/305) between 2015-2019 compared to 28.4% (61/215) in 2010-2014 (P<0.001). Patients with a personal/family history of an adverse anesthetic event were more frequently diagnosed as MH susceptible (133/220; 60.5%) than those without (47/120; 39.2%), (P < 0.001). Due to missing data, 180 medical records were excluded. CONCLUSION The proportion of patients referred to MH-units without a personal/family history of an adverse anesthetic event has increased, with 39.2% (47/120) diagnosed as MH susceptible.
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McConnell H, Andrews TD, Field MA. Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants. PeerJ 2021; 9:e11774. [PMID: 34316407 PMCID: PMC8286708 DOI: 10.7717/peerj.11774] [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: 07/01/2020] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Background Pharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools-these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect. Methods Here we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations. Results As previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as 'benign'. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as 'benign'. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms. Conclusion In this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice.
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Affiliation(s)
- Hannah McConnell
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - T Daniel Andrews
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, Australia.,Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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Kristan A, Gašperšič J, Režen T, Kunej T, Količ R, Vuga A, Fink M, Žula Š, Anžej Doma S, Preložnik Zupan I, Pajič T, Podgornik H, Debeljak N. Genetic analysis of 39 erythrocytosis and hereditary hemochromatosis-associated genes in the Slovenian family with idiopathic erythrocytosis. J Clin Lab Anal 2021; 35:e23715. [PMID: 33534944 PMCID: PMC8059723 DOI: 10.1002/jcla.23715] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/10/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Erythrocytosis is a condition with an excessive number of erythrocytes, accompanied by an elevated haemoglobin and/or haematocrit value. Congenital erythrocytosis has a diverse genetic background with several genes involved in erythropoiesis. In clinical practice, nine genes are usually examined, but in approximately 70% of patients, no causative mutation can be identified. In this study, we screened 39 genes, aiming to identify potential disease-driving variants in the family with erythrocytosis of unknown cause. PATIENTS AND METHODS Two affected family members with elevated haemoglobin and/or haematocrit and negative for acquired causes and one healthy relative from the same family were selected for molecular-genetic analysis of 24 erythrocytosis and 15 hereditary haemochromatosis-associated genes with targeted NGS. The identified variants were further analysed for pathogenicity using various bioinformatic tools and review of the literature. RESULTS Of the 12 identified variants, two heterozygous variants, the missense variant c.471G>C (NM_022051.2) (p.(Gln157His)) in the EGLN1 gene and the intron variant c.2572-13A>G (NM_004972.3) in the JAK2 gene, were classified as low-frequency variants in European population. None of the two variants were present in a healthy family member. Variant c.2572-13A>G has potential impact on splicing by one prediction tool. CONCLUSION For the first time, we included 39 genes in the erythrocytosis clinical panel and identified two potential disease-driving variants in the Slovene family studied. Based on the reported functional in vitro studies combined with our bioinformatics analysis, we suggest further functional analysis of variant in the JAK2 gene and evaluation of a cumulative effect of both variants.
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Affiliation(s)
- Aleša Kristan
- Medical Centre for Molecular BiologyFaculty of MedicineInstitute of Biochemistry and Molecular GeneticsUniversity of LjubljanaLjubljanaSlovenia
| | - Jernej Gašperšič
- Medical Centre for Molecular BiologyFaculty of MedicineInstitute of Biochemistry and Molecular GeneticsUniversity of LjubljanaLjubljanaSlovenia
| | - Tadeja Režen
- Centre for Functional Genomics and Bio‐ChipsFaculty of MedicineInstitute of Biochemistry and Molecular GeneticsUniversity of LjubljanaLjubljanaSlovenia
| | - Tanja Kunej
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Rok Količ
- Kemomed Research and DevelopmentKemomed LtdKranjSlovenia
| | - Andrej Vuga
- Kemomed Research and DevelopmentKemomed LtdKranjSlovenia
| | - Martina Fink
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
| | - Špela Žula
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
| | - Saša Anžej Doma
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
| | - Irena Preložnik Zupan
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
- Department of Internal MedicineFaculty of MedicineUniversity of LjubljanaLjubljanaSlovenia
| | - Tadej Pajič
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
- Clinical Institute of Genomic MedicineUniversity Medical Centre LjubljanaLjubljanaSlovenia
| | - Helena Podgornik
- Clinical Department of HaematologyUniversity Medical Centre LjubljanaLjubljanaSlovenia
- Chair of Clinical BiochemistryFaculty of PharmacyUniversity of LjubljanaLjubljanaSlovenia
| | - Nataša Debeljak
- Medical Centre for Molecular BiologyFaculty of MedicineInstitute of Biochemistry and Molecular GeneticsUniversity of LjubljanaLjubljanaSlovenia
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9
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Relevance of pathogenicity prediction tools in human RYR1 variants of unknown significance. Sci Rep 2021; 11:3445. [PMID: 33564012 PMCID: PMC7873245 DOI: 10.1038/s41598-021-82024-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle metabolism characterized by generalized muscle rigidity, increased body temperature, rhabdomyolysis, hyperkalemia and severe metabolic acidosis. The underlying mechanism of MH involves excessive Ca2+ release from myotubes via the ryanodine receptor type 1 (RYR1) and the voltage-dependent L-type calcium channel (CACNA1S). As more than 300 variants of unknown significance have been detected to date, we examined whether freely available pathogenicity prediction tools are able to detect relevant MH causing variants. In this diagnostic accuracy study, blood samples from 235 individuals with a history of a clinical malignant hyperthermia or their close relatives were genetically screened for RYR1 variants of all 106 RYR1 exons and additionally for known variants of CACNA1S. In vitro contracture tests were conducted on muscle biopsies obtained from all individuals, independently of whether a pathogenic variant, a variant of unknown significance or no variant was detected. Comparisons were made to three established bioinformatic pathogenicity detection tools to identify the clinical impact of the variants of unknown significance. All detected genetic variants were tested for pathogenicity by three in silico approaches and compared to the in vitro contracture test. Sensitivity and specificity of exon screening of all individuals listed in our MH database was analyzed. Exon screening identified 97 (41%) of the 235 individuals as carriers of pathogenic variants. Variants of unknown significance were detected in 21 individuals. Variants of unknown significance were subdivided into 19 malignant-hyperthermia-susceptible individuals and 2 non-malignant-hyperthermia-susceptible individuals. All pathogenic variants as well as the malignant-hyperthermia-suspectible variants were correctly identified by the bioinformatic prediction tools. Sensitivity of in silico approaches ranged between 0.71 and 0.98 (Polyphen 0.94 [CI 95% 0.75; 0.99]; Sift 0.98 [CI 95% 0.81; 0.99]; MutationTaster 0.92 [CI 95% 0.75; 0.99]). Specificity differed depending on the used tool (Polphen 0.98 [CI 95% 0.32; 0.99]; Sift 0.98 [CI 95% 0.32; 0.99]; MutationTaster 0.00 [CI 95% 0.00; 0.60]). All pathogenic variants and variants of unknown significance were scored as probably damaging in individuals, demonstrating a high sensitivity. Specificity was very low in one of the three tested programs. However, due to potential genotype–phenotype discordance, bioinformatic prediction tools are currently of limited value in diagnosing pathogenicity of MH-susceptible variants.
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Jaravine V, Balmford J, Metzger P, Boerries M, Binder H, Boeker M. Annotation of Human Exome Gene Variants with Consensus Pathogenicity. Genes (Basel) 2020; 11:E1076. [PMID: 32938008 PMCID: PMC7563776 DOI: 10.3390/genes11091076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022] Open
Abstract
A novel approach is developed to address the challenge of annotating with phenotypic effects those exome variants for which relevant empirical data are lacking or minimal. The predictive annotation method is implemented as a stacked ensemble of supervised base-learners, including distributed random forest and gradient boosting machines. Ensemble models were trained and cross-validated on evidence-based categorical variant effect annotations from the ClinVar database, and were applied to 84 million non-synonymous single nucleotide variants (SNVs). The consensus model combined 39 functional mutation impacts, cross-species conservation score, and gene indispensability score. The indispensability score, accounting for differences in variant pathogenicities including in essential and mutation-tolerant genes, considerably improved the predictions. The consensus combination is consistent with as many input scores as possible while minimizing false predictions. The input scores are ranked based on their ability to predict effects. The score rankings and categorical phenotypic variant effect predictions are aimed for direct use in clinical and biological applications to prioritize human exome variants and mutations.
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Affiliation(s)
- Victor Jaravine
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.B.); (H.B.); (M.B.)
| | - James Balmford
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.B.); (H.B.); (M.B.)
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (P.M.); (M.B.)
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg im Breisgau, Germany; (P.M.); (M.B.)
| | - Harald Binder
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.B.); (H.B.); (M.B.)
| | - Martin Boeker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.B.); (H.B.); (M.B.)
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Yeh HM, Liao MH, Chu CL, Lin YH, Sun WZ, Lai LP, Chen PL. Next-generation sequencing and bioinformatics to identify genetic causes of malignant hyperthermia. J Formos Med Assoc 2020; 120:883-892. [PMID: 32919876 DOI: 10.1016/j.jfma.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/02/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND/PURPOSE Malignant hyperthermia (MH) is a life-threatening pharmacogenetic disease with only two known causative genes, RYR1 and CACNA1S. Both are huge genes containing numerous exons, and they reportedly only account for 50-70% of known MH patients. Next-generation sequencing (NGS) technology and bioinformatics could help delineate the genetic diagnosis of MH and several MH-like clinical presentations. METHODS We established a capture-based targeted NGS sequencing framework to examine the whole genomic regions of RYR1, CACNA1S and the 16.6 Kb mitochondrial genome, as well as 12 other genes related to excitation-contraction coupling and/or skeletal muscle calcium homeostasis. We applied bioinformatics analyses to the variants identified in this study and also to the 48 documented RYR1 pathogenic variants. RESULTS The causative variants were identified in seven of the eight (87.5%) MH families, but in none of the 10 individuals classified as either normal controls (N = 2) or patients displaying MH-like clinical features later found to be caused by other etiologies (N = 8). We showed that RYR1 c.1565A>G (p.Tyr522Cys)(rs118192162) could be a genetic hot spot in the Taiwanese population. Bioinformatics analyses demonstrated low population frequencies and predicted damaging effects from all known pathogenic RYR1 variants. We estimated that more than one in 1149 individuals worldwide carry MH pathogenic variants at RYR1. CONCLUSION NGS and bioinformatics are sensitive and specific tools to examine RYR1 and CACNA1S for the genetic diagnosis of MH. Pathogenic variants in RYR1 can be found in the majority of MH patients in Taiwan.
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Affiliation(s)
- Huei-Ming Yeh
- Department of Anesthesiology National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Hua Liao
- Scientist, Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Lin Chu
- Department of Anesthesiology, National Taiwan University Hospital, Yun-Lin Branch, Yunlin, Taiwan
| | - Yin-Hung Lin
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Zen Sun
- Department of Anesthesiology National Taiwan University Hospital, Taipei, Taiwan
| | - Ling-Ping Lai
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
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12
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Chen CH, Bournat JC, Wilken N, Rosenfeld JA, Zhang J, Seth A, Jorgez CJ. Variants in ALX4 and their association with genitourinary defects. Andrology 2020; 8:1243-1255. [PMID: 32385972 DOI: 10.1111/andr.12815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Genitourinary anomalies occur in approximately 1% of humans, but in most cases, the cause is unknown. Aristaless-like homeobox 4 (ALX4) is an important homeodomain transcription factor. ALX4 mutations in humans and mouse have been associated with craniofacial defects and genitourinary anomalies such as cryptorchidism and epispadias. OBJECTIVES To investigate the presence and the functional impact of ALX4 variants in patients with genitourinary defects. MATERIALS AND METHODS Two separate patient cohorts were analyzed. One includes clinical exome-sequencing (ES) data from 7500 individuals. The other includes 52 ALX4 Sanger-sequenced individuals with bladder exstrophy-epispadias complex (BEEC). Dual luciferase assays were conducted to investigate the functional transcriptional impact of ALX4 variants in HeLa cells and HEK293 cells. RESULTS A total of 41 distinct ALX4 heterozygous missense variants were identified in the ES cohort with 15 variants present as recurrent in multiple patients. p.G369E and p.L373F were the only two present in individuals with genitourinary defects. A p.L373F heterozygous variant was also identified in one of the 52 individuals in the BEEC cohort. p.L373F and p.G369E were tested in vitro as both are considered damaging by MutationTaster, although only p.G369E was considered damaging by PolyPhen-2. p.L373F did not alter transcriptional activity in HeLa and HEK293 cells. p.G369E caused a significant 3.4- and 1.8-fold decrease in transcriptional activities relative to wild-type ALX4 in HEK293 and HeLa cells, respectively. DISCUSSION AND CONCLUSIONS Our study supports the idea that transcription factors like ALX4 could influence the normal development of the GU tract in humans as demonstrated in mouse models as ALX4 variant p.G369E (predicted pathogenic by multiple databases) affects ALX4 function in vitro. Variant p.L373F (predicted pathogenic by only MutationTaster) did not affect ALX4 function in vitro. Exon-sequence information and mouse genetics provide important insights into the complex mechanisms driving genitourinary defects allowing the association of transcriptional defects with congenital disorders.
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Affiliation(s)
- Ching H Chen
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Juan C Bournat
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Wilken
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA.,Department of Urology, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Jason Zhang
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Abhishek Seth
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA.,Department of Urology, Baylor College of Medicine, Houston, TX, USA.,Division of Urology, Department of Surgery, Texas Children's Hospital, Houston, TX, USA
| | - Carolina J Jorgez
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, USA.,Department of Urology, Baylor College of Medicine, Houston, TX, USA.,Division of Urology, Department of Surgery, Texas Children's Hospital, Houston, TX, USA
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13
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Functional analysis of newly identified RYR1 variants in patients susceptible to malignant hyperthermia. J Anesth 2020; 34:658-665. [PMID: 32535660 DOI: 10.1007/s00540-020-02803-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/23/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE This study aimed to evaluate whether the three ryanodine receptor type 1 (RYR1) variants (p.Ser2345Thr, p.Ser2345Arg, and p.Lys3367Arg) which we identified in Japanese malignant hyperthermia (MH) patients with a clinical grading scale rank of 6 were causative for MH. METHODS We prepared human embryonic kidney (HEK)-293 cells transfected with wild-type RYR1 or one of the RYR1 variants, along with myotubes cultured from muscle pieces. Calcium kinetics were examined by calculating the 340/380-nm ratio under various caffeine and 4-chloro-m-cresol (4CmC) concentrations with the ratiometric dye Fura-2 AM. Half-maximal effective concentration (EC50) values were calculated from dose-response curves. Statistical analysis was based on one-way analysis of variance with a Dunnett's multiple comparison test, using a P value < 0.05 as evidence of statistical significance. RESULTS In functional analysis using HEK-293 cells, we found significant reductions in the EC50 of p.Ser2345Thr and p.Ser2345Arg in comparison with wild-type RYR1 (P < 0.001), while the EC50 of p.Lys3367Arg was not significantly different (P = 0.062 for caffeine and P > 0.999 for 4CmC). On the other hand, functional analysis using myotubes showed significant differences in the EC50 values for all variants (P < 0.001 for all comparisons). CONCLUSIONS p.Ser2345Thr and p.Ser2345Arg appear capable of causing a calcium metabolism disorder that leads to the onset of MH, and p.Ser2345Arg can be considered as a diagnostic mutation, because it meets the European Malignant Hyperthermia Group criteria. However, patients with p.Lys3367Arg might have mutations in genes other than RYR1 that are capable of causing MH.
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Choi MH, Yang JO, Min JS, Lee JJ, Jun SY, Lee YJ, Yoon JY, Jeon SJ, Byeon I, Kang JW, Kim NS. A Novel X-Linked Variant of IQSEC2 is Associated with Lennox-Gastaut Syndrome and Mild Intellectual Disability in Three Generations of a Korean Family. Genet Test Mol Biomarkers 2019; 24:54-58. [PMID: 31829726 DOI: 10.1089/gtmb.2019.0177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aim: Lennox-Gastaut syndrome (LGS) is a severe type of childhood-onset epilepsy with multiple types of seizures, specific discharges on electroencephalography, and intellectual disability. However, LGS-related genes are largely unknown. To identify causative genes related to LGS, we collected and analyzed data from a three-generation Korean family in which one member had LGS and two had intellectual disability. Methods: Genomic DNAs were extracted from blood samples of all participants and used in whole-exome sequencing (WES). Genetic variants were detected by the Genome Analysis Toolkit and confirmed by Sanger sequencing. Variant pathogenicity was evaluated by prediction programs and the American College of Medical Genetics criteria. The LGS patient had generalized slow spike-and-wave discharges, multiple types of seizures, and developmental delay. Results: Analyses of the WES data from the family revealed a novel variant (c.1048G>A, p.Ala350Thr) in the IQ motif and Sec7 domain 2 (IQSEC2). This variant is within a highly evolutionarily conserved IQ-like motif, indicating a decrease in the calmodulin-binding capacity or α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid transmission. The hemizygous variant in the male with LGS was a maternally inherited X-linked variant from the heterozygous maternal grandmother and mother, both of whom had intellectual disability. Conclusion: These findings indicate that the variant of IQSEC2 triggered both LGS and intellectual disability dependent on sex in this family. We report a novel X-linked inherited IQSEC2 variant for LGS and intellectual disability, which enhances the spectrum of variants in the IQ-like motif of IQSEC2.
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Affiliation(s)
- Min-Hyuk Choi
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jin Ok Yang
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ju-Sik Min
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jeong-Ju Lee
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soo-Young Jun
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Yong-Jae Lee
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ji-Yong Yoon
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Su-Jin Jeon
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Iksu Byeon
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Joon-Won Kang
- Department of Pediatrics and Medical Science, Chungnam National University Hospital, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Nam-Soon Kim
- Rare-Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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Kolovou G, Cokkinos P, Bilianou H, Kolovou V, Katsiki N, Mavrogeni S. Non-traumatic and non-drug-induced rhabdomyolysis. Arch Med Sci Atheroscler Dis 2019; 4:e252-e263. [PMID: 32368681 PMCID: PMC7191942 DOI: 10.5114/amsad.2019.90152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/10/2019] [Indexed: 01/19/2023] Open
Abstract
Rhabdomyolysis (RM), a fortunately rare disease of the striated muscle cells, is a complication of non-traumatic (congenital (glycogen storage disease, discrete mitochondrial myopathies and various muscular dystrophies) or acquired (alcoholic myopathy, systemic diseases, arterial occlusion, viral illness or bacterial sepsis)) and traumatic conditions. Additionally, RM can occur in some individuals under specific circumstances such as toxic substance use and illicit drug abuse. Lipid-lowering drugs in particular are capable of causing RM. This comprehensive review will focus on non-traumatic and non-drug-induced RM. Moreover, the pathology of RM, its clinical manifestation and biochemical effects, and finally its management will be discussed.
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Affiliation(s)
- Genovefa Kolovou
- Cardiology Department, Onassis Cardiac Surgery Center, Athens, Greece
| | - Philip Cokkinos
- Cardiology Department, Onassis Cardiac Surgery Center, Athens, Greece
| | | | - Vana Kolovou
- Cardiology Department, Onassis Cardiac Surgery Center, Athens, Greece
- Molecular Immunology Laboratory, Onassis Cardiac Surgery Center, Athens, Greece
| | - Niki Katsiki
- First Department of Internal Medicine, Division of Endocrinology-Metabolism, Diabetes Center, AHEPA University Hospital, Thessaloniki, Greece
| | - Sophie Mavrogeni
- Cardiology Department, Onassis Cardiac Surgery Center, Athens, Greece
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16
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Isackson PJ, Wang J, Zia M, Spurgeon P, Levesque A, Bard J, James S, Nowak N, Lee TK, Vladutiu GD. RYR1 and CACNA1S genetic variants identified with statin-associated muscle symptoms. Pharmacogenomics 2018; 19:1235-1249. [PMID: 30325262 DOI: 10.2217/pgs-2018-0106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To examine the genetic differences between subjects with statin-associated muscle symptoms and statin-tolerant controls. MATERIALS & METHODS Next-generation sequencing was used to characterize the exomes of 76 subjects with severe statin-associated muscle symptoms and 50 statin-tolerant controls. RESULTS 12 probably pathogenic variants were found within the RYR1 and CACNA1S genes in 16% of cases with severe statin-induced myopathy representing a fourfold increase over variants found in statin-tolerant controls. Subjects with probably pathogenic RYR1 or CACNA1S variants had plasma CK 5X to more than 400X the upper limit of normal in addition to having muscle symptoms. CONCLUSIONS Genetic variants within the RYR1 and CACNA1S genes are likely to be a major contributor to the susceptibility to statin-associated muscle symptoms.
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Affiliation(s)
- Paul J Isackson
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA
| | - Jianxin Wang
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Mohammad Zia
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Paul Spurgeon
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Adrian Levesque
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Jonathan Bard
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Smitha James
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Norma Nowak
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Tae Keun Lee
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA
| | - Georgirene D Vladutiu
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA.,Departments of Neurology & Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14214, USA
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Figueroa L, Kraeva N, Manno C, Toro S, Ríos E, Riazi S. Abnormal calcium signalling and the caffeine-halothane contracture test. Br J Anaesth 2018; 122:32-41. [PMID: 30579404 PMCID: PMC6334558 DOI: 10.1016/j.bja.2018.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/16/2018] [Accepted: 08/06/2018] [Indexed: 01/20/2023] Open
Abstract
Background The variable clinical presentation of malignant hyperthermia (MH), a disorder of calcium signalling, hinders its diagnosis and management. Diagnosis relies on the caffeine–halothane contracture test, measuring contraction forces upon exposure of muscle to caffeine or halothane (FC and FH, respectively). Patients with above-threshold FC or FH are diagnosed as MH susceptible. Many patients test positive to halothane only (termed ‘HH’). Our objective was to determine the characteristics of these HH patients, including their clinical symptoms and features of cytosolic Ca2+ signalling related to excitation–contraction coupling in myotubes. Methods After institutional ethics committee approval, recruited patients undergoing contracture testing at Toronto's MH centre were assigned to three groups: HH, doubly positive (HS), and negative patients (HN). A clinical index was assembled from musculoskeletal symptoms and signs. An analogous calcium index summarised four measures in cultured myotubes: resting [Ca2+]cytosol, frequency of spontaneous cytosolic Ca2+ events, Ca2+ waves, and cell-wide Ca2+ spikes after electrical stimulation. Results The highest values of both indexes were found in the HH group; the differences in calcium index between HH and the other groups were statistically significant. The principal component analysis confirmed the unique cell-level features of the HH group, and identified elevated resting [Ca2+]cytosol and spontaneous event frequency as the defining HH characteristics. Conclusions These findings suggest that HH pathogenesis stems from excess Ca2+ leak through sarcoplasmic reticulum channels. This identifies HH as a separate diagnostic group and opens their condition to treatment based on understanding of pathophysiological mechanisms.
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Affiliation(s)
- L Figueroa
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA
| | - N Kraeva
- Malignant Hyperthermia Investigation Unit of the University Health Network, Toronto, ON, Canada; Department of Anaesthesia & Pain Management, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - C Manno
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA
| | - S Toro
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA
| | - E Ríos
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA.
| | - S Riazi
- Malignant Hyperthermia Investigation Unit of the University Health Network, Toronto, ON, Canada; Department of Anaesthesia & Pain Management, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
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18
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Genetic epidemiology of malignant hyperthermia in the UK. Br J Anaesth 2018; 121:944-952. [PMID: 30236257 DOI: 10.1016/j.bja.2018.06.028] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/01/2018] [Accepted: 06/20/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Gaps in our understanding of genetic susceptibility to malignant hyperthermia (MH) limit the application and interpretation of genetic diagnosis of the condition. Our aim was to define the prevalence and role of variants in the three genes implicated in MH susceptibility in the largest comprehensively phenotyped MH cohort worldwide. METHODS We initially included one individual from each positive family tested in the UK MH Unit since 1971 to detect variants in RYR1, CACNA1S, or STAC3. Screening for genetic variants has been ongoing since 1991 and has involved a range of techniques, most recently next generation sequencing. We assessed the pathogenicity of variants using standard guidelines, including family segregation studies. The prevalence of recurrent variants of unknown significance was compared with the prevalence reported in a large database of sequence variants in low-risk populations. RESULTS We have confirmed MH susceptibility in 795 independent families, for 722 of which we have a DNA sample. Potentially pathogenic variants were found in 555 families, with 25 RYR1 and one CACNA1S variants previously unclassified recurrent variants significantly over-represented (P<1×10-7) in our cohort compared with the Exome Aggregation Consortium database. There was genotype-phenotype discordance in 86 of 328 families suitable for segregation analysis. We estimate non-RYR1/CACNA1S/STAC3 susceptibility occurs in 14-23% of MH families. CONCLUSIONS Our data provide current estimates of the role of variants in RYR1, CACNA1S, and STAC3 in susceptibility to MH in a predominantly white European population.
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Williams JK, Feero WG, Veenstra DL, Starkweather A, Cashion AK. Considerations in initiating genomic screening programs in health care systems. Nurs Outlook 2018; 66:570-575. [PMID: 30093136 DOI: 10.1016/j.outlook.2018.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/12/2018] [Accepted: 06/17/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Janet K Williams
- College of Nursing, The University of Iowa, Iowa City, IA; American Academy of Nursing, Washington D.C..
| | | | | | - Angela Starkweather
- American Academy of Nursing, Washington D.C.; School of Nursing, University of Connecticut, Storrs, CT
| | - Ann K Cashion
- American Academy of Nursing, Washington D.C.; National Institute of Nursing Research, National Institutes of Health, Bethesda, MD
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Otsuki S, Yasuda T, Mukaida K, Noda Y, Kanzaki R, Miyoshi H, Kondo T, Hamada H, Kawamoto M. Myotoxicity of local anesthetics is equivalent in individuals with and without predisposition to malignant hyperthermia. J Anesth 2018; 32:616-623. [DOI: 10.1007/s00540-018-2526-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/19/2018] [Indexed: 01/25/2023]
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Todd JJ, Razaqyar MS, Witherspoon JW, Lawal TA, Mankodi A, Chrismer IC, Allen C, Meyer MD, Kuo A, Shelton MS, Amburgey K, Niyazov D, Fequiere P, Bönnemann CG, Dowling JJ, Meilleur KG. Novel Variants in Individuals with RYR1-Related Congenital Myopathies: Genetic, Laboratory, and Clinical Findings. Front Neurol 2018; 9:118. [PMID: 29556213 PMCID: PMC5845096 DOI: 10.3389/fneur.2018.00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/19/2018] [Indexed: 12/23/2022] Open
Abstract
The ryanodine receptor 1-related congenital myopathies (RYR1-RM) comprise a spectrum of slow, rare neuromuscular diseases. Affected individuals present with a mild-to-severe symptomatology ranging from proximal muscle weakness, hypotonia and joint contractures to scoliosis, ophthalmoplegia, and respiratory involvement. Although there is currently no FDA-approved treatment for RYR1-RM, our group recently conducted the first clinical trial in this patient population (NCT02362425). This study aimed to characterize novel RYR1 variants with regard to genetic, laboratory, muscle magnetic resonance imaging (MRI), and clinical findings. Genetic and histopathology reports were obtained from participant's medical records. Alamut Visual Software was used to determine if participant's variants had been previously reported and to assess predicted pathogenicity. Physical exams, pulmonary function tests, T1-weighted muscle MRI scans, and blood measures were completed during the abovementioned clinical trial. Six novel variants (two de novo, three dominant, and one recessive) were identified in individuals with RYR1-RM. Consistent with established RYR1-RM histopathology, cores were observed in all biopsies, except Case 6 who exhibited fiber-type disproportion. Muscle atrophy and impaired mobility with Trendelenburg gait were the most common clinical symptoms and were identified in all cases. Muscle MRI revealed substantial inter-individual variation in fatty infiltration corroborating the heterogeneity of the disease. Two individuals with dominant RYR1 variants exhibited respiratory insufficiency: a clinical symptom more commonly associated with recessive RYR1-RM cases. This study demonstrates that a genetics-led approach is suitable for the diagnosis of suspected RYR1-RM which can be corroborated through histopathology, muscle MRI and clinical examination.
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Affiliation(s)
- Joshua J Todd
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Muslima S Razaqyar
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Jessica W Witherspoon
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Tokunbor A Lawal
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Ami Mankodi
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke--NINDS (NIH), Bethesda, MD, United States
| | - Irene C Chrismer
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Carolyn Allen
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Mary D Meyer
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Anna Kuo
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Monique S Shelton
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
| | - Kim Amburgey
- Division of Neurology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Medical Center, New Orleans, LA, United States
| | - Pierre Fequiere
- Division of Neurology, Children's of Alabama, Birmingham, AL, United States
| | - Carsten G Bönnemann
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke--NINDS (NIH), Bethesda, MD, United States
| | - James J Dowling
- Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, Hospital for Sick Children, Toronto, ON, Canada
| | - Katherine G Meilleur
- Neuromuscular Symptoms Unit, National Institute of Nursing Research (NIH), Bethesda, MD, United States
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22
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Abstract
BACKGROUND Given the etiologic heterogeneity of disease classification using clinical phenomenology, we employed contemporary criteria to classify variants associated with myoclonic epilepsy with ragged-red fibers (MERRF) syndrome and to assess the strength of evidence of gene-disease associations. Standardized approaches are used to clarify the definition of MERRF, which is essential for patient diagnosis, patient classification, and clinical trial design. METHODS Systematic literature and database search with application of standardized assessment of gene-disease relationships using modified Smith criteria and of variants reported to be associated with MERRF using modified Yarham criteria. RESULTS Review of available evidence supports a gene-disease association for two MT-tRNAs and for POLG. Using modified Smith criteria, definitive evidence of a MERRF gene-disease association is identified for MT-TK. Strong gene-disease evidence is present for MT-TL1 and POLG. Functional assays that directly associate variants with oxidative phosphorylation impairment were critical to mtDNA variant classification. In silico analysis was of limited utility to the assessment of individual MT-tRNA variants. With the use of contemporary classification criteria, several mtDNA variants previously reported as pathogenic or possibly pathogenic are reclassified as neutral variants. CONCLUSIONS MERRF is primarily an MT-TK disease, with pathogenic variants in this gene accounting for ~90% of MERRF patients. Although MERRF is phenotypically and genotypically heterogeneous, myoclonic epilepsy is the clinical feature that distinguishes MERRF from other categories of mitochondrial disorders. Given its low frequency in mitochondrial disorders, myoclonic epilepsy is not explained simply by an impairment of cellular energetics. Although MERRF phenocopies can occur in other genes, additional data are needed to establish a MERRF disease-gene association. This approach to MERRF emphasizes standardized classification rather than clinical phenomenology, thus improving patient diagnosis and clinical trial design.
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23
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Hopkins PM, Gupta PK, Bilmen JG. Malignant hyperthermia. HANDBOOK OF CLINICAL NEUROLOGY 2018; 157:645-661. [DOI: 10.1016/b978-0-444-64074-1.00038-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Abstract
This article reviews advancements in the genetics of malignant hyperthermia, new technologies and approaches for its diagnosis, and the existing limitations of genetic testing for malignant hyperthermia. It also reviews the various RYR1-related disorders and phenotypes, such as myopathies, exertional rhabdomyolysis, and bleeding disorders, and examines the connection between these disorders and malignant hyperthermia.
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25
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Anandan C, Cipriani MA, Laughlin RS, Niu Z, Milone M. Rhabdomyolysis and fluctuating asymptomatic hyperCKemia associated with CACNA1S variant. Eur J Neurol 2017; 25:417-419. [PMID: 29193480 DOI: 10.1111/ene.13528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/24/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND PURPOSE CACNA1S encodes Cav 1.1, a voltage sensor for muscle excitation-contraction coupling, which activates the ryanodine receptor 1 (RYR1) leading to calcium release from the sarcoplasmic reticulum. CACNA1S mutations cause hypokalemic periodic paralysis, malignant hyperthermia and congenital myopathy. RYR1 mutations result in congenital myopathy, malignant hyperthermia and rhabdomyolysis. METHODS The aim was to describe a novel phenotype associated with a CACNA1S variant at a site previously linked to hypokalemic periodic paralysis. RESULTS The patient presented with fluctuating asymptomatic creatine kinase elevation after an episode of rhabdomyolysis but has no history of periodic paralysis. His muscle biopsy showed core-like structures occurring mainly in type 2 fibers. He carries a novel Cav 1.1 variant (p.Arg528Leu) affecting a highly conserved amino acid. Different mutations at the same location cause hypokalemic periodic paralysis. CONCLUSION This case underscores the similarity between the phenotypes caused by mutations in two functionally linked proteins, RYR1 and Cav 1.1.
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Affiliation(s)
- C Anandan
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - M A Cipriani
- Department of Family Medicine, Mayo Clinic, Rochester, MN, USA
| | - R S Laughlin
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Z Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - M Milone
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
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26
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Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV. Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. Hum Mutat 2017; 38:1051-1063. [PMID: 28817247 PMCID: PMC5746193 DOI: 10.1002/humu.23293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 11/07/2022]
Abstract
The exponential growth of genomic variants uncovered by next-generation sequencing necessitates efficient and accurate computational analyses to predict their functional effects. A number of computational methods have been developed for the task, but few unbiased comparisons of their performance are available. To fill the gap, The Critical Assessment of Genome Interpretation (CAGI) comprehensively assesses phenotypic predictions on newly collected experimental datasets. Here, we present the results of the SUMO conjugase challenge where participants were predicting functional effects of missense mutations in human SUMO-conjugating enzyme UBE2I. The performance of the predictors is similar to each other and is far from perfection. Evolutionary information from sequence alignments dominates the success: deleterious mutations at conserved positions and benign mutations at variable positions are accurately predicted. Prediction accuracy of other mutations remains unsatisfactory, and this fast-growing field of research is yet to learn the use of spatial structure information to improve the predictions significantly.
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Affiliation(s)
- Jing Zhang
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
| | - Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario M5G 1X5, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Song Sun
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario M5G 1X5, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Atina G Cote
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario M5G 1X5, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Frederick P. Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario M5G 1X5, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Computer Science University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Nick V. Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
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27
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de la Campa EÁ, Padilla N, de la Cruz X. Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence. BMC Genomics 2017; 18:569. [PMID: 28812538 PMCID: PMC5558188 DOI: 10.1186/s12864-017-3914-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Strict guidelines delimit the use of computational information in the clinical setting, due to the still moderate accuracy of in silico tools. These guidelines indicate that several tools should always be used and that full coincidence between them is required if we want to consider their results as supporting evidence in medical decision processes. Application of this simple rule certainly decreases the error rate of in silico pathogenicity assignments. However, when predictors disagree this rule results in the rejection of potentially valuable information for a number of variants. In this work, we focus on these variants of the protein sequence and develop specific predictors to help improve the success rate of their annotation. Results We have used a set of 59,442 protein sequence variants (15,723 pathological and 43,719 neutral) from 228 proteins to identify those cases for which pathogenicity predictors disagree. We have repeated this process for all the possible combinations of five known methods (SIFT, PolyPhen-2, PON-P2, CADD and MutationTaster2). For each resulting subset we have trained a specific pathogenicity predictor. We find that these specific predictors are able to discriminate between neutral and pathogenic variants, with a success rate different from random. They tend to outperform the constitutive methods but this trend decreases as the performance of the constitutive predictor improves (e.g. with PON-P2 and PolyPhen-2). We also find that specific methods outperform standard consensus methods (Condel and CAROL). Conclusion Focusing development efforts on the case of variants for which known methods disagree we may obtain pathogenicity predictors with improved performances. Although we have not yet reached the success rate that allows the use of this computational evidence in a clinical setting, the simplicity of the approach indicates that more advanced methods may reach this goal in a close future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3914-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Álvarez de la Campa
- Research Unit in Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. .,ICREA, Barcelona, Spain.
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28
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Bjorksten AR, Gillies RL, Hockey BM, Du Sart D. Sequencing of genes involved in the movement of calcium across human skeletal muscle sarcoplasmic reticulum: continuing the search for genes associated with malignant hyperthermia. Anaesth Intensive Care 2017; 44:762-768. [PMID: 27832566 DOI: 10.1177/0310057x1604400625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genetic basis of malignant hyperthermia (MH) is not fully characterised and likely involves more than just the currently classified mutations in the gene encoding the skeletal muscle ryanodine receptor (RYR1) and the gene encoding the α1 subunit of the dihydropyridine receptor (CACNA1S). In this paper we sequence other genes involved in calcium trafficking within skeletal muscle in patients with positive in vitro contracture tests, searching for alternative genes associated with MH. We identified four rare variants in four different genes (CACNB1, CASQ1, SERCA1 and CASQ2) encoding proteins involved in calcium handling in skeletal muscle in a cohort of 30 Australian MH susceptible probands in whom prior complete sequencing of RYR1 and CACNA1S had yielded no rare variants. These four variants have very low minor allele frequencies and while it is tempting to speculate that they have a role in MH, they remain at present variants of unknown significance. Nevertheless they provide the basis for a new set of functional studies, which may indeed identify novel players in MH.
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Affiliation(s)
- A R Bjorksten
- Senior Scientist, Malignant Hyperthermia Diagnostic Unit, Department of Anaesthesia and Pain Management, Royal Melbourne Hospital, Anaesthesia, Perioperative and Pain Medicine Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Victorian Clinical Genetics Service Molecular Genetics Laboratory, Murdoch Children's Research Institut
| | - R L Gillies
- Head, Malignant Hyperthermia Diagnostic Unit, Department of Anaesthesia and Pain Management, Royal Melbourne Hospital, Anaesthesia, Perioperative and Pain Medicine Unit, University of Melbourne, Victoria
| | - B M Hockey
- Malignant Hyperthermia Diagnostic Unit, Department of Anaesthesia and Pain Management, Royal Melbourne Hospital, Consultant Anaesthetist, Anaesthesia, Perioperative and Pain Medicine Unit, University of Melbourne, Victoria
| | - D Du Sart
- Research Affiliate/Head, Victorian Clinical Genetics Service Molecular Genetics Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria
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29
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Abath Neto O, Moreno CDAM, Malfatti E, Donkervoort S, Böhm J, Guimarães JB, Foley AR, Mohassel P, Dastgir J, Bharucha-Goebel DX, Monges S, Lubieniecki F, Collins J, Medne L, Santi M, Yum S, Banwell B, Salort-Campana E, Rendu J, Fauré J, Yis U, Eymard B, Cheraud C, Schneider R, Thompson J, Lornage X, Mesrob L, Lechner D, Boland A, Deleuze JF, Reed UC, Oliveira ASB, Biancalana V, Romero NB, Bönnemann CG, Laporte J, Zanoteli E. Common and variable clinical, histological, and imaging findings of recessive RYR1-related centronuclear myopathy patients. Neuromuscul Disord 2017; 27:975-985. [PMID: 28818389 DOI: 10.1016/j.nmd.2017.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/10/2017] [Accepted: 05/25/2017] [Indexed: 01/04/2023]
Abstract
Mutations in RYR1 give rise to diverse skeletal muscle phenotypes, ranging from classical central core disease to susceptibility to malignant hyperthermia. Next-generation sequencing has recently shown that RYR1 is implicated in a wide variety of additional myopathies, including centronuclear myopathy. In this work, we established an international cohort of 21 patients from 18 families with autosomal recessive RYR1-related centronuclear myopathy, to better define the clinical, imaging, and histological spectrum of this disorder. Early onset of symptoms with hypotonia, motor developmental delay, proximal muscle weakness, and a stable course were common clinical features in the cohort. Ptosis and/or ophthalmoparesis, facial weakness, thoracic deformities, and spinal involvement were also frequent but variable. A common imaging pattern consisted of selective involvement of the vastus lateralis, adductor magnus, and biceps brachii in comparison to adjacent muscles. In addition to a variable prominence of central nuclei, muscle biopsy from 20 patients showed type 1 fiber predominance and a wide range of intermyofibrillary architecture abnormalities. All families harbored compound heterozygous mutations, most commonly a truncating mutation combined with a missense mutation. This work expands the phenotypic characterization of patients with recessive RYR1-related centronuclear myopathy by highlighting common and variable clinical, histological, and imaging findings in these patients.
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Affiliation(s)
- Osorio Abath Neto
- Departamento de Neurologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil; Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France; Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | | | - Edoardo Malfatti
- Center for Research in Myology, Sorbonne University, Pitié-Salpêtrière Hospital Group, Paris, France
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | - Johann Böhm
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | | | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | - Jahannaz Dastgir
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | | | - Soledad Monges
- Servicio de Neurología y Servicio de Patologia, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Neurología y Servicio de Patologia, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | - James Collins
- Department of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Līvija Medne
- Individualized Medical Genetics Center, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mariarita Santi
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sabrina Yum
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brenda Banwell
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Emmanuelle Salort-Campana
- APHM, Dept. Neurology, Neuromuscular & ALS Reference Center, La Timone Univ. Hospital, France Aix Marseille Université, INSERM, GMGF, Marseille, France
| | - John Rendu
- Dept. Biochemistry, Molecular Biochemistry & Genetics, Toxicology & Pharmacology, Grenoble Alpes University, GIN Inst. Neurosciences, Grenoble, France
| | - Julien Fauré
- Dept. Biochemistry, Molecular Biochemistry & Genetics, Toxicology & Pharmacology, Grenoble Alpes University, GIN Inst. Neurosciences, Grenoble, France
| | - Uluc Yis
- Division of Child Neurology, Department of Pediatrics, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Bruno Eymard
- Paris-Est Neuromuscular Center, APHP - GH Pitié-Salpêtrière, Paris, France
| | - Chrystel Cheraud
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Raphaël Schneider
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France; Department of Computer Science, ICube, UMR 7357, CNRS, Strasbourg, France
| | - Julie Thompson
- Department of Computer Science, ICube, UMR 7357, CNRS, Strasbourg, France
| | - Xaviere Lornage
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Lilia Mesrob
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Doris Lechner
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | | | - Umbertina Conti Reed
- Departamento de Neurologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Acary Souza Bulle Oliveira
- Setor de Doenças Neuromusculares, Departamento de Neurologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Valérie Biancalana
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France; Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hopital Civil, Strasbourg, France
| | - Norma B Romero
- Center for Research in Myology, Sorbonne University, Pitié-Salpêtrière Hospital Group, Paris, France
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institutes of Health, Bethesda, MD, USA
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Edmar Zanoteli
- Departamento de Neurologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil.
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Novel RAG1 mutation and the occurrence of mycobacterial and Chromobacterium violaceum infections in a case of leaky SCID. Microb Pathog 2017; 109:114-119. [PMID: 28552805 DOI: 10.1016/j.micpath.2017.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 05/19/2017] [Accepted: 05/23/2017] [Indexed: 12/14/2022]
Abstract
Severe combined immunodeficiency (SCID) is a potentially fatal primary immunodeficiency (PID) that is caused by mutations in genes such as IL2RG, JAK3, IL7RA, RAG1, RAG2, and ADA. The products of these genes are involved in the development of several immune cells such as T, B and natural killer (NK) cells. Most of the SCID forms are autosomal recessive with the exception of IL2RG defects that cause an X-linked SCID. Among the different SCID types, there is a rare SCID form called leaky SCID, which is less severe when compared to the other classical SCID phenotypes. Leaky SCID can be caused by hypomorphic mutations in RAG1 and RAG2 that result in only partial loss of enzymatic function of the proteins respectively encoded by these genes. Here we report a novel missense mutation (c. 307C > T/p.H103Y) in the RAG1 gene in a patient with leaky SCID. In addition, we characterize the clinical and immunological features of this patient that developed along with other severe and recurrent infections such as mycobacterial diseases (BCGitis and pulmonary tuberculosis), the first occurrence of Chromobacterium violaceum in a patient with SCID. Understanding the increased susceptibility to mycobacteria presented by the patient, in which a functional investigation of IL-12/IFN-γ axis was performed, which demonstrated reduced production of IFN-γ in the supernatans of peripheral blood mononuclear cell cultures from the patient compared with those from healthy subjects. In conclusion, our data expands the molecular and clinical spectrum associated with the leaky SCID phenotype.
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31
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Kraeva N, Sapa A, Dowling JJ, Riazi S. Malignant hyperthermia susceptibility in patients with exertional rhabdomyolysis: a retrospective cohort study and updated systematic review. Can J Anaesth 2017; 64:736-743. [DOI: 10.1007/s12630-017-0865-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/23/2017] [Accepted: 03/13/2017] [Indexed: 01/24/2023] Open
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32
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Assessment of in silico protein sequence analysis in the clinical classification of variants in cancer risk genes. J Community Genet 2017; 8:87-95. [PMID: 28050887 PMCID: PMC5386911 DOI: 10.1007/s12687-016-0289-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 11/17/2022] Open
Abstract
Missense variants represent a significant proportion of variants identified in clinical genetic testing. In the absence of strong clinical or functional evidence, the American College of Medical Genetics recommends that these findings be classified as variants of uncertain significance (VUS). VUSs may be reclassified to better inform patient care when new evidence is available. It is critical that the methods used for reclassification are robust in order to prevent inappropriate medical management strategies and unnecessary, life-altering surgeries. In an effort to provide evidence for classification, several in silico algorithms have been developed that attempt to predict the functional impact of missense variants through amino acid sequence conservation analysis. We report an analysis comparing internally derived, evidence-based classifications with the results obtained from six commonly used algorithms. We compiled a dataset of 1118 variants in BRCA1, BRCA2, MLH1, and MSH2 previously classified by our laboratory’s evidence-based variant classification program. We compared internally derived classifications with those obtained from the following in silico tools: Align-GVGD, CONDEL, Grantham Analysis, MAPP-MMR, PolyPhen-2, and SIFT. Despite being based on similar underlying principles, all algorithms displayed marked divergence in accuracy, specificity, and sensitivity. Overall, accuracy ranged from 58.7 to 90.8% while the Matthews Correlation Coefficient ranged from 0.26–0.65. CONDEL, a weighted average of multiple algorithms, did not perform significantly better than its individual components evaluated here. These results suggest that the in silico algorithms evaluated here do not provide reliable evidence regarding the clinical significance of missense variants in genes associated with hereditary cancer.
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Expanding the clinical and genetic spectrum of G6PD deficiency: The occurrence of BCGitis and novel missense mutation. Microb Pathog 2017; 102:160-165. [DOI: 10.1016/j.micpath.2016.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 12/23/2022]
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