1
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Gopinath C, Rompicherla R, Mathias GP, Patil R, Poornachandra B, Vinekar A, Mochi TB, Braganza S, Shetty KB, Kumaramanickavel G, Ghosh A. Inherited retinal disorders: a genotype-phenotype correlation in an Indian cohort and the importance of genetic testing and genetic counselling. Graefes Arch Clin Exp Ophthalmol 2023:10.1007/s00417-022-05955-5. [PMID: 36648511 DOI: 10.1007/s00417-022-05955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/10/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Recent advances in sequencing technologies have enabled radical and rapid progress in the genetic diagnosis of inherited retinal disorders (IRDs). Although the list of gene variations continues to grow, it lacks the genetic etiology of ethnic groups like South Asians. Differences in racial backgrounds and consanguinity add to genetic heterogeneity and phenotypic overlaps. METHODS This retrospective study includes documented data from the Gen-Eye clinic from years 2014 to 2019. Medical records and pedigrees of 591 IRD patients of Indian origin and genetic reports of 117 probands were reviewed. Genotype-phenotype correlations were performed to classify as correlating, non-correlating and unsolved cases. RESULTS Among the 591 patients, we observed a higher prevalence of clinically diagnosed retinitis pigmentosa (38.9%) followed by unspecified diagnoses (28.5%). Consanguinity was reported to be high (55.6%) in this cohort. Among the variants identified in 117 probands, 36.4% of variants were pathogenic, 19.2% were likely pathogenic, and 44.4% were of uncertain significance. Among the pathogenic and likely pathogenic variants, autosomal recessive inheritance showed higher prevalence. About 35% (41/117) of cases showed genotype-phenotype correlation. Within the correlating cases, retinitis pigmentosa and Stargardt disease were predominant. Novel variants identified in RP, Stargardt, and LCA are reported here. CONCLUSION This first-of-a-kind report on an Indian cohort contributes to existing knowledge and expansion of variant databases, presenting relevant and plausible novel variants. Phenotypic overlap and variability lead to a differential diagnosis and hence a clear genotype-phenotype correlation helps in precise clinical confirmation. The study also emphasizes the importance of genetic counselling and testing for personalized vision care in a tertiary eye hospital.
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Affiliation(s)
- Chitra Gopinath
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
| | - Ramya Rompicherla
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
| | - Grace Priyaranjini Mathias
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
| | - Rajeshwari Patil
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
| | - B Poornachandra
- Vitreo-Retina Services, Narayana Nethralaya, Bangalore, 560010, India
| | - Anand Vinekar
- Vitreo-Retina Services, Narayana Nethralaya, Bangalore, 560010, India
| | | | - Sherine Braganza
- Vitreo-Retina Services, Narayana Nethralaya, Bangalore, 560010, India
| | - K Bhujang Shetty
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
- Vitreo-Retina Services, Narayana Nethralaya, Bangalore, 560010, India
| | - Govindasamy Kumaramanickavel
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India
| | - Anuprita Ghosh
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, 560099, India.
- Gen-Eye Clinic, Narayana Nethralaya, Bangalore, 560099, India.
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2
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Galán-Vidal J, Socuéllamos PG, Baena-Nuevo M, Contreras L, González T, Pérez-Poyato MS, Valenzuela C, González-Lamuño D, Gandarillas A. A novel loss-of-function mutation of the voltage-gated potassium channel Kv10.2 involved in epilepsy and autism. Orphanet J Rare Dis 2022; 17:345. [PMID: 36068614 PMCID: PMC9446776 DOI: 10.1186/s13023-022-02499-z] [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: 01/27/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Novel developmental mutations associated with disease are a continuous challenge in medicine. Clinical consequences caused by these mutations include neuron and cognitive alterations that can lead to epilepsy or autism spectrum disorders. Often, it is difficult to identify the physiological defects and the appropriate treatments. Results We have isolated and cultured primary cells from the skin of a patient with combined epilepsy and autism syndrome. A mutation in the potassium channel protein Kv10.2 was identified. We have characterised the alteration of the mutant channel and found that it causes loss of function (LOF). Primary cells from the skin displayed a very striking growth defect and increased differentiation. In vitro treatment with various carbonic anhydrase inhibitors with various degrees of specificity for potassium channels, (Brinzolamide, Acetazolamide, Retigabine) restored the activation capacity of the mutated channel. Interestingly, the drugs also recovered in vitro the expansion capacity of the mutated skin cells. Furthermore, treatment with Acetazolamide clearly improved the patient regarding epilepsy and cognitive skills. When the treatment was temporarily halted the syndrome worsened again. Conclusions By in vitro studying primary cells from the patient and the activation capacity of the mutated protein, we could first, find a readout for the cellular defects and second, test pharmaceutical treatments that proved to be beneficial. The results show the involvement of a novel LOF mutation of a Potassium channel in autism syndrome with epilepsy and the great potential of in vitro cultures of primary cells in personalised medicine of rare diseases.
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Affiliation(s)
- Jesús Galán-Vidal
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain
| | - Paula G Socuéllamos
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - María Baena-Nuevo
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Lizbeth Contreras
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain
| | - Teresa González
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - María S Pérez-Poyato
- Neuropediatric, University Hospital Marqués de Valdecilla, 39008, Santander, Spain
| | - Carmen Valenzuela
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain. .,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.
| | - Domingo González-Lamuño
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain. .,Paediatric Department, University of Cantabria University, Marqués de Valdecilla Hospital, 39008, Santander, Spain.
| | - Alberto Gandarillas
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain. .,INSERM, Occitanie Méditerranée, 34394, Montpellier, France.
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3
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Wang X, Junqing L, Huang T. CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data. Comput Biol Chem 2022; 99:107720. [DOI: 10.1016/j.compbiolchem.2022.107720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
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4
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Barbosa-Gouveia S, Vázquez-Mosquera ME, González-Vioque E, Hermida-Ameijeiras Á, Sánchez-Pintos P, de Castro MJ, León SR, Gil-Fournier B, Domínguez-González C, Camacho Salas A, Negrão L, Fineza I, Laranjeira F, Couce ML. Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies. J Clin Med 2022; 11:jcm11102750. [PMID: 35628876 PMCID: PMC9143479 DOI: 10.3390/jcm11102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
Neuromuscular diseases are genetically highly heterogeneous, and differential diagnosis can be challenging. Over a 3-year period, we prospectively analyzed 268 pediatric and adult patients with a suspected diagnosis of inherited neuromuscular disorder (INMD) using comprehensive gene-panel analysis and next-generation sequencing. The rate of diagnosis increased exponentially with the addition of genes to successive versions of the INMD panel, from 31% for the first iteration (278 genes) to 40% for the last (324 genes). The global mean diagnostic rate was 36% (97/268 patients), with a diagnostic turnaround time of 4–6 weeks. Most diagnoses corresponded to muscular dystrophies/myopathies (68.37%) and peripheral nerve diseases (22.45%). The most common causative genes, TTN, RYR1, and ANO5, accounted for almost 30% of the diagnosed cases. Finally, we evaluated the utility of the differential diagnosis tool Phenomizer, which established a correlation between the phenotype and molecular findings in 21% of the diagnosed patients. In summary, comprehensive gene-panel analysis of all genes implicated in neuromuscular diseases facilitates a rapid diagnosis and provides a high diagnostic yield.
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Affiliation(s)
- Sofia Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
| | - Maria Eugenia Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Emiliano González-Vioque
- Department of Clinical Biochemistry, Puerta de Hierro-Majadahonda University Hospital, 28222 Majadahonda, Spain;
| | - Álvaro Hermida-Ameijeiras
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Paula Sánchez-Pintos
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Maria José de Castro
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Soraya Ramiro León
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Belén Gil-Fournier
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Cristina Domínguez-González
- Neuromuscular Unit, Imas12 Research Institute, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Camacho Salas
- Pediatric Neurology Unit, Hospital Universitario 12 de Octubre, Complutense University of Madrid, 28041 Madrid, Spain;
| | - Luis Negrão
- Neuromuscular Diseases Unit, Neurology Service, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal;
| | - Isabel Fineza
- Pediatric Neurology Department, Child Developmental Center, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra Coimbra Portugal, 3000-075 Coimbra, Portugal;
| | - Francisco Laranjeira
- Biochemical Genetics Unit, Centro de Genética Médica Doutor Jacinto Magalhães, 4050-466 Porto, Portugal;
| | - Maria Luz Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
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Hieu NLT, Thu NTM, Ngan LTA, Van LTK, Huy DP, Linh PTT, Mai NTQ, Hien HTD, Hang DTT. Genetic analysis using targeted exome sequencing of 53 Vietnamese children with developmental and epileptic encephalopathies. Am J Med Genet A 2022; 188:2048-2060. [PMID: 35365919 DOI: 10.1002/ajmg.a.62741] [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: 08/15/2021] [Revised: 01/14/2022] [Accepted: 03/13/2022] [Indexed: 11/07/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) refers to a group of rare and severe neurodevelopmental disorders where genetic etiologies can play a major role. This study aimed to elucidate the genetic etiologies of a cohort of 53 Vietnamese patients with DEE. All patients were classified into known electroclinical syndromes where possible. Exome sequencing (ES) followed by a targeted analysis on 294 DEE-related genes was then performed. Patients with identified causative variants were followed for 6 months to determine the impact of genetic testing on their treatment. The diagnostic yield was 38.0% (20/53), which was significantly higher in the earlier onset group (<12 months) than in the later onset group (≥12 months). The 19 identified variants belonged to 11 genes with various cellular functions. Genes encoding ion channels especially sodium voltage-gated channel were the most frequently involved. Most variants were missense variants and located in key protein functional domains. Four variants were novel and four had been reported previously but in different phenotypes. Within 6 months of further follow-up, treatment changes were applied for six patients based on the identified disease-causing variants, with five patients showing a positive impact. This is the first study in Vietnam to analyze the genetics of DEE. This study confirms the strong involvement of genetic etiologies in DEE, especially early onset DEE. The study also contributes to clarify the genotype-phenotype correlations of DEE and highlights the efficacy of targeted ES in the diagnosis and treatment of DEE.
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Affiliation(s)
- Nguyen Le Trung Hieu
- Neurology Department, Children Hospital 2, Ho Chi Minh City, Vietnam.,University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Le Tran Anh Ngan
- Neurology Department, Children Hospital 2, Ho Chi Minh City, Vietnam
| | - Le Thi Khanh Van
- Neurology Department, Children Hospital 2, Ho Chi Minh City, Vietnam
| | - Do Phuoc Huy
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Pham Thi Truc Linh
- Functional Genomic Unit, DNA Medical Technology Company, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Mai
- Research Center for Genetics and Reproductive Health, School of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Huynh Thi Dieu Hien
- Research Center for Genetics and Reproductive Health, School of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Do Thi Thu Hang
- Research Center for Genetics and Reproductive Health, School of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
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Agaoglu NB, Unal B, Akgun Dogan O, Zolfagharian P, Shairfli P, Karakurt A, Can Senay B, Kizilboga T, Yildiz J, Dinler Doganay G, Doganay L. Determining the Accuracy of Next Generation Sequencing Based Copy Number Variation Analysis in Hereditary Breast and Ovarian Cancer. Expert Rev Mol Diagn 2022; 22:239-246. [PMID: 35240897 DOI: 10.1080/14737159.2022.2048373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are commonly associated with malignancies, including hereditary breast and ovarian cancers. Next generation sequencing (NGS) provides solutions for CNV detection in a single run. This study aimed to compare the accuracy of CNV detection by NGS analysing tool against Multiplex Ligation Dependent Probe Amplification (MLPA). RESEARCH DESIGN AND METHODS In total, 1276 cases were studied by targeted NGS panels and 691 cases (61 calls in 58 NGS-CNV positive and 633 NGS-CNV negative cases) were validated by MLPA. RESULTS Twenty-eight (46%) NGS-CNV positive calls were consistent, whereas 33 (54%) calls showed discordance with MLPA. Two cases were detected as SNV by the NGS and CNV by the MLPA analysis. In total, 2% of the cases showed an MLPA confirmed CNV region in BRCA1/2. The results of this study showed that despite the high false positive call rate of the NGS-CNV algorithm, there were no false negative calls. The cases that were determined to be negative by the NGS and positive by the MLPA were actually carrying SNVs that were located on the MLPA probe binding sites. CONCLUSION The diagnostic performance of NGS-CNV analysis is promising; however, the need for confirmation by different methods remains.
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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Medical Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Busra Unal
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Payam Zolfagharian
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Pari Shairfli
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Aylin Karakurt
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Burak Can Senay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tugba Kizilboga
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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7
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Kim MJ, Lee S, Yun H, Cho SI, Kim B, Lee JS, Chae JH, Sun C, Park SS, Seong MW. Consistent count region-copy number variation (CCR-CNV): an expandable and robust tool for clinical diagnosis of copy number variation at the exon level using next-generation sequencing data. Genet Med 2021; 24:663-672. [PMID: 34906491 DOI: 10.1016/j.gim.2021.10.025] [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: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Despite the importance of exonic copy number variations (CNVs) in human genetic diseases, reliable next-generation sequencing-based methods for detecting them are unavailable. We developed an expandable and robust exonic CNV detection tool called consistent count region (CCR)-CNV. METHODS In total, about 1000 samples of the truth set were used for validating CCR-CNV. We compared CCR-CNV performance with 2 well-known CNV tools. Finally, to overcome the limitations of CCR-CNV, we devised a combined approach. RESULTS The mean sensitivity and specificity of CCR-CNV alone were above 95%, which was superior to that of other CNV tools, such as DECoN and Atlas-CNV. However, low covered region and positive predictive value and high false discovery rate act as obstacles to its use in clinical settings. The combined approach showed much improved performance than CCR-CNV alone. CONCLUSION In this study, we present a novel diagnostic tool that allows the identification of exonic CNVs with high confidence using various reagents and clinical next-generation sequencing platforms. We validated this method using the largest multiple ligation-dependent probe amplification-confirmed data set, including sufficient copy normal control data. The approach, combined with existing CNV tools, allows the implementation of CCR-CNV in clinical settings.
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Affiliation(s)
- Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Kim
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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8
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Marmontel O, Rollat-Farnier PA, Wozny AS, Charrière S, Vanhoye X, Simonet T, Chatron N, Collin-Chavagnac D, Nony S, Dumont S, Mahl M, Jacobs C, Janin A, Caussy C, Poinsot P, Tauveron I, Bardel C, Millat G, Peretti N, Moulin P, Marçais C, Di Filippo M. Development of a new expanded next-generation sequencing panel for genetic diseases involved in dyslipidemia. Clin Genet 2020; 98:589-594. [PMID: 33111339 DOI: 10.1111/cge.13832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The aim of this study was to provide an efficient tool: reliable, able to increase the molecular diagnosis performance, to facilitate the detection of copy number variants (CNV), to assess genetic risk scores (wGRS) and to offer the opportunity to explore candidate genes. Custom SeqCap EZ libraries, NextSeq500 sequencing and a homemade pipeline enable the analysis of 311 dyslipidemia-related genes. In the training group (48 DNA from patients with a well-established molecular diagnosis), this next-generation sequencing (NGS) workflow showed an analytical sensitivity >99% (n = 532 variants) without any false negative including a partial deletion of one exon. In the prospective group, from 25 DNA from patients without prior molecular analyses, 18 rare variants were identified in the first intention panel genes, allowing the diagnosis of monogenic dyslipidemia in 11 patients. In six other patients, the analysis of minor genes and wGRS determination provided a hypothesis to explain the dyslipidemia. Remaining data from the whole NGS workflow identified four patients with potentially deleterious variants. This NGS process gives a major opportunity to accede to an enhanced understanding of the genetic of dyslipidemia by simultaneous assessment of multiple genetic determinants.
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Affiliation(s)
- Oriane Marmontel
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France.,Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
| | | | - Anne-Sophie Wozny
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Sybil Charrière
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Xavier Vanhoye
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Thomas Simonet
- Cellule BioInformatique, Hospices Civils de Lyon, Bron Cedex, France
| | | | - Delphine Collin-Chavagnac
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Séverine Nony
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Sabrina Dumont
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Muriel Mahl
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Chantal Jacobs
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Alexandre Janin
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Cyrielle Caussy
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Département Endocrinologie, Diabète et Nutrition, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre-Bénite, France
| | - Pierre Poinsot
- Service de Gastroentérologie Hépatologie et Nutrition Pédiatrique, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Igor Tauveron
- Service d'endocrinologie, CHU G. Montpied, Clermont-Ferrand, France
| | - Claire Bardel
- Cellule BioInformatique, Hospices Civils de Lyon, Bron Cedex, France
| | - Gilles Millat
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France
| | - Noël Peretti
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Service de Gastroentérologie Hépatologie et Nutrition Pédiatrique, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Philippe Moulin
- Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France.,Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, GHE, Hospices Civils de Lyon, Bron Cedex, France
| | - Christophe Marçais
- Service de Biochimie et Biologie Moléculaire Sud, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Mathilde Di Filippo
- Service de Biochimie et Biologie moléculaire Grand Est, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon, Bron Cedex, France.,Univ-Lyon, CarMeN laboratory, Inserm U1060, INRA U1397, Université Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
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9
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Fernández-Marmiesse A, Roca I, Díaz-Flores F, Cantarín V, Pérez-Poyato MS, Fontalba A, Laranjeira F, Quintans S, Moldovan O, Felgueroso B, Rodríguez-Pedreira M, Simón R, Camacho A, Quijada P, Ibanez-Mico S, Domingno MR, Benito C, Calvo R, Pérez-Cejas A, Carrasco ML, Ramos F, Couce ML, Ruiz-Falcó ML, Gutierrez-Solana L, Martínez-Atienza M. Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients. Front Neurosci 2019; 13:1135. [PMID: 31780880 PMCID: PMC6856296 DOI: 10.3389/fnins.2019.01135] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
In order to characterize the genetic architecture of epilepsy in a pediatric population from the Iberian Peninsula (including the Canary Islands), we conducted targeted exome sequencing of 246 patients with infantile-onset seizures with or without neurodevelopmental delay. We detected 107 variants in 48 different genes, which were implicated in neuronal excitability, neurodevelopment, synaptic transmission, and metabolic pathways. In 104 cases (42%) we detected variant(s) that we classified as pathogenic or likely pathogenic. Of the 48 mutated genes, 32 were dominant, 8 recessive and 8 X-linked. Of the patients for whom family studies could be performed and in whom pathogenic variants were identified in dominant or X-linked genes, 82% carried de novo mutations. The involvement of small copy number variations (CNVs) is 9%. The use of progressively updated custom panels with high mean vertical coverage enabled establishment of a definitive diagnosis in a large proportion of cases (42%) and detection of CNVs (even duplications) with high fidelity. In 10.5% of patients we detected associations that are pending confirmation via functional and/or familial studies. Our findings had important consequences for the clinical management of the probands, since a large proportion of the cohort had been clinically misdiagnosed, and their families were subsequently able to avail of genetic counseling. In some cases, a more appropriate treatment was selected for the patient in question, or an inappropriate treatment discontinued. Our findings suggest the existence of modifier genes that may explain the incomplete penetrance of some epilepsy-related genes. We discuss possible reasons for non-diagnosis and future research directions. Further studies will be required to uncover the roles of structural variants, epimutations, and oligogenic inheritance in epilepsy, thereby providing a more complete molecular picture of this disease. In summary, given the broad phenotypic spectrum of most epilepsy-related genes, efficient genomic tools like the targeted exome sequencing panel described here are essential for early diagnosis and treatment, and should be implemented as first-tier diagnostic tools for children with epilepsy without a clear etiologic basis.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain.,Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain
| | - Iria Roca
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain.,Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain
| | - Felícitas Díaz-Flores
- Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain
| | - Verónica Cantarín
- Neuropediatrics Unit, Niño Jesús Clinical University Hospital, Madrid, Spain
| | | | - Ana Fontalba
- Genetics Unit, Marqués de Valdecilla Clinical University Hospital, Santander, Spain
| | - Francisco Laranjeira
- Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar Do Porto, Porto, Portugal
| | - Sofia Quintans
- Neuropediatrics Unit, Santa María Hospital, Lisbon, Portugal
| | - Oana Moldovan
- Genetics Unit, Santa María Hospital, Lisbon, Portugal
| | - Blanca Felgueroso
- Neuropediatrics Unit, Teresa Herrera Child's Hospital, A Coruña, Spain
| | | | - Rogelio Simón
- Neuropediatrics Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain
| | - Ana Camacho
- Neuropediatrics Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain.,Department of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Pilar Quijada
- Metabolic Disorders Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain
| | - Salvador Ibanez-Mico
- Neuropediatrics Unit, Virgen de la Arrixaca Clinical University Hospital, Murcia, Spain
| | - Mª Rosario Domingno
- Neuropediatrics Unit, Virgen de la Arrixaca Clinical University Hospital, Murcia, Spain
| | - Carmen Benito
- Genetics Unit, Clinical University Hospital of Málaga, Málaga, Spain
| | - Rocío Calvo
- Neuropediatrics Unit, Clinical University Hospital of Málaga, Málaga, Spain
| | - Antonia Pérez-Cejas
- Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain
| | - Mª Llanos Carrasco
- Neuropediatrics Unit, Clinical University Hospital Severo Ochoa, Leganés, Madrid, Spain
| | - Feliciano Ramos
- Clinical Genetics Unit, Pediatrics, Clinical University Hospital of Zaragoza, Zaragoza, Spain
| | - Mª Luz Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mª Luz Ruiz-Falcó
- Neuropediatrics Unit, Niño Jesús Clinical University Hospital, Madrid, Spain
| | | | - Margarita Martínez-Atienza
- Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain.,Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain.,Molecular Genetics Unit, Virgen de las Nieves Clinical University Hospital, Granada, Spain
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