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Miyahira AK, Kamran SC, Jamaspishvili T, Marshall CH, Maxwell KN, Parolia A, Zorko NA, Pienta KJ, Soule HR. Disrupting prostate cancer research: Challenge accepted; report from the 2023 Coffey-Holden Prostate Cancer Academy Meeting. Prostate 2024; 84:993-1015. [PMID: 38682886 DOI: 10.1002/pros.24721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION The 2023 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, themed "Disrupting Prostate Cancer Research: Challenge Accepted," was convened at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA, from June 22 to 25, 2023. METHODS The 2023 marked the 10th Annual CHPCA Meeting, a discussion-oriented scientific think-tank conference convened annually by the Prostate Cancer Foundation, which centers on innovative and emerging research topics deemed pivotal for advancing critical unmet needs in prostate cancer research and clinical care. The 2023 CHPCA Meeting was attended by 81 academic investigators and included 40 talks across 8 sessions. RESULTS The central topic areas covered at the meeting included: targeting transcription factor neo-enhancesomes in cancer, AR as a pro-differentiation and oncogenic transcription factor, why few are cured with androgen deprivation therapy and how to change dogma to cure metastatic prostate cancer without castration, reducing prostate cancer morbidity and mortality with genetics, opportunities for radiation to enhance therapeutic benefit in oligometastatic prostate cancer, novel immunotherapeutic approaches, and the new era of artificial intelligence-driven precision medicine. DISCUSSION This article provides an overview of the scientific presentations delivered at the 2023 CHPCA Meeting, such that this knowledge can help in facilitating the advancement of prostate cancer research worldwide.
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Affiliation(s)
- Andrea K Miyahira
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Jamaspishvili
- Department of Pathology and Laboratory Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Catherine H Marshall
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kara N Maxwell
- Department of Medicine-Hematology/Oncology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medicine Service, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Abhijit Parolia
- Department of Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas A Zorko
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- University of Minnesota Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
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Savad S, Modarressi MH, Younesi S, Seifi-Alan M, Samadaian N, Masoomy M, Dianatpour M, Norouzi S, Amidi S, Boroumand A, Ashrafi MR, Ronagh A, Eslami M, Hashemnejad M, Nourian S, Mohammadi S, Taheri Amin MM, Heidari M, Seifi-Alan M, Shojaaldini Ardakani H, Aghamahdi F, Khalilian S, Ghafouri-Fard S. A Comprehensive Overview of NF1 Mutations in Iranian Patients. Neuromolecular Med 2024; 26:28. [PMID: 38954284 DOI: 10.1007/s12017-024-08790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/30/2024] [Indexed: 07/04/2024]
Abstract
Neurofibromatosis type 1 (NF1) is a genetic disorder caused by mutations in the NF1 gene. This disorder shows nearly complete penetrance and high phenotypic variability. We used the whole-exome sequencing technique to identify mutations in 32 NF1 cases from 22 Iranian families. A total of 31 variants, including 30 point mutations and one large deletion, were detected. In eight cases, variants were inherited, while they were sporadic in the remaining. Seven novel variants, including c.5576 T > G, c.6658_6659insC, c.2322dupT, c.92_93insAA, c.4360C > T, c.3814C > T, and c.4565_4566delinsC, were identified. The current study is the largest in terms of the sample size of Iranian NF1 cases with identified mutations. The results can broaden the spectrum of NF1 mutations and facilitate the process of genetic counseling in the affected families.
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Affiliation(s)
| | | | - Sarang Younesi
- Prenatal Screening Department, Nilou Laboratory, Tehran, Iran
| | - Mahnaz Seifi-Alan
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Mona Masoomy
- Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehdi Dianatpour
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Human Genetic, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | | | - Mahmoud Reza Ashrafi
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Ataxia Clinic, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ronagh
- Department of Pediatrics Neurologists, Shahid Bahonar Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Eslami
- Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Hashemnejad
- Department of Obstetrics and Gynecology, School of Medicine, Kamali Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Shahab Nourian
- Department of Pediatrics Endocrinology and Metabolisms, Emam Ali Hospital, Alborz University of Medical Sciences and Health Services, Karaj, Iran
| | - Sanaz Mohammadi
- Comprehensive Medical Genetics Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Morteza Heidari
- Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Ataxia Clinic, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahin Seifi-Alan
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Fatemeh Aghamahdi
- Department of Pediatrics, Alborz University of Medical Sciences, Karaj, Iran
| | - Sheyda Khalilian
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Mohd Nippah NF, Abu N, Ab Mutalib NS, Alias H. Advances in next-generation sequencing for relapsed pediatric acute lymphoblastic leukemia: current insights and future directions. Front Genet 2024; 15:1394523. [PMID: 38894724 PMCID: PMC11183504 DOI: 10.3389/fgene.2024.1394523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Leukemia is one of the most common cancers in children; and its genetic diversity in the landscape of acute lymphoblastic leukemia (ALL) is important for diagnosis, risk assessment, and therapeutic approaches. Relapsed ALL remains the leading cause of cancer deaths among children. Almost 20% of children who are treated for ALL and achieve complete remission experience disease recurrence. Relapsed ALL has a poor prognosis, and relapses are more likely to have mutations that affect signaling pathways, chromatin patterning, tumor suppression, and nucleoside metabolism. The identification of ALL subtypes has been based on genomic alterations for several decades, using the molecular landscape at relapse and its clinical significance. Next-generation sequencing (NGS), also known as massive parallel sequencing, is a high-throughput, quick, accurate, and sensitive method to examine the molecular landscape of cancer. This has undoubtedly transformed the study of relapsed ALL. The implementation of NGS has improved ALL genomic analysis, resulting in the recent identification of various novel molecular entities and a deeper understanding of existing ones. Thus, this review aimed to consolidate and critically evaluate the most current information on relapsed pediatric ALL provided by NGS technology. In this phase of targeted therapy and personalized medicine, identifying the capabilities, benefits, and drawbacks of NGS will be essential for healthcare professionals and researchers offering genome-driven care. This would contribute to precision medicine to treat these patients and help improve their overall survival and quality of life.
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Affiliation(s)
- Nur Farhana Mohd Nippah
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Hamidah Alias
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
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Zhang X, Xu L, Pan E, Sun X, Ding X. Partial remission with sintilimab monotherapy in a patient carrying a CD274 amplification in refractory diffuse large B‑cell lymphoma: A case report. Oncol Lett 2024; 27:289. [PMID: 38736746 PMCID: PMC11083924 DOI: 10.3892/ol.2024.14423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/22/2024] [Indexed: 05/14/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with varying characteristics, in terms of genomic variation, cell morphology and clinical presentation. At present, only ~66% of patients are cured with initial treatment and those with refractory DLBCL exhibit a poor prognosis. Thus, further investigations into novel effective treatment options for DLBCL are required. The present study reports the case of a patient resistant to multiple therapies, including rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) plus enzastaurin (trial no. CTR20171560), GemOx plus lenalidomide and selinexor (trial no. ATG-010-DLBCL-001). The patient harbored a CD274 amplification, as identified via next-generation sequencing (NGS), and exhibited a high programmed death-ligand 1 Tumor Proportion Score of up to 95%. Consequently, the patient was treated with sintilimab monotherapy and the response lasted for 12 months of follow-up without major immune-related adverse events. This case highlights the role of NGS technology in selecting treatment options for refractory DLBCL. Furthermore, the results of the present study suggest that sintilimab may have potential in the treatment of patients with refractory DLBCL.
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Affiliation(s)
- Xian Zhang
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Liye Xu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Evenki Pan
- Department of Medical Services, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210031, P.R. China
| | - Xiuhua Sun
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Xiaolei Ding
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
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Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [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: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
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Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Goel S, Deshpande S, Dhaniwala N, Singh R, Suneja A, Jadawala VH. A Comprehensive Review of Genetic Variations in Collagen-Encoding Genes and Their Implications in Intervertebral Disc Degeneration. Cureus 2024; 16:e52708. [PMID: 38384607 PMCID: PMC10880043 DOI: 10.7759/cureus.52708] [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: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
This comprehensive review examines the intricate relationship between genetic variations in collagen-encoding genes and their implications in intervertebral disc degeneration (IVDD). Intervertebral disc degeneration is a prevalent spinal condition characterized by structural and functional changes in intervertebral discs (IVDs), and understanding its genetic underpinnings is crucial for advancing diagnostic and therapeutic strategies. The review begins by exploring the background and importance of collagen in IVDs, emphasizing its role in providing structural integrity. It then delves into the significance of genetic variations within collagen-encoding genes, categorizing and discussing their potential impact on disc health. The methods employed in studying these variations, such as genome-wide association studies (GWASs) and next-generation sequencing (NGS), are also reviewed. The subsequent sections analyze existing literature to establish associations between genetic variations and IVDD, unraveling molecular mechanisms linking genetic factors to disc degeneration. The review concludes with a summary of key findings, implications for future research and clinical practice, and a reflection on the importance of understanding genetic variations in collagen-encoding genes to diagnose and treat IVDD. The insights gleaned from this review contribute to our understanding of IVDD and hold promise for the development of personalized interventions based on individual genetic profiles.
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Affiliation(s)
- Sachin Goel
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sanjay Deshpande
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Nareshkumar Dhaniwala
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Rahul Singh
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anmol Suneja
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Vivek H Jadawala
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Gowda VK, Reddy VS, Srinivasan VM, Vamyanmane DK. The Combined Neurogenetic Disorders; Blended Phenotype of Metachromatic Leukodystrophy (MLD) and Glutaric Aciduria Type 1 (GA -1) in an Indian Child. Ann Indian Acad Neurol 2024; 27:103-105. [PMID: 38495240 PMCID: PMC10941903 DOI: 10.4103/aian.aian_772_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/11/2023] [Indexed: 03/19/2024] Open
Affiliation(s)
- Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Viveka Santhosh Reddy
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Varunvenkat M Srinivasan
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
| | - Dhananjaya K Vamyanmane
- Department of Pediatric Radiology, Indira Gandhi Institute of Child Health, Bengaluru, Karnataka, India
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Yang T, Luo X, Liu Y, Lin M, Zhao Q, Zhang W, Chen Z, Dong M, Wang J, Wang Q, Zhang X, Zhong T. Next-generation sequencing analysis of the molecular spectrum of thalassemia in Southern Jiangxi, China. Hum Genomics 2023; 17:77. [PMID: 37592328 PMCID: PMC10436446 DOI: 10.1186/s40246-023-00520-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Thalassemia is an extremely prevalent monogenic inherited blood disorder in southern China. It is important to comprehensively understand the molecular spectrum of thalassemia in an area with such a high prevalence of thalassemia before taking appropriate actions for the prevention and treatment of this disorder. Herein, we explored the clinical feasibility of using next-generation sequencing (NGS) for large-scale population screening to illustrate the prevalence and spectrum of thalassemia in Southern Jiangxi. METHODS Blood samples collected from 136,312 residents of reproductive age in Southern Jiangxi were characterized for thalassemia by NGS. A retrospective analysis was then conducted on blood samples determined to be positive for thalassemia. RESULTS In total, 19,827 (14.545%) subjects were diagnosed as thalassemia carriers, and the thalassemia prevalence rate significantly varied by geographical region (p < 0.001). A total of 40 α-thalassemia genotypes including 21 rare genotypes were identified, with -@-SEA/αα being the most prevalent genotype. 42 β-thalassemia genotypes including 27 rare genotypes were identified, with the most common mutation IVS II-654 C > T accounting for 35.257% of these β-thalassemia genotypes. Furthermore, 74 genotypes were identified among 608 individuals with combined α- and β-thalassemia. Notably, most individuals with rare thalassemia mutations had mildly abnormal hematologic parameters including microcytic hypochromia. CONCLUSIONS Our findings demonstrate the great heterogeneity and diverse spectrum of thalassemia in Southern Jiangxi, emphasizing the importance and necessity of persistent prevention and control of thalassemia in this region. Additionally, our findings further suggest that NGS can effectively identify rare mutations and reduce the misdiagnosis rate of thalassemia.
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Affiliation(s)
- Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Xuemei Luo
- Ganzhou Municipal Health Commission, Ganzhou, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Qinfei Zhao
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Zhigang Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Minghua Dong
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Junli Wang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qi Wang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Xiaokang Zhang
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China.
| | - Tianyu Zhong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China.
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
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Magdy Mohamed Abdelaziz Barakat S, Sallehuddin R, Yuhaniz SS, R. Khairuddin RF, Mahmood Y. Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges. PeerJ Comput Sci 2023; 9:e1180. [PMID: 37547391 PMCID: PMC10403225 DOI: 10.7717/peerj-cs.1180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/27/2023] [Indexed: 08/08/2023]
Abstract
Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization. Results Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach. Conclusion We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
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Affiliation(s)
| | - Roselina Sallehuddin
- Computer Science, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Siti Sophiayati Yuhaniz
- Advanced Informatics Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Kuala Lumpur, Kuala Lumpur, Malaysia
| | | | - Yasir Mahmood
- Faculty of Information Technology, The University of Lahore, Lahore, Lahore, Pakistan
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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Schaflinger E, Enko D. Die Bedeutung der Hochdurchsatz-Sequenzierung in der medizinisch genetischen Diagnostik und Beratung. Dtsch Med Wochenschr 2022; 147:1336-1341. [DOI: 10.1055/a-1924-6646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
ZusammenfassungNext-Generation-Sequencing ist ein modernes diagnostisches Hochdurchsatz-Verfahren (Multi-Gen-Analysen), durch dessen Einsatz sowohl hereditäre Krebserkrankungen (Tumordispositionssyndrome, Keimbahndiagnostik) als auch somatische Alterationen in Tumoren besser abgeklärt werden können. Der breitere Einsatz dieser Technologie im medizinischen Alltag zeigt das tatsächliche Ausmaß der interindividuellen genetischen Variabilität. Wichtige Bedeutung hat dieses Verfahren für die Untersuchung von heterogenen genetischen Erkrankungen (z. B. Tumorerkrankungen, neurodegenerativen und -muskulären Erkrankungen) erlangt. Weitere Indikationsgebiete stellen die Pharmakogenetik sowie die nicht invasive Pränataldiagnostik dar. Es ist zu erwarten, dass dieses diagnostische Mittel eine breite klinische Anwendung finden wird. Mit der rasanten Zunahme und Komplexität genetischer Dateninformationen nimmt die richtige Interpretation und Übermittlung der Befunde in der humangenetischen Beratung (Keimbahndiagnostik) einen hohen Stellenwert ein. Die genetische Beratung muss entsprechend neu ausgerichtet und adaptiert werden.
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Affiliation(s)
| | - Dietmar Enko
- Klinisches Institut für Medizinische und Chemische Labordiagnostik, Medizinische Universität Graz
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Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3457806. [PMID: 36212714 PMCID: PMC9537002 DOI: 10.1155/2022/3457806] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Background Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.
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Affiliation(s)
- Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mirza Jawad ul Hasnain
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Syed Hassan Abbas
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mahmoud F. Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Naeem Aslam
- Department of Computer Science, NFCIET, Khanewal Road, Multan, Pakistan
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13
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Lee JH, Kim MG, Kim DY, Shin HW, Kang H, Koo BS, Kim KK. Effectiveness of an integrative medicine approach to improve cognitive dysfunction and dementia: An observational study. Medicine (Baltimore) 2022; 101:e30301. [PMID: 36197176 PMCID: PMC9509052 DOI: 10.1097/md.0000000000030301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Despite the urgent need to control dementia, an effective treatment has yet to be developed. Along with the Korean government's policy of cooperation between conventional medicine (CM) and Korean medicine (KM), integrative medical services for dementia patients are being provided. This study aimed to compare the integrative medical clinic (IMC) for dementia used by Dongguk University Hospitals (DUH) with other service models and to review the characteristics and treatment outcomes of patients who had visited DUH over the past 5 years. Patients' electronic medical records from May 2015 to June 2020 were searched and their data were analyzed to evaluate the IMC's service model. Patient demographic and clinical characteristics, diagnostic tests, and treatment patterns for CM and KM were collected. The proportion of patients who did not show worsening cognitive function was described in detail. A strength of the DUH integrative medicine clinic is its ability to manage both KM and CM patients in the same space at the same time. Among the 82 patients who visited the clinic during our study period, 56 remained for data analysis after we excluded patients who met the exclusion criteria; nineteen patients had diagnoses of mild cognitive impairment. Among collaboration patterns, the first visit to the IMC had the highest proportion (55.4%). Among diagnosed tests in CM, laboratory tests and neuropsychological tests were used the most. In KM, a heart rate variability test was frequently used. The most common CM treatment prescribed was anticonvulsants, with 22 patients (39.2%) receiving donepezil, whereas the most frequent KM treatments were acupuncture (82.1%) and herbal medicine (78.6%). Twelve patients were followed up with the Mini-Mental State Examination, and 8 demonstrated either no worsening or improved cognition (baseline Mini-Mental State Examination range: 21-26). All 8 patients had mild cognitive impairment including 6 with amnestic, multidomain impairment. This study searched for a way to improve cognitive dysfunction and dementia using an integrative approach, and it shows promising results for mild cognitive impairment. However, more precisely designed follow-up studies are needed to address the present work's limitations of a retrospective study design and a small sample size.
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Affiliation(s)
- Ji Hyun Lee
- Woorisaam Oriental Medicine Clinic, Goyang, South Korea
| | - Man Gi Kim
- Department of Oriental Neuropsychiatry, Dongguk University Ilsan Korean Medicine Hospital, Goyang, South Korea
- Department of Oriental Neuropsychiatry, Graduate School of Dongguk University, Seoul, South Korea
| | - Do Yeun Kim
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Goyang, South Korea
| | - Hye-Won Shin
- UCI Memory Impairments and Neurological Disorders (UCI MIND), Irvine, CA, USA
- RIIID Medical Group of Irvine, Irvine, CA, USA
| | - Hakmook Kang
- Biostatistics and Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA
| | - Byung Soo Koo
- Department of Oriental Neuropsychiatry, Dongguk University Ilsan Korean Medicine Hospital, Goyang, South Korea
- Department of Oriental Neuropsychiatry, Graduate School of Dongguk University, Seoul, South Korea
- *Correspondence: Byung Soo Koo, Department of Oriental Neuropsychiatry, Dongguk University Ilsan Korean Medicine Hospital, Goyang 10326, South Korea (e-mail: ) and Kwang Ki Kim, Department of Neurology, Dongguk University Ilsan Hospital, Goyang, 10326, South Korea (e-mail: )
| | - Kwang Ki Kim
- Department of Neurology, Dongguk University Ilsan Hospital, Goyang, South Korea
- *Correspondence: Byung Soo Koo, Department of Oriental Neuropsychiatry, Dongguk University Ilsan Korean Medicine Hospital, Goyang 10326, South Korea (e-mail: ) and Kwang Ki Kim, Department of Neurology, Dongguk University Ilsan Hospital, Goyang, 10326, South Korea (e-mail: )
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14
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Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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Mahmud S, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Paul GK, Chung S, Saleh MA, Alshehri S, Ghoneim MM, Alruwaily M, Kim B. Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs's cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mst. Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sanghyun Chung
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
| | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Momammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Maha Alruwaily
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
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16
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Kruse J, Mueller R, Aghdassi AA, Lerch MM, Salloch S. Genetic Testing for Rare Diseases: A Systematic Review of Ethical Aspects. Front Genet 2022; 12:701988. [PMID: 35154238 PMCID: PMC8826556 DOI: 10.3389/fgene.2021.701988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022] Open
Abstract
Genetic testing is associated with many ethical challenges on the individual, organizational and macro level of health care systems. The provision of genetic testing for rare diseases in particular requires a full understanding of the complexity and multiplicity of related ethical aspects. This systematic review presents a detailed overview of ethical aspects relevant to genetic testing for rare diseases as discussed in the literature. The electronic databases Pubmed, Science Direct and Web of Science were searched, resulting in 55 relevant publications. From the latter, a total of 93 different ethical aspects were identified. These ethical aspects were structured into three main categories (process of testing, consequences of the test outcome and contextual challenges) and 20 subcategories highlighting the diversity and complexity of ethical aspects relevant to genetic testing for rare diseases. This review can serve as a starting point for the further in-depth investigation of particular ethical issues, the education of healthcare professionals regarding this matter and for informing international policy development on genetic testing for rare diseases.
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Affiliation(s)
- Judith Kruse
- Institute of Ethics and History of Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Regina Mueller
- Institute of Ethics and History of Medicine, Medical Faculty, University Tübingen, Tübingen, Germany
| | - Ali A Aghdassi
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | | | - Sabine Salloch
- Institute of Ethics, History and Philosophy of Medicine, Hannover Medical School, Hannover, Germany
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17
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Yang XA. Editorial: Next Generation Sequencing (NGS) for Rare Diseases Diagnosis. Front Genet 2022; 12:808042. [PMID: 35003232 PMCID: PMC8733941 DOI: 10.3389/fgene.2021.808042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xiu-An Yang
- Laboratory of Genetic Engineering and Genomics, School of Basic Medical Sciences, Chengde Medical University, Chengde, China.,Hebei Key Laboratory of Nerve Injury and Repair, Chengde Medical University, Chengde, China
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18
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Huebner T, Steffens M, Scholl C. Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe. Mol Diagn Ther 2021; 26:89-103. [PMID: 34905151 PMCID: PMC8766366 DOI: 10.1007/s40291-021-00567-x] [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] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
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19
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Oliveira Netto AB, Brusius-Facchin AC, Leistner-Segal S, Kubaski F, Josahkian J, Giugliani R. Detection of Mosaic Variants in Mothers of MPS II Patients by Next Generation Sequencing. Front Mol Biosci 2021; 8:789350. [PMID: 34805285 PMCID: PMC8602069 DOI: 10.3389/fmolb.2021.789350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Mucopolysaccharidosis type II is an X-linked lysosomal storage disorder caused by mutations in the IDS gene that encodes the iduronate-2-sulfatase enzyme. The IDS gene is located on the long arm of the X-chromosome, comprising 9 exons, spanning approximately 24 kb. The analysis of carriers, in addition to detecting mutations in patients, is essential for genetic counseling, since the risk of recurrence for male children is 50%. Mosaicism is a well-known phenomenon described in many genetic disorders caused by a variety of mechanisms that occur when a mutation arises in the early development of an embryo. Sanger sequencing is limited in detecting somatic mosaicism and sequence change levels of less than 20% may be missed. The Next Generation Sequencing (NGS) has been increasingly used in diagnosis. It is a sensitive and fast method for the detection of somatic mosaicism. Compared to Sanger sequencing, which represents a cumulative signal, NGS technology analyzes the sequence of each DNA read in a sample. NGS might therefore facilitate the detection of mosaicism in mothers of MPS II patients. The aim of this study was to reanalyze, by NGS, all MPS II mothers that showed to be non-carriers by Sanger analysis. Twelve non-carriers were selected for the reanalysis on the Ion PGM and Ion Torrent S5 platform, using a custom panel that includes the IDS gene. Results were visualized in the Integrative Genomics Viewer (IGV). We were able to detected the presence of the variant previously found in the index case in three of the mothers, with frequencies ranging between 13 and 49% of the reads. These results suggest the possibility of mosaicism in the mothers. The use of a more sensitive technology for detecting low-level mosaic mutations is essential for accurate recurrence-risk estimates. In our study, the NGS analysis showed to be an effective methodology to detect the mosaic event.
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Affiliation(s)
- Alice Brinckmann Oliveira Netto
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil
| | - Ana Carolina Brusius-Facchin
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Sandra Leistner-Segal
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil
| | - Francyne Kubaski
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Juliana Josahkian
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,Department of Clinical Medicine, Hospital Universitario de Santa Maria (HUSM), Santa Maria, Brazil
| | - Roberto Giugliani
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Brazil
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20
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Gburek-Augustat J, Schoene-Bake JC, Bültmann E, Haack T, Buchert R, Synofzik M, Biskup S, Feuerhake F, Sorge I, Hartmann H. Pitfalls in Genetic Diagnostics: Why Phenotyping is Essential. Neuropediatrics 2021; 52:274-283. [PMID: 33791999 DOI: 10.1055/s-0041-1726306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
New genetic testing technologies have revolutionized medicine within the past years. It is foreseeable that the development will continue with the introduction of new techniques. Nevertheless, despite improved technology, an exact clinical description of the phenotype is still necessary and it is important to critically question findings, both before initiating genetic testing and when interpreting the results. We present four brief case vignettes to point out difficulties associated with correctly interpreting genetic findings.
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Affiliation(s)
- Janina Gburek-Augustat
- Division of Neuropediatrics, University Hospital, Hospital for Children and Adolescents, Leipzig, Germany.,Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany.,Department of Neuropediatrics, Developmental Neurology, Social Paediatrics, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - Jan-Christoph Schoene-Bake
- Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany.,Gemeinschaftspraxis fuer Humangenetik, Hamburg, Germany
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Tobias Haack
- Department of Medical Genetics and Applied Genomics, Rare Disease Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Rebecca Buchert
- Department of Medical Genetics and Applied Genomics, Rare Disease Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | | | - Ina Sorge
- Department of Pediatric Radiology, University Hospital Leipzig, Leipzig, Germany
| | - Hans Hartmann
- Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
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21
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Davison GW, Irwin RE, Walsh CP. The metabolic-epigenetic nexus in type 2 diabetes mellitus. Free Radic Biol Med 2021; 170:194-206. [PMID: 33429021 DOI: 10.1016/j.freeradbiomed.2020.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The prevalence of type 2 diabetes mellitus (T2DM) continues to rise globally. Yet the aetiology and pathophysiology of this noncommunicable, polygenic disease, is poorly understood. Lifestyle factors, such as poor dietary intake, lack of exercise, and abnormal glycaemia, are purported to play a role in disease onset and progression, and these environmental factors may disrupt specific epigenetic mechanisms, leading to a reprogramming of gene transcription. The hyperglycaemic cell per se, alters epigenetics through chemical modifications to DNA and histones via metabolic intermediates such as succinate, α-ketoglutarate and O-GlcNAc. To illustrate, α-ketoglutarate is considered a salient co-factor in the activation of the ten-eleven translocation (TET) dioxygenases, which drives DNA demethylation. On the contrary, succinate and other mitochondrial tricarboxylic acid cycle intermediates, inhibit TET activity predisposing to a state of hypermethylation. Hyperglycaemia depletes intracellular ascorbic acid, and damages DNA by enhancing the production of reactive oxygen species (ROS); this compromised cell milieu exacerbates the oxidation of 5-methylcytosine alongside a destabilisation of TET. These metabolic connections may regulate DNA methylation, affecting gene transcription and pancreatic islet β-cell function in T2DM. This complex interrelationship between metabolism and epigenetic alterations may provide a conceptual foundation for understanding how pathologic stimuli modify and control the intricacies of T2DM. As such, this narrative review will comprehensively evaluate and detail the interplay between metabolism and epigenetic modifications in T2DM.
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Affiliation(s)
- Gareth W Davison
- Ulster University, Sport and Exercise Sciences Research Institute, Newtownabbey, Northern Ireland, UK.
| | - Rachelle E Irwin
- Ulster University, Genomic Medicine Research Group, Biomedical Sciences Research Institute, Coleraine, Northern Ireland, UK
| | - Colum P Walsh
- Ulster University, Genomic Medicine Research Group, Biomedical Sciences Research Institute, Coleraine, Northern Ireland, UK
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22
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Yuan J, Chen F, Fan D, Jiang Q, Xue Z, Zhang J, Yu X, Li K, Qu J, Su J. EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases. NAR Genom Bioinform 2021; 3:lqab050. [PMID: 34085038 PMCID: PMC8168129 DOI: 10.1093/nargab/lqab050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/22/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Eye diseases are remarkably common and encompass a large and diverse range of morbidities that affect different components of the visual system and visual function. With advances in omics technology of eye disorders, genome-scale datasets have been rapidly accumulated in genetics and epigenetics field. However, the efficient collection and comprehensive analysis of different kinds of omics data are lacking. Herein, we developed EyeDiseases (https://eyediseases.bio-data.cn/), the first database for multi-omics data integration and interpretation of human eyes diseases. It contains 1344 disease-associated genes with genetic variation, 1774 transcription files of bulk cell expression and single-cell RNA-seq, 105 epigenomics data across 185 kinds of human eye diseases. Using EyeDiseases, we investigated SARS-CoV-2 potential tropism in eye infection and found that the SARS-CoV-2 entry factors, ACE2 and TMPRSS2 are highly correlated with cornea and keratoconus, suggest that ocular surface cells are susceptible to infection by SARS-CoV-2. Additionally, integrating analysis of Age-related macular degeneration (AMD) GWAS loci and co-expression data revealed 9 associated genes involved in HIF-1 signaling pathway and voltage-gate potassium channel complex. The EyeDiseases provides a valuable resource for accelerating the discovery and validation of candidate loci and genes contributed to the molecular diagnosis and therapeutic vulnerabilities with various eyes diseases.
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Affiliation(s)
- Jian Yuan
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Fukun Chen
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Dandan Fan
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Qi Jiang
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Zhengbo Xue
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Ji Zhang
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Xiangyi Yu
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Kai Li
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, Zhejiang, China
| | - Jia Qu
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou 325027, China
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
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23
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The importance of genetic testing for dystonia patients and translational research. J Neural Transm (Vienna) 2021; 128:473-481. [PMID: 33876307 PMCID: PMC8099821 DOI: 10.1007/s00702-021-02329-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 12/28/2022]
Abstract
Genetic testing through a variety of methods is a fundamental but underutilized approach for establishing the precise genetic diagnosis in patients with heritable forms of dystonia. Our knowledge of numerous dystonia-related genes, variants that they may contain, associated clinical presentations, and molecular disease mechanism may have significant translational potential for patients with genetically confirmed dystonia or their family members. Importantly, genetic testing permits the assembly of patient cohorts pertinent for dystonia-related research and developing therapeutics. Here we review the genetic testing approaches relevant to dystonia patients, and summarize and illustrate the multifold benefits of establishing an accurate molecular diagnosis for patients imminently or for translational research in the long run.
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Magrinelli F, Balint B, Bhatia KP. Challenges in Clinicogenetic Correlations: One Gene - Many Phenotypes. Mov Disord Clin Pract 2021; 8:299-310. [PMID: 33816657 PMCID: PMC8015894 DOI: 10.1002/mdc3.13165] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/02/2020] [Accepted: 12/19/2020] [Indexed: 12/25/2022] Open
Abstract
Background Progress in genetics – particularly the advent of next‐generation sequencing (NGS) – has enabled an unparalleled gene discovery and revealed unmatched complexity of genotype–phenotype correlations in movement disorders. Among other things, it has emerged that mutations in one and the same gene can cause multiple, often markedly different phenotypes. Consequently, movement disorder specialists have increasingly experienced challenges in clinicogenetic correlations. Objectives To deconstruct biological phenomena and mechanistic bases of phenotypic heterogeneity in monogenic movement disorders and neurodegenerative diseases. To discuss the evolving role of movement disorder specialists in reshaping disease phenotypes in the NGS era. Methods This scoping review details phenomena contributing to phenotypic heterogeneity and their underlying mechanisms. Results Three phenomena contribute to phenotypic heterogeneity, namely incomplete penetrance, variable expressivity and pleiotropy. Their underlying mechanisms, which are often shared across phenomena and non‐mutually exclusive, are not fully elucidated. They involve genetic factors (ie, different mutation types, dynamic mutations, somatic mosaicism, intragenic intra‐ and inter‐allelic interactions, modifiers and epistatic genes, mitochondrial heteroplasmy), epigenetic factors (ie, genomic imprinting, X‐chromosome inactivation, modulation of genetic and chromosomal defects), and environmental factors. Conclusion Movement disorders is unique in its reliance on clinical judgment to accurately define disease phenotypes. This has been reaffirmed by the NGS revolution, which provides ever‐growing sequencing data and fuels challenges in variant pathogenicity assertions for such clinically heterogeneous disorders. Deep phenotyping, with characterization and continual updating of “core” phenotypes, and comprehension of determinants of genotype–phenotype complex relationships are crucial for clinicogenetic correlations and have implications for the diagnosis, treatment and counseling.
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Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology University College London London United Kingdom.,Department of Neurosciences, Biomedicine and Movement Sciences University of Verona Verona Italy
| | - Bettina Balint
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology University College London London United Kingdom.,Department of Neurology University Hospital Heidelberg Heidelberg Germany
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology University College London London United Kingdom
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Gannamani R, van der Veen S, van Egmond M, de Koning TJ, Tijssen MAJ. Challenges in Clinicogenetic Correlations: One Phenotype - Many Genes. Mov Disord Clin Pract 2021; 8:311-321. [PMID: 33816658 PMCID: PMC8015914 DOI: 10.1002/mdc3.13163] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 12/11/2022] Open
Abstract
Background In the field of movement disorders, what you see (phenotype) is seldom what you get (genotype). Whereas 1 phenotype was previously associated to 1 gene, the advent of next‐generation sequencing (NGS) has facilitated an exponential increase in disease‐causing genes and genotype–phenotype correlations, and the “one‐phenotype‐many‐genes” paradigm has become prominent. Objectives To highlight the “one‐phenotype‐many‐genes” paradigm by discussing the main challenges, perspectives on how to address them, and future directions. Methods We performed a scoping review of the various aspects involved in identifying the underlying molecular cause of a movement disorder phenotype. Results The notable challenges are (1) the lack of gold standards, overlap in clinical spectrum of different movement disorders, and variability in the interpretation of classification systems; (2) selecting which patients benefit from genetic tests and the choice of genetic testing; (3) problems in the variant interpretation guidelines; (4) the filtering of variants associated with disease; and (5) the lack of standardized, complete, and up‐to‐date gene lists. Perspectives to address these include (1) deep phenotyping and genotype–phenotype integration, (2) adherence to phenotype‐specific diagnostic algorithms, (3) implementation of current and complementary bioinformatic tools, (4) a clinical‐molecular diagnosis through close collaboration between clinicians and genetic laboratories, and (5) ongoing curation of gene lists and periodic reanalysis of genetic sequencing data. Conclusions Despite the rapidly emerging possibilities of NGS, there are still many steps to take to improve the genetic diagnostic yield. Future directions, including post‐NGS phenotyping and cohort analyses enriched by genotype–phenotype integration and gene networks, ought to be pursued to accelerate identification of disease‐causing genes and further improve our understanding of disease biology.
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Affiliation(s)
- Rahul Gannamani
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Department of Genetics University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Sterre van der Veen
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Martje van Egmond
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Tom J de Koning
- Department of Genetics University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands.,Pediatrics, Department of Clinical Sciences Lund University Lund Sweden
| | - Marina A J Tijssen
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
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26
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Xiao H, Zhou WH. [Application of RNA sequencing in clinical diagnosis of Mendelian disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1138-1142. [PMID: 33059815 PMCID: PMC7568994 DOI: 10.7499/j.issn.1008-8830.2005004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Gene panel and whole exome sequencing are now commonly used to detect Mendelian disease, but the current molecular diagnostic rate of DNA sequencing is only 35%-50%. In recent years, RNA sequencing emerges as a promising diagnostic method. It can detect new pathogenic mutations, and analyze allele-specific expression. This will be helpful to understand the relationship between disease genotype and phenotype, and can complement genome sequencing in order to expand the traditional genomic diagnostic methods of Mendelian disease. RNA sequencing is expected to become a routine tool for diagnosing Mendelian diseases. This article reviews the application of RNA sequencing in the clinical diagnosis of Mendelian disease.
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Affiliation(s)
- Hui Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai 201102, China.
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27
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Ergoren MC, Cobanogulları H, Temel SG, Mocan G. Functional coding/non-coding variants in EGFR, ROS1 and ALK genes and their role in liquid biopsy as a personalized therapy. Crit Rev Oncol Hematol 2020; 156:103113. [PMID: 33038629 DOI: 10.1016/j.critrevonc.2020.103113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Personalized medicine holds promise to tailor the treatment options for patients' unique genetic make-up, behavioral and environmental background. Liquid biopsy is non-invasive technique and precise diagnosis and treatment approach. Significantly, NGS technologies have revolutionized the genomic medicine by novel identifying SNPs, indel mutations in both coding and non-coding regions and also a promising technology to accelerate the early detection and finding new biomarkers for diagnosis and treatment. The number of the bioinformatics tools have been rapidly increasing with the aim of learning more about the detected mutations either they have a pathogenic role or not. EGFR, ROS1 and ALK genes are members of the RTK family. Until now, mutations within these genes have been associated with many cancers and involved in resistance formation to TKIs. This review article summarized the findings about the mostly investigated variations in EGFR, ROS1 and ALK genes and their potential role in liquid biopsy approach.
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Affiliation(s)
- Mahmut Cerkez Ergoren
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus.
| | - Havva Cobanogulları
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Histology & Embryology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa, Turkey
| | - Gamze Mocan
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; Department of Medical Pathology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus
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Amanat S, Requena T, Lopez-Escamez JA. A Systematic Review of Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders. Genes (Basel) 2020; 11:genes11090987. [PMID: 32854191 PMCID: PMC7564972 DOI: 10.3390/genes11090987] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Exome sequencing has been commonly used to characterize rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) and searching for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to the heritability of complex clinical traits. We conducted a systematic review to find evidence supporting the use of EP strategies in the search for rare variants in genetic studies of complex diseases and highlight the contribution of rare variations to the genetic structure of polygenic conditions. After assessing the quality of the retrieved records, we selected 19 genetic studies considering EPs to demonstrate genetic association. All studies successfully identified several rare or de novo variants, and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach for patients with an early onset of a disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.
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Affiliation(s)
- Sana Amanat
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
| | - Teresa Requena
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK;
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18016 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
- Correspondence: ; Tel.: +34-958-715-500-160
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Lopez-Escamez JA, Amanat S. Heritability and Genetics Contribution to Tinnitus. Otolaryngol Clin North Am 2020; 53:501-513. [DOI: 10.1016/j.otc.2020.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Strianese O, Rizzo F, Ciccarelli M, Galasso G, D’Agostino Y, Salvati A, Del Giudice C, Tesorio P, Rusciano MR. Precision and Personalized Medicine: How Genomic Approach Improves the Management of Cardiovascular and Neurodegenerative Disease. Genes (Basel) 2020; 11:E747. [PMID: 32640513 PMCID: PMC7397223 DOI: 10.3390/genes11070747] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Life expectancy has gradually grown over the last century. This has deeply affected healthcare costs, since the growth of an aging population is correlated to the increasing burden of chronic diseases. This represents the interesting challenge of how to manage patients with chronic diseases in order to improve health care budgets. Effective primary prevention could represent a promising route. To this end, precision, together with personalized medicine, are useful instruments in order to investigate pathological processes before the appearance of clinical symptoms and to guide physicians to choose a targeted therapy to manage the patient. Cardiovascular and neurodegenerative diseases represent suitable models for taking full advantage of precision medicine technologies applied to all stages of disease development. The availability of high technology incorporating artificial intelligence and advancement progress made in the field of biomedical research have been substantial to understand how genes, epigenetic modifications, aging, nutrition, drugs, microbiome and other environmental factors can impact health and chronic disorders. The aim of the present review is to address how precision and personalized medicine can bring greater clarity to the clinical and biological complexity of these types of disorders associated with high mortality, involving tremendous health care costs, by describing in detail the methods that can be applied. This might offer precious tools for preventive strategies and possible clues on the evolution of the disease and could help in predicting morbidity, mortality and detecting chronic disease indicators much earlier in the disease course. This, of course, will have a major effect on both improving the quality of care and quality of life of the patients and reducing time efforts and healthcare costs.
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Affiliation(s)
- Oriana Strianese
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Gennaro Galasso
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Ylenia D’Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Carmine Del Giudice
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
| | - Paola Tesorio
- Unit of Cardiology, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy;
| | - Maria Rosaria Rusciano
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
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31
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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32
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Dunn PJ, Maher BH, Albury CL, Stuart S, Sutherland HG, Maksemous N, Benton MC, Smith RA, Haupt LM, Griffiths LR. Tiered analysis of whole-exome sequencing for epilepsy diagnosis. Mol Genet Genomics 2020; 295:751-763. [DOI: 10.1007/s00438-020-01657-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
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Second case of Bardet-Biedl syndrome caused by biallelic variants in IFT74. Eur J Hum Genet 2020; 28:943-946. [PMID: 32144365 DOI: 10.1038/s41431-020-0594-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/26/2020] [Accepted: 02/18/2020] [Indexed: 02/02/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder of the cilia, often resulting in a phenotype of obesity, rod-cone dystrophy, a variable degree of intellectual disability, polydactyly, renal problems, and/or hypogonadism in males or genital abnormalities in females. We here report the case of an 11-year-old girl who presented with postaxial polydactyly, retinal dystrophy, and childhood obesity, suggesting Bardet-Biedl syndrome. She had no renal problems, developmental delay, or intellectual disability. Genetic testing revealed compound heterozygous variants in the IFT74 gene (c.371_372del p.Gln124Argfs*9 and c.16850-1G>T p.?). We here report the second patient with Bardet-Biedl syndrome due to biallelic IFT74 variants. Both patients have obesity, polydactyly, retinal dystrophy, and no renal abnormalities. The present case however, has normal intellect, whereas the other patient has intellectual disability. We hereby confirm IFT74 as a BBS gene and encourage diagnostic genetic testing laboratories to add IFT74 to their BBS gene panels.
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Wagner M, Lévy J, Jung-Klawitter S, Bakhtiari S, Monteiro F, Maroofian R, Bierhals T, Hempel M, Elmaleh-Bergès M, Kitajima JP, Kim CA, Salomao JG, Amor DJ, Cooper MS, Perrin L, Pipiras E, Neu A, Doosti M, Karimiani EG, Toosi MB, Houlden H, Jin SC, Si YC, Rodan LH, Venselaar H, Kruer MC, Kok F, Hoffmann GF, Strom TM, Wortmann SB, Tabet AC, Opladen T. Loss of TNR causes a nonprogressive neurodevelopmental disorder with spasticity and transient opisthotonus. Genet Med 2020; 22:1061-1068. [PMID: 32099069 DOI: 10.1038/s41436-020-0768-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE TNR, encoding Tenascin-R, is an extracellular matrix glycoprotein involved in neurite outgrowth and neural cell adhesion, proliferation and migration, axonal guidance, myelination, and synaptic plasticity. Tenascin-R is exclusively expressed in the central nervous system with highest expression after birth. The protein is crucial in the formation of perineuronal nets that ensheath interneurons. However, the role of Tenascin-R in human pathology is largely unknown. We aimed to establish TNR as a human disease gene and unravel the associated clinical spectrum. METHODS Exome sequencing and an online matchmaking tool were used to identify patients with biallelic variants in TNR. RESULTS We identified 13 individuals from 8 unrelated families with biallelic variants in TNR sharing a phenotype consisting of spastic para- or tetraparesis, axial muscular hypotonia, developmental delay, and transient opisthotonus. Four homozygous loss-of-function and four different missense variants were identified. CONCLUSION We establish TNR as a disease gene for an autosomal recessive nonprogressive neurodevelopmental disorder with spasticity and transient opisthotonus and highlight the role of central nervous system extracellular matrix proteins in the pathogenicity of spastic disorders.
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Affiliation(s)
- Matias Wagner
- Institute of Human Genetics, Faculty of Medicine, Technical University München, Munich, Germany. .,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany. .,Institut für Neurogenomik, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
| | - Jonathan Lévy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Sabine Jung-Klawitter
- Division of Neuropediatrics and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.,Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, USA
| | | | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Chong A Kim
- Genetic Unit, Instituto da Criança-HCFMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Julia G Salomao
- Genetic Unit, Instituto da Criança-HCFMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Monica S Cooper
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Laurence Perrin
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Eva Pipiras
- Department of Cytogenetics, Jean-Verdier Hospital, Paris 13 University, Embryology and Histology, AP-HP, Bondy, France
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mohammad Doosti
- Department of Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan G Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's, University, London, UK
| | - Mehran B Toosi
- Department of Pediatric Neurology, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Sheng Chih Jin
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | | | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.,Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil
| | - Georg F Hoffmann
- Division of Neuropediatrics and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany
| | - Tim M Strom
- Institute of Human Genetics, Faculty of Medicine, Technical University München, Munich, Germany
| | - Saskia B Wortmann
- Institute of Human Genetics, Faculty of Medicine, Technical University München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,University Childrens Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Anne-Claude Tabet
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France.,Neuroscience Department, Human Genetics and Cognitive Function Unit, Pasteur Institute, Paris, France
| | - Thomas Opladen
- Division of Neuropediatrics and Metabolic Medicine, University Children's Hospital, Heidelberg, Germany.
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Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects. Eur Neuropsychopharmacol 2020; 31:1-15. [PMID: 31866110 DOI: 10.1016/j.euroneuro.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/03/2018] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.
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Ren S, Chen X, Kong X, Chen Y, Wu Q, Jiao Z, Shi H. Identification of six novel variants in Waardenburg syndrome type II by next-generation sequencing. Mol Genet Genomic Med 2020; 8:e1128. [PMID: 31960627 PMCID: PMC7057110 DOI: 10.1002/mgg3.1128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 11/22/2022] Open
Abstract
Background Waardenburg syndrome (WS) is a dominantly inherited, genetically heterogeneous auditory‐pigmentary syndrome characterized by nonprogressive sensorineural hearing loss and iris discoloration. This study aimed to investigate the underlying molecular pathology in Chinese WS families. Methods A total of 13 patients with Waardenburg syndrome type II (WS2) from six unrelated Chinese families were enrolled. We investigated the mutation profile of genes related to congenital deafness in these families through a targeted sequencing technology and validated the candidate variants by Sanger sequencing. Results We identified six novel variants in microphthalmia‐associated transcription factor (MITF) and SRY‐box 10 (SOX10), which were predicted to be disease causing by in silico analysis. Our results showed that mutations in SOX10 and MITF are two major causes of deafness associated with WS, and de novo mutations were frequently found in probands with SOX10 mutations but not in those with MITF mutations. Conclusion Results showed that targeted next‐generation sequencing (NGS) enabled us to detect disease‐causing mutations with high accuracy, stability, speed and throughput. Our study extends the pathogenic mutation spectrum of MITF and SOX10.
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Affiliation(s)
- Shumin Ren
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaojie Chen
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yibing Chen
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qinghua Wu
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhihui Jiao
- Department of Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huirong Shi
- Department of obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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37
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Mayer AK, Balousha G, Sharkia R, Mahajnah M, Ayesh S, Schulze M, Buchert R, Zobor D, Azem A, Schöls L, Bauer P, Wissinger B. Unraveling the genetic cause of hereditary ophthalmic disorders in Arab societies from Israel and the Palestinian Authority. Eur J Hum Genet 2020; 28:742-753. [PMID: 31896775 DOI: 10.1038/s41431-019-0566-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/12/2019] [Accepted: 12/10/2019] [Indexed: 11/09/2022] Open
Abstract
Visual impairment due to inherited ophthalmic disorders is amongst the most common disabilities observed in populations practicing consanguineous marriages. Here we investigated the molecular genetic basis of an unselected broad range of ophthalmic disorders in 20 consanguineous families from Arab villages of Israel and the Palestinian Authority. Most patients had little or very poor prior clinical workup and were recruited in a field study. Homozygosity mapping followed by candidate gene sequencing applying conventional Sanger sequencing or targeted next generation sequencing was performed in six families. In the remaining 14 families, one affected subject per family was chosen for whole exome sequencing. We discovered likely disease-causing variants, all homozygous, in 19 of 20 independent families (95%) including a previously reported novel disease gene for congenital nystagmus associated with foveal hypoplasia. Moreover, we found a family in which disease-causing variants for two collagenopathies - Stickler and Knobloch syndrome - segregate within a large sibship. Nine of the 19 distinct variants observed in this study were novel. Our study demonstrated a very high molecular diagnostic yield for a highly diverse spectrum of rare ophthalmic disorders in Arab patients from Israel and the Palestinian Authority, even with very limited prior clinical investigation. We conclude that 'genetic testing first' may be an economic way to direct clinical care and to support proper genetic counseling and risk assessment in these families.
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Affiliation(s)
- Anja K Mayer
- Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany.,Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Ghassan Balousha
- Department of Pathology and Histology, Al-Quds University, Eastern Jerusalem, Palestinian Authority, Jerusalem, Israel
| | - Rajech Sharkia
- The Triangle Regional Research and Development Center, Kfar Qari', Israel.,Beit-Berl Academic College, Beit-Berl, Israel
| | - Muhammad Mahajnah
- Child Neurology and Development Center, Hillel-Yaffe Medical Center, Hadera, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Suhail Ayesh
- Molecular Genetic Laboratory, Al-Makassed Islamic Charitable Society Hospital, Jerusalem, Israel
| | - Martin Schulze
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany.,Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ditta Zobor
- University Eye Hospital, University of Tuebingen, Tuebingen, Germany
| | - Abdussalam Azem
- The School of Neurobiology, Biochemistry and Biophysics, George S. Wise faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ludger Schöls
- Hertie Institute for Brain Research, University of Tuebingen, Tuebingen, Germany.,German Center of Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany.
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38
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Fürst D, Tsamadou C, Neuchel C, Schrezenmeier H, Mytilineos J, Weinstock C. Next-Generation Sequencing Technologies in Blood Group Typing. Transfus Med Hemother 2019; 47:4-13. [PMID: 32110189 DOI: 10.1159/000504765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.
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Affiliation(s)
- Daniel Fürst
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christof Weinstock
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden Wuerttemberg/Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
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39
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Graziola F, Garone G, Stregapede F, Bosco L, Vigevano F, Curatolo P, Bertini E, Travaglini L, Capuano A. Diagnostic Yield of a Targeted Next-Generation Sequencing Gene Panel for Pediatric-Onset Movement Disorders: A 3-Year Cohort Study. Front Genet 2019; 10:1026. [PMID: 31737037 PMCID: PMC6828958 DOI: 10.3389/fgene.2019.01026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/24/2019] [Indexed: 11/17/2022] Open
Abstract
In recent years, genetic techniques of diagnosis have shown rapid development, resulting in a modified clinical approach to many diseases, including neurological disorders. Movement disorders, in particular those arising in childhood, pose a diagnostic challenge. First, from a purely phenomenological point of view, the correct clinical classification of signs and symptoms may be difficult and require expert evaluation. This is because the clinical picture is often a mixture of hyperkinetic and hypokinetic disorders, and within hyperkinetic movement disorders, combined phenotypes are not unusual. Second, although several genes that cause movement disorders in children are now well-known, many of them have only been described in adult populations or discovered in patients after many years of disease. Furthermore, diseases that alter their mechanisms from childhood to adulthood are still little known, and many phenotypes in children are the result of a disruption of normal neurodevelopment. High-throughput gene screening addresses these difficulties and has modified the approach to genetic diagnosis. In the exome-sequencing era, customized genetic panels now offer the ability to perform fast and low-cost screening of the genes commonly involved in the pathogenesis of the disease. Here, we describe a 3-year study using a customized gene panel for pediatric-onset movement disorders in a selected cohort of children and adolescents. We report a satisfying diagnostic yield, further confirming the usefulness of gene panel analysis.
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Affiliation(s)
- Federica Graziola
- Movement Disorders Clinic, Department of Neurosciences, Bambino Gesù Children’s Hospital, Rome, Italy
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giacomo Garone
- Movement Disorders Clinic, Department of Neurosciences, Bambino Gesù Children’s Hospital, Rome, Italy
- University Hospital Pediatric Department, Bambino Gesù Children’s Hospital, University of Rome Tor Vergata, Rome, Italy
| | - Fabrizia Stregapede
- Department of Neuroscience, Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesù Children’s Hospital, Rome, Italy
- Department of Sciences, Roma Tre University, Rome, Italy
| | - Luca Bosco
- Department of Neuroscience, Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Federico Vigevano
- Movement Disorders Clinic, Department of Neurosciences, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Paolo Curatolo
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Enrico Bertini
- Department of Neuroscience, Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Lorena Travaglini
- Department of Neuroscience, Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Alessandro Capuano
- Movement Disorders Clinic, Department of Neurosciences, Bambino Gesù Children’s Hospital, Rome, Italy
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40
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Dong Y, Branscum P. What Motivates Individuals to Get Obesity Related Direct-To-Consumer Genetic Tests? A Reasoned Action Approach. AMERICAN JOURNAL OF HEALTH EDUCATION 2019. [DOI: 10.1080/19325037.2019.1663379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Performance of Sequencing Assays in Diagnosis of Prosthetic Joint Infection: A Systematic Review and Meta-Analysis. J Arthroplasty 2019; 34:1514-1522.e4. [PMID: 31005434 DOI: 10.1016/j.arth.2019.02.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/08/2019] [Accepted: 02/20/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND A prompt, accurate diagnosis of prosthetic joint infection (PJI) allows early treatment, and with identification of the causative organism, sensitive antibiotics could be applied. However, routine methods cannot identify the causative organism under certain circumstances. Gene sequencing assays have unique superiority in promptness and broad coverage of pathogens, but evidence of its accuracy is quite limited. METHODS Of 247 citations identified for screening, 12 studies with 1965 patients in total were included. The diagnostic value of sequencing assays in PJI was systematically reviewed. Subgroup analysis was conducted to explore the source of heterogeneity. RESULTS Pooled sensitivity was 0.81 (95% confidence interval [CI], 0.73-0.87); pooled specificity was 0.94 (95% CI, 0.91-0.97); positive likelihood ratio was 14.2 (95% CI, 8.7-23.4); negative likelihood ratio was 0.20 (95% CI, 0.14-0.29); and the area under the curve was 0.94 (95% CI, 0.18-1.00). The results of subgroup analysis revealed that antibiotics reduced the sensitivity of sequencing-based diagnosis compared with withholding antibiotics before sampling (0.71 vs 0.94). In another subgroup analysis, sequencing by synthesis (Illumina sequencing) had better specificity than other next-generation sequencing methods (0.963 vs 0.829) and specificity similar to time-consuming and laborious Sanger sequencing (0.963 vs 0.967). CONCLUSION Sequencing assays had favorable diagnostic accuracy of PJI. When sequencing assays were applied to diagnosing PJI, an antibiotic-free interval before sampling may enhance the ability to detect the causative organism and, among next-generation sequencing methods, sequencing by synthesis seemed to have advantages over other methods in specificity.
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42
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Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet 2019; 104:466-483. [PMID: 30827497 PMCID: PMC6407525 DOI: 10.1016/j.ajhg.2019.01.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Gene-panel and whole-exome analyses are now standard methodologies for mutation detection in Mendelian disease. However, the diagnostic yield achieved is at best 50%, leaving the genetic basis for disease unsolved in many individuals. New approaches are thus needed to narrow the diagnostic gap. Whole-genome sequencing is one potential strategy, but it currently has variant-interpretation challenges, particularly for non-coding changes. In this study we focus on transcriptome analysis, specifically total RNA sequencing (RNA-seq), by using monogenetic neuromuscular disorders as proof of principle. We examined a cohort of 25 exome and/or panel "negative" cases and provided genetic resolution in 36% (9/25). Causative mutations were identified in coding and non-coding exons, as well as in intronic regions, and the mutational pathomechanisms included transcriptional repression, exon skipping, and intron inclusion. We address a key barrier of transcriptome-based diagnostics: the need for source material with disease-representative expression patterns. We establish that blood-based RNA-seq is not adequate for neuromuscular diagnostics, whereas myotubes generated by transdifferentiation from an individual's fibroblasts accurately reflect the muscle transcriptome and faithfully reveal disease-causing mutations. Our work confirms that RNA-seq can greatly improve diagnostic yield in genetically unresolved cases of Mendelian disease, defines strengths and challenges of the technology, and demonstrates the suitability of cell models for RNA-based diagnostics. Our data set the stage for development of RNA-seq as a powerful clinical diagnostic tool that can be applied to the large population of individuals with undiagnosed, rare diseases and provide a framework for establishing minimally invasive strategies for doing so.
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Affiliation(s)
- Hernan D Gonorazky
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Viswateja Nelakuditi
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Pouria Mashouri
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peiqui Wang
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dennis Kao
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Krish Ohri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Katherine D Mathews
- Departments of Pediatrics and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Andres N Osorio
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Hospital Universitari Sant Joan de Deu, Barcelona 08950, Spain; Center for the Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona 08950, Spain
| | - David Villanova
- GenomicTales Parc de la Mola, 10, AD700 Escaldes-Engordany, Andorra
| | - Dwi U Kemaladewi
- Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michael Brudno
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - James J Dowling
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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Abstract
PURPOSE Next-generation sequencing panels are particularly useful in identifying genetic diagnoses in patients with nonspecific clinical findings by allowing for analysis of many genes at once. The purpose of this study was to develop a simple, objective system to evaluate the quality of available next-generation sequencing panels. METHODS A list of potentially important features of next-generation sequencing panels generated from the literature was evaluated for accessibility and objectivity and distilled to a "core" set of quality features. This was then applied to a clinical setting using the example of epilepsy panels. Panels at 8 laboratories were rated based on several objective measures to create a scoring system that differentiated between labs in a clinically meaningful way. RESULTS There was substantial variability in 6 "core" test criteria, allowing for creation of a scoring system that clearly distinguished labs based on identified strengths and weaknesses of each panel. CONCLUSION We have demonstrated an objective method for comparing next-generation sequencing panels that can be applied or adapted to any clinical phenotype for which genetic testing is available. This method offers an unbiased approach to determining the ideal test for a given indication at a given time.
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Affiliation(s)
- Kaitlin Angione
- Department of Pediatrics, Section of Neurology, University of Colorado Denver, Aurora, CO, USA
| | - Melissa Gibbons
- Department of Pediatrics, Section of Neurology, University of Colorado Denver, Aurora, CO, USA
| | - Scott Demarest
- Department of Pediatrics, Section of Neurology, University of Colorado Denver, Aurora, CO, USA
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Zhang H, Li C, Li J, Hou S, Chen D, Yan H, Chen S, Liu S, Yin Z, Yang X, Tan J, Huang X, Zhang L, Fang J, Zhang C, Li W, Guo J, Lei D. Next-generation sequencing improves molecular epidemiological characterization of thalassemia in Chenzhou Region, P.R. China. J Clin Lab Anal 2019; 33:e22845. [PMID: 30809867 PMCID: PMC6528559 DOI: 10.1002/jcla.22845] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/19/2018] [Accepted: 01/03/2019] [Indexed: 12/23/2022] Open
Abstract
Objectives Thalassemia is a highly prevalent monogenic inherited disease in southern China. It is important to collect epidemiological data comprehensively for proper prevention and treatment. Methods In this study, blood samples collected from 15 807 residents of Chenzhou were primarily screened by hematological tests. A total of 3973 samples of suspected thalassemia carriers were further characterized by combined next‐generation sequencing (NGS) and Gap‐PCR. Results In total, 1704 subjects were diagnosed as thalassemia carriers with a total prevalence rate of 10.78%, including 943 α‐thalassemia carriers, 708 β‐thalassemia carriers, and 53 composite α and β‐thalassemia carriers. The prevalence rates of α‐thalassemia, β‐thalassemia, and composite α and β‐thalassemia were 5.97%, 4.48%, and 0.34%, respectively. Meanwhile, we characterized 19 α‐thalassemia variations and 21 β‐thalassemia variations in thalassemia carriers. Approximately 2.88% of thalassemia carriers would be missed by traditional genetic analysis. In addition, four novel thalassemia mutations and one novel abnormal hemoglobin mutation were identified. Conclusions Our data suggest a high prevalence of thalassemia and a diverse spectrum of thalassemia‐associated variations in Chenzhou. Also, combined NGS and Gap‐PCR is an effective thalassemia screening method. Our findings might be helpful for prevention and treatment of thalassemia in this region.
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Affiliation(s)
- Haoqing Zhang
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Caiyun Li
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Jianbiao Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shuai Hou
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Danjing Chen
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Haiying Yan
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Shiping Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Saijun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhenzhen Yin
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaoqin Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Jufang Tan
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Xiaoyan Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Liming Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Junbin Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Caifen Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Guo
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Dongzhu Lei
- Center of Prenatal Diagnosis, Chenzhou No. 1 People's Hospital, Chenzhou, China
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Zhou R, Wei Y, Sciacovelli L, Plebani M, Wang Q. A pilot study for establishing quality indicators in molecular diagnostics according to the IFCC WG-LEPS initiative: preliminary findings in China. ACTA ACUST UNITED AC 2018; 57:822-831. [PMID: 30838838 DOI: 10.1515/cclm-2018-0966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/29/2018] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Quality indicators (QIs) are crucial tools in measuring the quality of laboratory services. Based on the general QIs of the Working Group “Laboratory Errors and Patient Safety (WG-LEPS)” of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), specific QIs have been established in order to monitor and improve the quality of molecular diagnostics, and to assess the detection level of associated disease.
Methods
A survey was conducted on 46 independent commercial laboratories in China, investigated using questionnaires and on-site inspections. Specific QIs established were mainly based on the specific laboratory work-flow for molecular diagnoses. The specific QI results from three volunteer laboratories were collected and used to validate their effectiveness.
Results
Of the 46 laboratories participating in the study, 44 (95.7%), conducted molecular diagnostics. Of 13 specific established QIs, six were priority level 1, and seven, priority level 3. At pre-evaluation of data from the three volunteering laboratories, it was found that the newly classified specific QIs had outstanding advantages in error identification and risk reduction.
Conclusions
Novel specific QIs, a promising tool for monitoring and improving upon the total testing process in molecular diagnostics, can effectively contribute to ensuring patient safety.
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Affiliation(s)
- Rui Zhou
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Yali Wei
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
| | - Laura Sciacovelli
- Department of Laboratory Medicine, Padova University Hospital, Padova, Italy
| | - Mario Plebani
- Department of Laboratory Medicine, Padova University Hospital, Padova, Italy
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China
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46
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DiStefano JK, Kingsley CB. Identification of Disease Susceptibility Alleles in the Next Generation Sequencing Era. Methods Mol Biol 2018; 1706:3-16. [PMID: 29423790 DOI: 10.1007/978-1-4939-7471-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of next generation sequencing (NGS) technologies has transformed the study of human genetic variation. In less than a decade, NGS has facilitated the discovery of causal mutations in both rare, monogenic diseases and common, heterogeneous disorders, leading to unprecedented improvements in disease diagnosis and treatment strategies. Given the rapid evolution of NGS platforms, it is now possible to analyze whole genomes and exomes quickly and affordably. Further, emerging NGS applications, such as single-cell sequencing, have the power to address specific issues like somatic variation, which is yielding new insights into the role of somatic mutations in cancer and late-onset diseases. Despite limitations associated with current iterations of NGS technologies, the impact of this approach on identifying disease-causing variants has been significant. This chapter provides an overview of several NGS platforms and applications and discusses how these technologies can be used in concert with experimental and computational strategies to identify variants with a causative effect on disease development and progression.
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Affiliation(s)
- Johanna K DiStefano
- Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, 85004, USA.
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Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
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Kringel D, Kaunisto MA, Lippmann C, Kalso E, Lötsch J. Development of an AmpliSeq TM Panel for Next-Generation Sequencing of a Set of Genetic Predictors of Persisting Pain. Front Pharmacol 2018; 9:1008. [PMID: 30283335 PMCID: PMC6156278 DOI: 10.3389/fphar.2018.01008] [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: 05/24/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
Background: Many gene variants modulate the individual perception of pain and possibly also its persistence. The limited selection of single functional variants is increasingly being replaced by analyses of the full coding and regulatory sequences of pain-relevant genes accessible by means of next generation sequencing (NGS). Methods: An NGS panel was created for a set of 77 human genes selected following different lines of evidence supporting their role in persisting pain. To address the role of these candidate genes, we established a sequencing assay based on a custom AmpliSeqTM panel to assess the exomic sequences in 72 subjects of Caucasian ethnicity. To identify the systems biology of the genes, the biological functions associated with these genes were assessed by means of a computational over-representation analysis. Results: Sequencing generated a median of 2.85 ⋅ 106 reads per run with a mean depth close to 200 reads, mean read length of 205 called bases and an average chip loading of 71%. A total of 3,185 genetic variants were called. A computational functional genomics analysis indicated that the proposed NGS gene panel covers biological processes identified previously as characterizing the functional genomics of persisting pain. Conclusion: Results of the NGS assay suggested that the produced nucleotide sequences are comparable to those earned with the classical Sanger sequencing technique. The assay is applicable for small to large-scale experimental setups to target the accessing of information about any nucleotide within the addressed genes in a study cohort.
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Affiliation(s)
- Dario Kringel
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt, Germany
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Catharina Lippmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology, Frankfurt, Germany
| | - Eija Kalso
- Division of Pain Medicine, Department of Anesthesiology, Intensive Care and Pain Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology, Frankfurt, Germany
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Tomanin R, Karageorgos L, Zanetti A, Al-Sayed M, Bailey M, Miller N, Sakuraba H, Hopwood JJ. Mucopolysaccharidosis type VI (MPS VI) and molecular analysis: Review and classification of published variants in the ARSB gene. Hum Mutat 2018; 39:1788-1802. [PMID: 30118150 PMCID: PMC6282714 DOI: 10.1002/humu.23613] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/26/2023]
Abstract
Maroteaux–Lamy syndrome (MPS VI) is an autosomal recessive lysosomal storage disorder caused by pathogenic ARSB gene variants, commonly diagnosed through clinical findings and deficiency of the arylsulfatase B (ASB) enzyme. Detection of ARSB pathogenic variants can independently confirm diagnosis and render genetic counseling possible. In this review, we collect and summarize 908 alleles (201 distinct variants, including 3 polymorphisms previously considered as disease‐causing variants) from 478 individuals diagnosed with MPS VI, identified from literature and public databases. Each variant is further analyzed for clinical classification according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results highlight the heterogeneity of ARSB alleles, with most unique variants (59.5%) identified as missense and 31.7% of unique alleles appearing once. Only 18% of distinct variants were previously recorded in public databases with supporting evidence and clinical significance. ACMG recommends publishing clinical and biochemical data that accurately characterize pathogenicity of new variants in association with reporting specific alleles. Variants analyzed were sent to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), and MPS VI locus‐specific database (http://mps6-database.org) where they will be available. High clinical suspicion coupled with diagnostic testing for deficient ASB activity and timely submission and classification of ARSB variants with biochemical and clinical data in public databases is essential for timely diagnosis of MPS VI.
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Affiliation(s)
- Rosella Tomanin
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women's and Children's Health, University of Padova and "Fondazione Istituto di Ricerca Pediatrica Città della Speranza", Padova, Italy
| | - Litsa Karageorgos
- Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Alessandra Zanetti
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women's and Children's Health, University of Padova and "Fondazione Istituto di Ricerca Pediatrica Città della Speranza", Padova, Italy
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc., Novato, CA, United States
| | - Nicole Miller
- BioMarin Pharmaceutical Inc., Novato, CA, United States
| | - Hitoshi Sakuraba
- Department of Clinical Genetics, Meiji Pharmaceutical University, Tokyo, Japan
| | - John J Hopwood
- Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, Australia
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Stapleton M, Arunkumar N, Kubaski F, Mason RW, Tadao O, Tomatsu S. Clinical presentation and diagnosis of mucopolysaccharidoses. Mol Genet Metab 2018; 125:4-17. [PMID: 30057281 DOI: 10.1016/j.ymgme.2018.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 01/09/2023]
Abstract
Mucopolysaccharidoses (MPS) are estimated to affect1 in 25,000 live births although specific rates vary between the ethnic origin and country. MPS are a group of lysosomal storage disorders, which cause the buildup of GAG(s) due to insufficient or absent GAG-degrading enzymes. With seven types of MPS disorders and eleven subtypes, the MPS family presents unique challenges for early clinical diagnosis due to the molecular and clinical heterogeneity between groups and patients. Novel methods of early identification, particularly newborn screening through mass spectrometry, can change the flow of diagnosis, allowing enzyme and GAG quantification before the presentation of clinical symptoms improving outcomes. Genetic testing of patients and their families can also be conducted preemptively. This testing enables families to make informed decisions about family planning, leading to prenatal diagnosis. In this review, we discuss the clinical symptoms of each MPS type as they initially appear in patients, biochemical and molecular diagnostic methods, and the future of newborn screening for this group of disorders.
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Affiliation(s)
- Molly Stapleton
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Nivethitha Arunkumar
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Francyne Kubaski
- Department of Molecular Biology and Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Robert W Mason
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Orii Tadao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States; Department of Pediatrics, Shimane University, Shimane, Japan.
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