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Szakállas N, Barták BK, Valcz G, Nagy ZB, Takács I, Molnár B. Can long-read sequencing tackle the barriers, which the next-generation could not? A review. Pathol Oncol Res 2024; 30:1611676. [PMID: 38818014 PMCID: PMC11137202 DOI: 10.3389/pore.2024.1611676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.
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Affiliation(s)
- Nikolett Szakállas
- Department of Biological Physics, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
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Mastrangelo M, Galosi S, Cesario S, Renzi A, Campea L, Leuzzi V. Presenting Patterns of Genetically Determined Developmental Encephalopathies With Epilepsy and Movement Disorders: A Single Tertiary Center Retrospective Cohort Study. Front Neurol 2022; 13:855134. [PMID: 35795805 PMCID: PMC9251420 DOI: 10.3389/fneur.2022.855134] [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: 01/14/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThis paper aimed to evaluate the frequency of observation of genetically determined developmental encephalopathies with epilepsy and movement disorders in a specialistic center, the distribution of etiologies and presenting clinical hallmarks, and the mean times for the achievement of molecular genetic diagnosis.Patients and MethodsRetrospective data about clinical phenotypes, etiology, and diagnostic pathways were collected in all the genetically confirmed patients with developmental encephalopathies with epilepsy and movement disorders referred to our institution between 2010 and 2020. The cohort was divided into two groups according to the predominant movement disorder type: 1) Group A: patients with hyperkinetic movement disorders; 2) Group B: patients with hypokinetic movement disorders. Both groups were analyzed in terms of developmental, epileptic, and movement disorder phenotypes.ResultsThe cohort included 69 patients (Group A = 53; Group B = 16). The etiological spectrum was heterogeneous with a predominance of Rett and Angelman syndrome in Group A and neurodegenerative disorders in Group B. A moderate/severe intellectual disability was assessed in 58/69 patients (mean age at the first signs of developmental impairment = 1,87 ± 1,72 years). Group A included patients with an earlier onset of epileptic seizures (2,63 ± 3,15 vs. 4,45 ± 5,55 years of group B) and a predominant generalized motor semiology of seizures at the onset. Focal seizures were the main initial epileptic manifestations in Group B. Seizures were noticed earlier than movement disorders in Group A while the opposite occurred in Group B. A higher increase in molecular genetic diagnosis was obtained in the last five years. Mean diagnostic delay was longer in Group B than in Group A (12,26 ± 13,32 vs. 5.66 ± 6.41 years). Chorea as an initial movement disorder was associated with a significantly longer diagnostic delay and a higher age at etiological diagnosis.ConclusionsThis study suggested: (a) a higher frequency of genetic defects involving neurotransmission, neuronal excitability, or neural development in patients with hyperkinetic movement disorders; (b) a higher frequency of neurodegenerative courses and a longer diagnostic delay in patients with hypokinetic movement disorders.
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Affiliation(s)
- Mario Mastrangelo
- Child Neurology and Psychiatry Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Serena Galosi
- Child Neurology and Psychiatry Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Serena Cesario
- Child Neurology and Psychiatry Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Alessia Renzi
- Department of Dynamic and Clinical Psychology, and Health Studies, Sapienza University of Rome, Rome, Italy
| | - Lucilla Campea
- Child Neurology and Psychiatry Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Vincenzo Leuzzi
- Child Neurology and Psychiatry Unit, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
- *Correspondence: Vincenzo Leuzzi
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Xie D, Duan R, Li C, Xie Z, Wang A, Xiong L, Wei J, Xi H, Fang J, Yan H, Wang J, Zhang Y, Mao X, Wang J, Wang H. Study on the Economic Burden of Neurodevelopmental Diseases on Patients With Genetic Diagnosis. Front Public Health 2022; 10:887796. [PMID: 35615033 PMCID: PMC9126321 DOI: 10.3389/fpubh.2022.887796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To study the burden of neurodevelopmental diseases (NDDs) via cost-of-illness analysis of Chinese patients with genetic diagnosis. Methods We recruited NDD patients (0–18 years old) with genetic diagnosis (GD) from September 1, 2020 to January 30, 2021. We gathered basic information on the details of diagnosis, as well as the direct medical cost, direct non-healthcare cost and indirect cost before and after receiving GD. We corrected the cost for time biases by calculating the cost per day for each patient. Results For the 502 patients with NDDs, the mean age was 4.08 ± 3.47. The household income was 0.6 (0.4, 1.0) 10,000 CNY per-month on average. The direct medical cost, direct non-healthcare cost and indirect cost were 12.27 (7.36, 22.23) 10,000 CNY, 1.45 (0.73, 2.69)10,000 CNY and 14.14(4.80, 28.25) 10,000 CNY per patient, respectively. Every patient received 1.20 (0.34, 3.60) 10,000 CNY on average (15.91%) from insurance. The daily total cost after receiving GD were ~62.48% lower than those before GD (191.59 CNY vs. 71.45 CNY). The descend range of lab cost (95.77%, P < 0.05) was the largest, followed by drugs (91.39%, P < 0.05), hospitalization (90.85%, P < 0.05), and consultation (57.41%, P < 0.05). The cost of rehabilitation kept slightly increasing but there were no significant differences (P > 0.05). The daily direct medical cost of each patient fell by 75.26% (P < 0.05) from 311.79 CNY to 77.14 CNY when the diagnostic age was younger than 1, and declined by 49.30% (P < 0.05) and 8.97% (P > 0.05) when the diagnostic age was 1–3 and older than 3, respectively. Conclusions Early genetic diagnosis is crucial for to reducing the burden of disease because of the amount of money spent was lower when they are diagnosed at younger age. Patients with NDDs can incur a heavy economic burden, especially in rehabilitation cost and indirect cost, because the insurance coverage for patients is low, so it is urgent for governments to pay more attention to these issues.
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Affiliation(s)
- Donghua Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Department of Neurology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Li
- Children Health Hospital of Shenzhen City, Shenzhen, China
| | - Zhiqun Xie
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Aihua Wang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Lili Xiong
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Jianhui Wei
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Hui Xi
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Junqu Fang
- Department of Information Management, Maternal and Child Health Hospital of Hunan Province, Changsha, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Junyu Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiao Mao
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- *Correspondence: Xiao Mao
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
- Jingmin Wang
| | - Hua Wang
- NHC Key Laboratory of Birth Defect for Research and Prevention (Maternal and Child Health Hospital of Hunan Province), Changsha, China
- Hua Wang
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4
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Wang WL, Tu CF, Tan YQ. Insight on multiple morphological abnormalities of sperm flagella in male infertility: what is new? Asian J Androl 2021; 22:236-245. [PMID: 31210147 PMCID: PMC7275805 DOI: 10.4103/aja.aja_53_19] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The syndrome of multiple morphological abnormalities of the sperm flagella (MMAF) is a specific kind of asthenoteratozoospermia with a mosaic of flagellar morphological abnormalities (absent, short, bent, coiled, and irregular flagella). MMAF was proposed in 2014 and has attracted increasing attention; however, it has not been clearly understood. In this review, we elucidate the definition of MMAF from a systematical view, the difference between MMAF and other conditions with asthenoteratozoospermia or asthenozoospermia (such as primary mitochondrial sheath defects and primary ciliary dyskinesia), the knowledge regarding its etiological mechanism and related genetic findings, and the clinical significance of MMAF for intracytoplasmic sperm injection and genetic counseling. This review provides the basic knowledge for MMAF and puts forward some suggestions for further investigations.
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Affiliation(s)
- Wei-Li Wang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410078, China
| | - Chao-Feng Tu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410078, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410078, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410078, China.,National Engineering and Research Center of Human Stem Cell, Changsha 410078, China
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5
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Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
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6
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Kim YG, Kim MJ, Lee JS, Lee JA, Song JY, Cho SI, Park SS, Seong MW. SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use. J Mol Diagn 2020; 23:140-148. [PMID: 33246077 DOI: 10.1016/j.jmoldx.2020.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 01/03/2023] Open
Abstract
Despite the wide application of next-generation sequencing, Sanger sequencing still plays a necessary role in clinical laboratories. However, recent developments in the field of bioinformatics have focused mostly on next-generation sequencing, while tools for Sanger sequencing have shown little progress. In this study, SnackVar (https://github.com/Young-gonKim/SnackVar, last accessed June 22, 2020), a novel graphical user interface-based software for Sanger sequencing, was developed. All types of variants, including heterozygous insertion/deletion variants, can be identified by SnackVar with minimal user effort. The featured reference sequences of all of the genes are prestored in SnackVar, allowing for detected variants to be precisely described based on coding DNA references according to the nomenclature of the Human Genome Variation Society. Among 88 previously reported variants from four insertion/deletion-rich genes (BRCA1, APC, CALR, and CEBPA), the result of SnackVar agreed with reported results in 87 variants [98.9% (93.0%; 99.9%)]. The cause of one incorrect variant calling was proven to be erroneous base callings from poor-quality trace files. Compared with commercial software, SnackVar required less than one-half of the time taken for the analysis of a selected set of test cases. We expect SnackVar to be a cost-effective option for clinical laboratories performing Sanger sequencing.
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Affiliation(s)
- Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jung Ae Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ji Yun Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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7
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Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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8
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Caglayan AO, Gumus H, Sandford E, Kubisiak TL, Ma Q, Ozel AB, Per H, Li JZ, Shakkottai VG, Burmeister M. COQ4 Mutation Leads to Childhood-Onset Ataxia Improved by CoQ10 Administration. THE CEREBELLUM 2019; 18:665-669. [PMID: 30847826 DOI: 10.1007/s12311-019-01011-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahmet Okay Caglayan
- Department of Medical Genetics, School of Medicine, Demiroglu Bilim University, 34394, Istanbul, Turkey
| | - Hakan Gumus
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, Erciyes University, 38039, Kayseri, Turkey
| | - Erin Sandford
- Molecular & Behavioral Neuroscience Institute, University of Michigan, 5061 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Thomas L Kubisiak
- Molecular & Behavioral Neuroscience Institute, University of Michigan, 5061 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Qianyi Ma
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - A Bilge Ozel
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Huseyin Per
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, Erciyes University, 38039, Kayseri, Turkey
| | - Jun Z Li
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vikram G Shakkottai
- Department of Neurology, Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of Michigan, 5061 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA. .,Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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9
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Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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10
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Martinez G, Kherraf ZE, Zouari R, Fourati Ben Mustapha S, Saut A, Pernet-Gallay K, Bertrand A, Bidart M, Hograindleur JP, Amiri-Yekta A, Kharouf M, Karaouzène T, Thierry-Mieg N, Dacheux-Deschamps D, Satre V, Bonhivers M, Touré A, Arnoult C, Ray PF, Coutton C. Whole-exome sequencing identifies mutations in FSIP2 as a recurrent cause of multiple morphological abnormalities of the sperm flagella. Hum Reprod 2019; 33:1973-1984. [PMID: 30137358 DOI: 10.1093/humrep/dey264] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/13/2018] [Indexed: 12/30/2022] Open
Abstract
STUDY QUESTION Can whole-exome sequencing (WES) of infertile patients identify new genes responsible for multiple morphological abnormalities of the sperm flagella (MMAF)? SUMMARY ANSWER WES analysis of 78 infertile men with a MMAF phenotype permitted the identification of four homozygous mutations in the fibrous sheath (FS) interacting protein 2 (FSIP2) gene in four unrelated individuals. WHAT IS KNOWN ALREADY The use of high-throughput sequencing techniques revealed that mutations in the dynein axonemal heavy chain 1 (DNAH1) gene, and in the cilia and flagella associated protein 43 (CFAP43) and 44 (CFAP44) genes account for approximately one-third of MMAF cases thus indicating that other relevant genes await identification. STUDY DESIGN, SIZE, DURATION This was a retrospective genetics study of 78 patients presenting a MMAF phenotype who were recruited in three fertility clinics between 2008 and 2015. Control sperm samples were obtained from normospermic donors. Allelic frequency for control subjects was derived from large public databases. PARTICIPANTS/MATERIALS, SETTING, METHODS WES was performed for all 78 subjects. All identified variants were confirmed by Sanger sequencing. Relative mRNA expression levels for the selected candidate gene (FSIP2) was assessed by quantitative RT-PCR in a panel of normal human and mouse tissues. To characterize the structural and ultrastructural anomalies present in patients' sperm, immunofluorescence (IF) was performed on sperm samples from two subjects with a mutation and one control and transmission electron microscopy (TEM) analyses was performed on sperm samples from one subject with a mutation and one control. MAIN RESULTS AND THE ROLE OF CHANCE We identified four unrelated patients (4/78, 5.1%) with homozygous loss of function mutations in the FSIP2 gene, which encodes a protein of the sperm FS and is specifically expressed in human and mouse testis. None of these mutations were reported in control sequence databases. TEM analyses showed a complete disorganization of the FS associated with axonemal defects. IF analyses confirmed that the central-pair microtubules and the inner and outer dynein arms of the axoneme were abnormal in all four patients carrying FSIP2 mutations. Importantly, and in contrast to what was observed in patients with MMAF and mutations in other MMAF-related genes (DNAH1, CFAP43 and CFAP44), mutations in FSIP2 led to the absence of A-kinase anchoring protein 4 (AKAP4). LIMITATIONS, REASONS FOR CAUTION The low number of biological samples and the absence of a reliable anti-FSIP2 antibody prevented the formal demonstration that the FSIP2 protein was absent in sperm from subjects with a FSIP2 mutation. WIDER IMPLICATIONS OF THE FINDINGS Our findings indicate that FSIP2 is one of the main genes involved in MMAF syndrome. In humans, genes previously associated with a MMAF phenotype encoded axonemal-associated proteins (DNAH1, CFAP43 and CFAP44). We show here that FSIP2, a protein of the sperm FS, is also logically associated with MMAF syndrome as we showed that it is necessary for FS assembly and for the overall axonemal and flagellar biogenesis. As was suggested before in mouse and man, our results also suggest that defects in AKAP4, one of the main proteins interacting with FSIP2, would induce a MMAF phenotype. Finally, this work reinforces the demonstration that WES sequencing is a good strategy to reach a genetic diagnosis for patients with severe male infertility phenotypes. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the following grants: the 'MAS-Flagella' project financed by the French ANR and the DGOS for the program PRTS 2014 (14-CE15) and the 'Whole genome sequencing of patients with Flagellar Growth Defects (FGD)' project financed by the Fondation Maladies Rares for the program Séquençage à haut débit 2012. The authors have no conflict of interest.
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Affiliation(s)
- Guillaume Martinez
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | - Zine-Eddine Kherraf
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU de Grenoble, UM GI-DPI, Grenoble, France
| | - Raoudha Zouari
- Clinique des Jasmins, 23, Av. Louis BRAILLE 1002 Belvedere, Tunis, Tunisia
| | | | - Antoine Saut
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | | | - Anne Bertrand
- Grenoble Neuroscience Institute, INSERM 1216, Grenoble, France
| | - Marie Bidart
- CHU Grenoble Alpes, UM de Biochimie Génétique et Moléculaire, Grenoble, France
| | - Jean Pascal Hograindleur
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Amir Amiri-Yekta
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Biochimie Génétique et Moléculaire, Grenoble, France.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mahmoud Kharouf
- Clinique des Jasmins, 23, Av. Louis BRAILLE 1002 Belvedere, Tunis, Tunisia
| | - Thomas Karaouzène
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,University Grenoble Alpes/CNRS, TIMC-IMAG, Grenoble, France
| | | | - Denis Dacheux-Deschamps
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR, Bordeaux, France.,Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR-CNRS 5234, Bordeaux, France
| | - Véronique Satre
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | - Mélanie Bonhivers
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR, Bordeaux, France.,Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR-CNRS 5234, Bordeaux, France
| | - Aminata Touré
- INSERM U1016, Institut Cochin, Paris, France.,Centre National de la Recherche Scientifique UMR8104, Paris, France.,Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Christophe Arnoult
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Pierre F Ray
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU de Grenoble, UM GI-DPI, Grenoble, France
| | - Charles Coutton
- University Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
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11
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Exome sequencing in adult neurology practice: Challenges and rewards in a mixed resource setting. Clin Neurol Neurosurg 2018; 174:48-56. [DOI: 10.1016/j.clineuro.2018.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022]
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12
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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13
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Fogel BL. Genetic and genomic testing for neurologic disease in clinical practice. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:11-22. [PMID: 29325607 DOI: 10.1016/b978-0-444-63233-3.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The influence of genetics on neurologic disease is broad and it is becoming more common that clinicians are presented with a patient whose disease is likely of genetic origin. In the search for mutations causing Mendelian disorders, advances in genetic testing methodology have propelled modern neurologic practice beyond single-gene testing into the realm of genomic medicine, where routine evaluations encompass hundreds or thousands of genes, or even the entire exome, representing all protein-coding genes in the genome. The role of various single-gene, multigene, and genomic testing methods, including chromosomal microarray and next-generation sequencing, in the evaluation of neurologic disease is discussed here to provide a framework for their use in a modern neurologic practice. Understanding the inherent issues that arise during the interpretation of sequence variants as pathogenic or benign and the potential discovery of incidental medically relevant findings are important considerations for neurologists utilizing these tests clinically. Strategies for the evaluation of clinically heterogeneous disorders are presented to guide neurologists in the transition from single-gene to genomic considerations and toward the prospect of the widespread routine use of exome sequencing in the continuing goal to achieve more rapid and more precise diagnoses that will improve management and outcome in patients challenged by neurologic disease.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States.
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14
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Dong FN, Amiri-Yekta A, Martinez G, Saut A, Tek J, Stouvenel L, Lorès P, Karaouzène T, Thierry-Mieg N, Satre V, Brouillet S, Daneshipour A, Hosseini SH, Bonhivers M, Gourabi H, Dulioust E, Arnoult C, Touré A, Ray PF, Zhao H, Coutton C. Absence of CFAP69 Causes Male Infertility due to Multiple Morphological Abnormalities of the Flagella in Human and Mouse. Am J Hum Genet 2018; 102:636-648. [PMID: 29606301 DOI: 10.1016/j.ajhg.2018.03.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/05/2018] [Indexed: 10/17/2022] Open
Abstract
The multiple morphological abnormalities of the flagella (MMAF) phenotype is among the most severe forms of sperm defects responsible for male infertility. The phenotype is characterized by the presence in the ejaculate of immotile spermatozoa with severe flagellar abnormalities including flagella being short, coiled, absent, and of irregular caliber. Recent studies have demonstrated that MMAF is genetically heterogeneous, and genes thus far associated with MMAF account for only one-third of cases. Here we report the identification of homozygous truncating mutations (one stop-gain and one splicing variant) in CFAP69 of two unrelated individuals by whole-exome sequencing of a cohort of 78 infertile men with MMAF. CFAP69 encodes an evolutionarily conserved protein found at high levels in the testis. Immunostaining experiments in sperm from fertile control individuals showed that CFAP69 localized to the midpiece of the flagellum, and the absence of CFAP69 was confirmed in both individuals carrying CFPA69 mutations. Additionally, we found that sperm from a Cfap69 knockout mouse model recapitulated the MMAF phenotype. Ultrastructural analysis of testicular sperm from the knockout mice showed severe disruption of flagellum structure, but histological analysis of testes from these mice revealed the presence of all stages of the seminiferous epithelium, indicating that the overall progression of spermatogenesis is preserved and that the sperm defects likely arise during spermiogenesis. Together, our data indicate that CFAP69 is necessary for flagellum assembly/stability and that in both humans and mice, biallelic truncating mutations in CFAP69 cause autosomal-recessive MMAF and primary male infertility.
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15
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Abstract
The autosomal-recessive cerebellar ataxias comprise more than half of the known genetic forms of ataxia and represent an extensive group of clinically heterogeneous disorders that can occur at any age but whose onset is typically prior to adulthood. In addition to ataxia, patients often present with polyneuropathy and clinical symptoms outside the nervous system. The most common of these diseases is Friedreich ataxia, caused by mutation of the frataxin gene, but recent advances in genetic analysis have greatly broadened the ever-expanding number of causative genes to over 50. In this review, the clinical neurogenetics of the recessive cerebellar ataxias will be discussed, including updates on recently identified novel ataxia genes, advancements in unraveling disease-specific molecular pathogenesis leading to ataxia, potential treatments under development, technologic improvements in diagnostic testing such as clinical exome sequencing, and what the future holds for clinicians and geneticists.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States.
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16
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Pang SYY, Teo KC, Hsu JS, Chang RSK, Li M, Sham PC, Ho SL. The role of gene variants in the pathogenesis of neurodegenerative disorders as revealed by next generation sequencing studies: a review. Transl Neurodegener 2017; 6:27. [PMID: 29046784 PMCID: PMC5639582 DOI: 10.1186/s40035-017-0098-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
The clinical diagnosis of neurodegenerative disorders based on phenotype is difficult in heterogeneous conditions with overlapping symptoms. It does not take into account the disease etiology or the highly variable clinical course even amongst patients diagnosed with the same disorder. The advent of next generation sequencing (NGS) has allowed for a system-wide, unbiased approach to identify all gene variants in the genome simultaneously. With the plethora of new genes being identified, genetic rather than phenotype-based classification of Mendelian diseases such as spinocerebellar ataxia (SCA), hereditary spastic paraplegia (HSP) and Charcot-Marie-Tooth disease (CMT) has become widely accepted. It has also become clear that gene variants play a role in common and predominantly sporadic neurodegenerative diseases such as Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). The observation of pleiotropy has emerged, with mutations in the same gene giving rise to diverse phenotypes, which further increases the complexity of phenotype-genotype correlation. Possible mechanisms of pleiotropy include different downstream effects of different mutations in the same gene, presence of modifier genes, and oligogenic inheritance. Future directions include development of bioinformatics tools and establishment of more extensive public genotype/phenotype databases to better distinguish deleterious gene variants from benign polymorphisms, translation of genetic findings into pathogenic mechanisms through in-vitro and in-vivo studies, and ultimately finding disease-modifying therapies for neurodegenerative disorders.
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Affiliation(s)
- Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Kay-Cheong Teo
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Jacob Shujui Hsu
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Richard Shek-Kwan Chang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Miaoxin Li
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China.,Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, People's Republic of China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
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17
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Valera JM, Diaz T, Petty LE, Quintáns B, Yáñez Z, Boerwinkle E, Muzny D, Akhmedov D, Berdeaux R, Sobrido MJ, Gibbs R, Lupski JR, Geschwind DH, Perlman S, Below JE, Fogel BL. Prevalence of spinocerebellar ataxia 36 in a US population. NEUROLOGY-GENETICS 2017; 3:e174. [PMID: 28761930 PMCID: PMC5515602 DOI: 10.1212/nxg.0000000000000174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/10/2017] [Indexed: 12/12/2022]
Abstract
Objective: To assess the prevalence and clinical features of individuals affected by spinocerebellar ataxia 36 (SCA36) at a large tertiary referral center in the United States. Methods: A total of 577 patients with undiagnosed sporadic or familial cerebellar ataxia comprehensively evaluated at a tertiary referral ataxia center were molecularly evaluated for SCA36. Repeat primed PCR and fragment analysis were used to screen for the presence of a repeat expansion in the NOP56 gene. Results: Fragment analysis of triplet repeat primed PCR products identified a GGCCTG hexanucleotide repeat expansion in intron 1 of NOP56 in 4 index cases. These 4 SCA36-positive families comprised 2 distinct ethnic groups: white (European) (2) and Asian (Japanese [1] and Vietnamese [1]). Individuals affected by SCA36 exhibited typical clinical features with gait ataxia and age at onset ranging between 35 and 50 years. Patients also suffered from ataxic or spastic limbs, altered reflexes, abnormal ocular movement, and cognitive impairment. Conclusions: In a US population, SCA36 was observed to be a rare disorder, accounting for 0.7% (4/577 index cases) of disease in a large undiagnosed ataxia cohort.
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Affiliation(s)
- Juliana M Valera
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Tatyana Diaz
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Lauren E Petty
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Beatriz Quintáns
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Zuleima Yáñez
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Eric Boerwinkle
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Donna Muzny
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Dmitry Akhmedov
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Rebecca Berdeaux
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Maria J Sobrido
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Richard Gibbs
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - James R Lupski
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Daniel H Geschwind
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Susan Perlman
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Jennifer E Below
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Brent L Fogel
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
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Wolf SM, Thyagarajan B, Fogel BL. The need to develop a patient-centered precision medicine model for adults with chronic disability. Expert Rev Mol Diagn 2017; 17:415-418. [PMID: 28325089 DOI: 10.1080/14737159.2017.1309976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Susan M Wolf
- a Law School, Medical School, Consortium on Law and Values in Health, Environment & the Life Sciences , University of Minnesota , Minneapolis , MN , USA
| | - Bharat Thyagarajan
- b Department of Laboratory Medicine and Pathology , University of Minnesota , Minneapolis , MN , USA
| | - Brent L Fogel
- c University of California-Los Angeles (UCLA) , Departments of Neurology and Human Genetics , Los Angeles , CA , USA
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19
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Bonifati V. Will New Genetic Techniques Like Exome Sequencing and Others Obviate the Need for Clinical Expertise? Yes. Mov Disord Clin Pract 2017; 4:36-38. [PMID: 30713946 DOI: 10.1002/mdc3.12438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/08/2016] [Accepted: 08/12/2016] [Indexed: 12/24/2022] Open
Affiliation(s)
- Vincenzo Bonifati
- Department of Clinical Genetics Erasmus Medical Center Rotterdam the Netherlands
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Abstract
PURPOSE OF REVIEW The landscape of genetic diagnostic testing has changed dramatically with the introduction of next-generation clinical exome sequencing (CES), which provides an unbiased analysis of all protein-coding sequences in the roughly 21,000 genes in the human genome. Use of this testing, however, is currently limited in clinical neurologic practice by the lack of a framework for appropriate use and payer coverage. RECENT FINDINGS CES can be cost-effective due to its high diagnostic yield in comparison to other genetic tests in current use and should be utilized as a routine diagnostic test in patients with heterogeneous neurologic phenotypes facing a broad genetic differential diagnosis. CES can eliminate the need for escalating sequences of conventional neurodiagnostic tests. SUMMARY This review discusses the role of clinical exome sequencing in neurologic disease, including its benefits to patients, limitations, appropriate use, and billing. We also provide a reference template policy for payer use when considering testing requests.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics and Departments of Neurology and Human Genetics (BLF), David Geffen School of Medicine, University of California Los Angeles; Health Policy Consultant (SS-M), Santa Maria, CA; and NeuroDevelopmental Science Center and the Department of Pediatrics (BHC), Akron Children's Hospital, OH
| | - Saty Satya-Murti
- Program in Neurogenetics and Departments of Neurology and Human Genetics (BLF), David Geffen School of Medicine, University of California Los Angeles; Health Policy Consultant (SS-M), Santa Maria, CA; and NeuroDevelopmental Science Center and the Department of Pediatrics (BHC), Akron Children's Hospital, OH
| | - Bruce H Cohen
- Program in Neurogenetics and Departments of Neurology and Human Genetics (BLF), David Geffen School of Medicine, University of California Los Angeles; Health Policy Consultant (SS-M), Santa Maria, CA; and NeuroDevelopmental Science Center and the Department of Pediatrics (BHC), Akron Children's Hospital, OH
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