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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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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [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: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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Glotov OS, Chernov AN, Glotov AS. Human Exome Sequencing and Prospects for Predictive Medicine: Analysis of International Data and Own Experience. J Pers Med 2023; 13:1236. [PMID: 37623486 PMCID: PMC10455459 DOI: 10.3390/jpm13081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Today, whole-exome sequencing (WES) is used to conduct the massive screening of structural and regulatory genes in order to identify the allele frequencies of disease-associated polymorphisms in various populations and thus detect pathogenic genetic changes (mutations or polymorphisms) conducive to malfunctional protein sequences. With its extensive capabilities, exome sequencing today allows both the diagnosis of monogenic diseases (MDs) and the examination of seemingly healthy populations to reveal a wide range of potential risks prior to disease manifestation (in the future, exome sequencing may outpace costly and less informative genome sequencing to become the first-line examination technique). This review establishes the human genetic passport as a new WES-based clinical concept for the identification of new candidate genes, gene variants, and molecular mechanisms in the diagnosis, prediction, and treatment of monogenic, oligogenic, and multifactorial diseases. Various diseases are addressed to demonstrate the extensive potential of WES and consider its advantages as well as disadvantages. Thus, WES can become a general test with a broad spectrum pf applications, including opportunistic screening.
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Affiliation(s)
- Oleg S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of Experimental Medical Virology, Molecular Genetics and Biobanking of Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
| | - Alexander N. Chernov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
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Marzano F, Chiara M, Consiglio A, D’Amato G, Gentile M, Mirabelli V, Piane M, Savio C, Fabiani M, D’Elia D, Sbisà E, Scarano G, Lonardo F, Tullo A, Pesole G, Faienza MF. Whole-Exome and Transcriptome Sequencing Expands the Genotype of Majewski Osteodysplastic Primordial Dwarfism Type II. Int J Mol Sci 2023; 24:12291. [PMID: 37569667 PMCID: PMC10418986 DOI: 10.3390/ijms241512291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Microcephalic Osteodysplastic Primordial Dwarfism type II (MOPDII) represents the most common form of primordial dwarfism. MOPD clinical features include severe prenatal and postnatal growth retardation, postnatal severe microcephaly, hypotonia, and an increased risk for cerebrovascular disease and insulin resistance. Autosomal recessive biallelic loss-of-function genomic variants in the centrosomal pericentrin (PCNT) gene on chromosome 21q22 cause MOPDII. Over the past decade, exome sequencing (ES) and massive RNA sequencing have been effectively employed for both the discovery of novel disease genes and to expand the genotypes of well-known diseases. In this paper we report the results both the RNA sequencing and ES of three patients affected by MOPDII with the aim of exploring whether differentially expressed genes and previously uncharacterized gene variants, in addition to PCNT pathogenic variants, could be associated with the complex phenotype of this disease. We discovered a downregulation of key factors involved in growth, such as IGF1R, IGF2R, and RAF1, in all three investigated patients. Moreover, ES identified a shortlist of genes associated with deleterious, rare variants in MOPDII patients. Our results suggest that Next Generation Sequencing (NGS) technologies can be successfully applied for the molecular characterization of the complex genotypic background of MOPDII.
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Affiliation(s)
- Flaviana Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Arianna Consiglio
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Gabriele D’Amato
- Neonatal Intensive Care Unit, Di Venere Hospital, 70012 Bari, Italy
| | | | - Valentina Mirabelli
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy;
| | | | - Marco Fabiani
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Domenica D’Elia
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Elisabetta Sbisà
- Institute for Biomedical Technologies, ITB-CNR, 70126 Bari, Italy; (A.C.); (V.M.); (D.D.); (E.S.)
| | - Gioacchino Scarano
- Medical Genetics Unit, AORN “San Pio”, Hosp. “G. Rummo”, 82100 Benevento, Italy; (G.S.); (F.L.)
| | - Fortunato Lonardo
- Medical Genetics Unit, AORN “San Pio”, Hosp. “G. Rummo”, 82100 Benevento, Italy; (G.S.); (F.L.)
| | - Apollonia Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM–CNR, 70126 Bari, Italy; (F.M.); (A.T.)
- Department of Biosciences, Biotechnology and Biofarmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Maria Felicia Faienza
- Pediatric Section, Department of Precision and Regenerative Medicine and Ionian Area, University “A. Moro” of Bari, 70124 Bari, Italy
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Zhang K, Lin G, Han Y, Peng R, Li J. Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient-Parent Trio Sample: Pilot Study for Neurodevelopmental Disorder de Novo Variants. J Mol Diagn 2023; 25:378-387. [PMID: 37208049 DOI: 10.1016/j.jmoldx.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient-parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. One of the 26 challenging variants was identified by all laboratories, whereas all 26 variants were identified by only nine laboratories. The lack of identification of mosaic variants was often due to the bioinformatics analysis that excluded the variant. For missing intended heterozygous variants, probable root causes were related to the technical bioinformatics pipeline and variant interpretation and reporting. For each missing variant, there may be more than one probable reason from the different laboratories. There was considerable variation in interlaboratory performance for detecting challenging variants using trio-based ES. This finding may have important implications for the design and validation of tests for different variant types in clinical laboratories, especially for technically challenging variants, and necessary workflow modification can potentially improve trio-based ES performance.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
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Miziak B, Czuczwar SJ. Approaches for the discovery of drugs that target K Na 1.1 channels in KCNT1-associated epilepsy. Expert Opin Drug Discov 2022; 17:1313-1328. [PMID: 36408599 DOI: 10.1080/17460441.2023.2150164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
INTRODUCTION There are approximately 70 million people with epilepsy and about 30% of patients are not satisfactorily treated. A link between gene mutations and epilepsy is well documented. A number of pathological variants of KCNT1 gene (encoding the weakly voltage-dependent sodium-activated potassium channel - KNa 1.1) mutations has been found. For instance, epilepsy of infancy with migrating focal seizures, autosomal sleep-related hypermotor epilepsy or Ohtahara syndrome have been associated with KCNT1 gene mutations. AREAS COVERED Several methods for studies on KNa 1.1 channels have been reviewed - patch clamp analysis, Förster resonance energy transfer spectroscopy and whole-exome sequencing. The authors also review available drugs for the management of KCNT1 epilepsies. EXPERT OPINION The current methods enable deeper insights into electrophysiology of KNa 1.1 channels or its functioning in different activation states. It is also possible to identify a given KCNT1 mutation. Quinidine and cannabidiol show variable efficacy as add-on to baseline antiepileptic drugs so more effective treatments are required. A combined approach with the methods shown above, in silico methods and the animal model of KCNT1 epilepsies seems likely to create personalized treatment of patients with KCNT1 gene mutations.
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Affiliation(s)
- Barbara Miziak
- Department of Pathophysiology, Medical University of Lublin, Lublin, Poland
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Zhu X, Peng M, Yin Y, Zhang Y, Zheng D, Peng Z, Cheng J, Yang S, Wang J. Identification of a novel ANK1 mutation in a Chinese family with hereditary spherocytosis: A case report. Exp Ther Med 2022; 25:4. [PMID: 36561627 PMCID: PMC9748711 DOI: 10.3892/etm.2022.11704] [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: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
The present study describes the clinical profile and ankyrin 1 (ANK1) mutation status of a Chinese family with hereditary spherocytosis (HS). A young male patient (proband) was diagnosed with HS after presenting with anaemia and jaundice. The Coombs test was negative and spherocytes were found in peripheral blood smears. Magnetic resonance imaging showed splenomegaly and splenic iron depositions. The red blood cell osmotic fragility test was positive. The eosin-5'-maleimide binding test showed reduced mean channel fluorescence. Whole-exome sequencing revealed a novel ANK1 mutation (c.4707G>A), resulting in a nonsense mutation (p.Trp1569*). The patient's father, paternal aunt and paternal grandmother exhibited comparable clinical symptoms and Sanger sequencing confirmed the same mutation in these family members. To the best of our knowledge, an HS pedigree with this novel ANK1 nonsense mutation has not been previously reported. At the same time, the unique clinical presentation of this pedigree helps our understanding of the heterogeneity of clinical manifestations of HS.
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Affiliation(s)
- Xiaoning Zhu
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Mengyun Peng
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yue Yin
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yurong Zhang
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ding Zheng
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhaoxuan Peng
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jun Cheng
- Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Song Yang
- Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100020, P.R. China,Correspondence to: Professor Jing Wang, Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, 182 Chunhui Road, Longmatan, Luzhou, Sichuan 646000, P.R. China
| | - Jing Wang
- Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China,Correspondence to: Professor Jing Wang, Department of Hepatobiliary Disease, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, 182 Chunhui Road, Longmatan, Luzhou, Sichuan 646000, P.R. China
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Zhang K, Yu L, Lin G, Li J. A multi-laboratory assessment of clinical exome sequencing for detection of hereditary disease variants: 4441 ClinVar variants for clinical genomic test development and validation. Clin Chim Acta 2022; 535:99-107. [PMID: 35985503 DOI: 10.1016/j.cca.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Whole-exome sequencing (WES) technology has become an essential tool in the clinical diagnostic for rare genetic disorders, however, the issues that reduce testing precision, sensitivity, and concordance are not clear under routine testing conditions. The study is to systematically evaluate the comparability of clinical WES testing results in laboratories under routine conditions. METHODS We designed a multi-laboratory study across 24 participating laboratories in China. We assessed sequencing quality across capture methods and sequencing platforms, benchmarked the impact of coverage and callable regions on detecting single nucleotide variants (SNVs), small insertions and deletions (Indels) under the same computational approaches, and compared the sensitivity, precision and reproducibility on detecting mutations across laboratories. RESULTS High inter-laboratory variability on variants detection were found across participating laboratories. Sample DNA concentration and sequencing evenness are two major variables that lead to the coverage variation. The difference in bioinformatics tools and computational settings affect the sensitivity and precision of the final output. Besides, copy-number variants (CNVs) identification is less reproducible than SNVs and Indels in the WES testing. We also compiled a list of 4441 low coverage ClinVar variants of 1176 genes from this study, which can be used as a source for creating in silico and synthetic DNA reference materials for clinical genetic disorder detection. CONCLUSIONS The considerable inter-laboratory variability seen in both sequencing coverage evenness and variants detection highlights the urgent need to improve the precision, sensitivity and comparability of the results generated across different laboratories. The list of low coverage variants can have important implications for the development and validation of clinical genetic disorder tests by laboratories. This study also serves to best practice inform guidelines for detecting clinical genetic disorders by exome sequencing.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Lijia Yu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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van Hoolwerff M, Rodríguez Ruiz A, Bouma M, Suchiman HED, Koning RI, Jost CR, Mulder AA, Freund C, Guilak F, Ramos YFM, Meulenbelt I. High-impact FN1 mutation decreases chondrogenic potential and affects cartilage deposition via decreased binding to collagen type II. SCIENCE ADVANCES 2021; 7:eabg8583. [PMID: 34739320 PMCID: PMC8570604 DOI: 10.1126/sciadv.abg8583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Osteoarthritis is the most prevalent joint disease worldwide, yet progress in development of effective disease-modifying treatments is slow because of lack of insight into the underlying disease pathways. Therefore, we aimed to identify the causal pathogenic mutation in an early-onset osteoarthritis family, followed by functional studies in human induced pluripotent stem cells (hiPSCs) in an in vitro organoid cartilage model. We demonstrated that the identified causal missense mutation in the gelatin-binding domain of the extracellular matrix protein fibronectin resulted in significant decreased binding capacity to collagen type II. Further analyses of formed hiPSC-derived neo-cartilage tissue highlighted that mutated fibronectin affected chondrogenic capacity and propensity to a procatabolic osteoarthritic state. Together, we demonstrate that binding of fibronectin to collagen type II is crucial for fibronectin downstream gene expression of chondrocytes. We advocate that effective treatment development should focus on restoring or maintaining proper binding between fibronectin and collagen type II.
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Affiliation(s)
- Marcella van Hoolwerff
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Alejandro Rodríguez Ruiz
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marga Bouma
- LUMC hiPSC Hotel, Leiden University Medical Center, Leiden, Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, Netherlands
| | - H. Eka D. Suchiman
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Roman I. Koning
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Carolina R. Jost
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Aat A. Mulder
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Christian Freund
- LUMC hiPSC Hotel, Leiden University Medical Center, Leiden, Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, Netherlands
| | - Farshid Guilak
- Department of Orthopedic Surgery, Washington University and Shriners Hospitals for Children, St. Louis, MO, USA
| | - Yolande F. M. Ramos
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
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12
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Rabbani B, Khorgami M, Dalili M, Zamani N, Mahdieh N, Gollob MH. Novel cases of pediatric sudden cardiac death secondary to TRDN mutations presenting as long QT syndrome at rest and catecholaminergic polymorphic ventricular tachycardia during exercise: The TRDN arrhythmia syndrome. Am J Med Genet A 2021; 185:3433-3445. [PMID: 34415104 DOI: 10.1002/ajmg.a.62464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
TRDN mutations cause catecholaminergic polymorphic ventricular tachycardia (CPVT) but may present with abnormal electrocardiogram (ECG) findings provoking a diagnosis of long QT syndrome (LQTS). We report two novel cases of sudden cardiac death in children due to mutations of TRDN, providing further insight into this rare and aggressive inherited arrhythmia syndrome. Whole exome sequencing (WES) was performed in two unrelated children who experienced cardiac arrest during exercise and were negative for targeted testing of LQTS. WES identified a novel homozygous splice-site mutation in both patients, denoted c.22+1G>T, absent from gnomAD and suggesting a founder variant in the Iranian population. We now summarize the genetic architecture of all reported TRDN-related patients, including 27 patients from 21 families. The average age-onset was 30 months (range 1-10) for all cases. Adrenergic-mediated cardiac events were common, occurring in 23 of 27 cases (85%). LQTS was diagnosed in 10 cases (37%), CPVT in 10 (37%) cases, and in 7 cases. No phenotypic diagnosis was provided. Five cases (15%) had evidence for associated skeletal myopathy. Four missense TRDN variants (24%) were observed in diseased cases, while the remaining variants reflect putative loss-of-function (LOF) mutations. No disease phenotype was reported in 26 heterozygous carriers. In conclusion, TRDN mutations cause a rare autosomal recessive arrhythmia syndrome presenting with adrenergic-mediated arrhythmic events, but with ECG abnormalities leading to a diagnosis of LQTS in a proportion of cases. Heterozygous carriers are free of disease manifestations.
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Affiliation(s)
- Bahareh Rabbani
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadrafi Khorgami
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Dalili
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Nasrin Zamani
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Arrhythmia Service, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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13
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Remec ZI, Trebusak Podkrajsek K, Repic Lampret B, Kovac J, Groselj U, Tesovnik T, Battelino T, Debeljak M. Next-Generation Sequencing in Newborn Screening: A Review of Current State. Front Genet 2021; 12:662254. [PMID: 34122514 PMCID: PMC8188483 DOI: 10.3389/fgene.2021.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Newborn screening was first introduced at the beginning of the 1960s with the successful implementation of the first phenylketonuria screening programs. Early expansion of the included disorders was slow because each additional disorder screened required a separate test. Subsequently, the technological advancements of biochemical methodology enabled the scaling-up of newborn screening, most notably with the implementation of tandem mass spectrometry. In recent years, we have witnessed a remarkable progression of high-throughput sequencing technologies, which has resulted in a continuous decrease of both cost and time required for genetic analysis. This has enabled more widespread use of the massive multiparallel sequencing. Genomic sequencing is now frequently used in clinical applications, and its implementation in newborn screening has been intensively advocated. The expansion of newborn screening has raised many clinical, ethical, legal, psychological, sociological, and technological concerns over time. This review provides an overview of the current state of next-generation sequencing regarding newborn screening including current recommendations and potential challenges for the use of such technologies in newborn screening.
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Affiliation(s)
- Ziga I. Remec
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katarina Trebusak Podkrajsek
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Barbka Repic Lampret
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovac
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tine Tesovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marusa Debeljak
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
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14
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Marinakis NM, Svingou M, Veltra D, Kekou K, Sofocleous C, Tilemis FN, Kosma K, Tsoutsou E, Fryssira H, Traeger-Synodinos J. Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders. Am J Med Genet A 2021; 185:2561-2571. [PMID: 34008892 DOI: 10.1002/ajmg.a.62338] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/10/2022]
Abstract
About 6000 to 7000 different rare disorders with suspected genetic etiologies have been described and almost 4500 causative gene(s) have been identified. The advent of next-generation sequencing (NGS) technologies has revolutionized genomic research and diagnostics, representing a major advance in the identification of pathogenic genetic variations. This study presents a 3-year experience from an academic genetics center, where 400 patients were referred for genetic analysis of disorders with unknown etiology. A phenotype-driven proband-only exome sequencing (ES) strategy was applied for the investigation of rare disorders, in the context of optimizing ES diagnostic yield and minimizing costs and time to definitive diagnosis. Overall molecular diagnostic yield reached 53% and characterized 243 pathogenic variants in 210 cases, 85 of which were novel and 148 known, contributing information to the community of disease and variant databases. ES provides an opportunity to resolve the genetic etiology of disorders and support appropriate medical management and genetic counseling. In cases with complex phenotypes, the identification of complex genotypes may contribute to more comprehensive clinical management. In the context of effective multidisciplinary collaboration between clinicians and laboratories, ES provides an efficient and appropriate tool for first-tier genomic analysis.
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Affiliation(s)
- Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eirini Tsoutsou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
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15
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Keller N, Paketci C, Altmueller J, Fuhrmann N, Wunderlich G, Schrank B, Unver O, Yilmaz S, Boostani R, Karimiani EG, Motameny S, Thiele H, Nürnberg P, Maroofian R, Yis U, Wirth B, Karakaya M. Genomic variants causing mitochondrial dysfunction are common in hereditary lower motor neuron disease. Hum Mutat 2021; 42:460-472. [PMID: 33600046 DOI: 10.1002/humu.24181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 02/10/2021] [Indexed: 11/08/2022]
Abstract
Hereditary lower motor neuron diseases (LMND) other than 5q-spinal muscular atrophy (5q-SMA) can be classified according to affected muscle groups. Proximal and distal forms of non-5q-SMA represent a clinically and genetically heterogeneous spectrum characterized by significant overlaps with axonal forms of Charcot-Marie-Tooth (CMT) disease. A consensus for the best approach to molecular diagnosis needs to be reached, especially in light of continuous novel gene discovery and falling costs of next-generation sequencing (NGS). We performed exome sequencing (ES) in 41 families presenting with non-5q-SMA or axonal CMT, 25 of which had undergone a previous negative neuromuscular disease (NMD) gene panel analysis. The total diagnostic yield of ES was 41%. Diagnostic success in the cohort with a previous NMD-panel analysis was significantly extended by ES, primarily due to novel gene associated-phenotypes and uncharacteristic phenotypic presentations. We recommend early ES for individuals with hereditary LMND presenting uncharacteristic or significantly overlapping features. As mitochondrial dysfunction was the underlying pathomechanism in 47% of the solved individuals, we highlight the sensitivity of the anterior horn cell and peripheral nerve to mitochondrial imbalance as well as the necessity to screen for mitochondrial disorders in individuals presenting predominant lower motor neuron symptoms.
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Affiliation(s)
- Natalie Keller
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Cem Paketci
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
| | - Gilbert Wunderlich
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
- Department of Neurology, University Hospital Cologne, Cologne, Germany
| | - Bertold Schrank
- Department of Neurology, DKD HELIOS Kliniken, Wiesbaden, Germany
| | - Olcay Unver
- Department of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Sanem Yilmaz
- Department of Pediatric Neurology, Ege University, Izmir, Turkey
| | - Reza Boostani
- Department of Neurology, Ghaem Hospital, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Uluc Yis
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Brunhilde Wirth
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Mert Karakaya
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
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16
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Bakshi D, Katoch A, Chakraborty S, Shah R, Sharma B, Bhat A, Verma S, Bhat GR, Nagpal A, Vaishnavi S, Goswami A, Kumar R. ANKLE1 as New Hotspot Mutation for Breast Cancer in Indian Population and Has a Role in DNA Damage and Repair in Mammalian Cells. Front Genet 2021; 11:609758. [PMID: 33584808 PMCID: PMC7873468 DOI: 10.3389/fgene.2020.609758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer has replaced cervical cancer as being the most common and having the highest mortality among women in India. ANKLE gene is conserved among organisms during evolutionary succession and is a member of LEM family proteins in lower metazoans and is involved in critical functions in the nuclear architecture, gene expression and cell signaling. ANKLE1 is the human orthologous of LEM-3 and is involved in DNA damage response and DNA repair. Whole Exome Sequencing (WES) of paired breast cancer samples was performed and ANKLE1 was found to be a new possible hotspot for predisposition of breast cancer. The mass array genotyping for breast cancer variant rs2363956 further confirmed the ANKLE1 association with the studied population of breast cancer. To elucidate the role of ANKLE1 in DNA damage, it was knocked down in MCF-7 breast cancer cell line and the expression of γH2AX was assessed. ANKLE1 knockdown cells displayed elevated levels of γ-H2AX foci in response to the cisplatin induced replication stress. The localization pattern of ANKLE1 further emphasized the role of ANKLE1 in DNA repair process. We observed that ANKLE1 is required for maintaining genomic stability and plays a role in DNA damage and repair process. These findings provided a molecular basis for the suspected role of ANKLE1 in human breast cancer and suggested an important role of this gene in controlling breast cancer development among women in India.
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Affiliation(s)
| | - Archana Katoch
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Souneek Chakraborty
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ruchi Shah
- Shri Mata Vaishno Devi University, Katra, India
| | | | - Amrita Bhat
- Shri Mata Vaishno Devi University, Katra, India
| | | | | | | | | | - Anindya Goswami
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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17
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Clinical impact of genomic testing in patients with suspected monogenic kidney disease. Genet Med 2020; 23:183-191. [PMID: 32939031 PMCID: PMC7790755 DOI: 10.1038/s41436-020-00963-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Methods We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Results ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design.
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18
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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19
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Nicolaides NC, Kanaka-Gantenbein C, Papadopoulou-Marketou N, Sertedaki A, Chrousos GP, Papassotiriou I. Emerging technologies in pediatrics: the paradigm of neonatal diabetes mellitus. Crit Rev Clin Lab Sci 2020; 57:522-531. [PMID: 32356495 DOI: 10.1080/10408363.2020.1752141] [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] [Indexed: 10/24/2022]
Abstract
In the era of precision medicine, the tremendous progress in next-generation sequencing technologies has allowed the identification of an ever-increasing number of genes associated with known Mendelian disorders. Neonatal diabetes mellitus is a rare, genetically heterogeneous endocrine disorder diagnosed before 6 months of age. It may occur alone or in the context of genetic syndromes. Neonatal diabetes mellitus has been linked with genetic defects in at least 26 genes to date. Novel mutations in these disease-causing genes are being reported, giving us a better knowledge of the molecular events that occur upon insulin biosynthesis and secretion from the pancreatic β-cell. Of great importance, some of the identified genes encode proteins that can be therapeutically targeted by drugs per os, leading to transitioning from insulin to sulfonylureas. In this review, we provide an overview of pancreatic β-cell physiology, present the clinical manifestations and the genetic causes of the different forms of neonatal diabetes, and discuss the application of next-generation sequencing methods in the diagnosis and therapeutic management of neonatal diabetes and on research in this area.
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Affiliation(s)
- Nicolas C Nicolaides
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nektaria Papadopoulou-Marketou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Amalia Sertedaki
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Ioannis Papassotiriou
- Department of Clinical Biochemistry, "Aghia Sophia" Children's Hospital, Athens, Greece.,IFCC Emerging Technologies Division, Emerging Technologies in Pediatric Laboratory Medicine (C-ETPLM), Milano, Italy
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20
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Cao P, Miao B, Xu Y, Fan Q, Zhang Q, Zhang G, Zhou C, Xu Y. Role of gene polymorphisms related to progesterone elevation in women undergoing long GnRH agonist protocols. Reprod Biomed Online 2020; 40:381-392. [PMID: 32204850 DOI: 10.1016/j.rbmo.2019.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/27/2019] [Accepted: 12/10/2019] [Indexed: 11/29/2022]
Abstract
RESEARCH QUESTION Can single-nucleotide polymorphisms (SNP) of genes related to progesterone synthesis predict the risk of premature serum progesterone elevation in women undergoing gonadotrophin-releasing hormone agonist protocols for ovarian stimulation? DESIGN A total of 765 women were divided into high progesterone and normal progesterone groups according to progesterone concentration on the day of human chorionic gonadotrophin (HCG) administration, with the 75th percentile as the threshold between the group. Associations were analysed of genetic information from whole exome sequencing and the clinical characteristics of the two groups to identify the relationship between SNP, haplotypes and serum progesterone elevation. RESULTS Among 40 common SNP of eight genes (FSHR, LHCGR, ESR1, ESR2, PGR, HSD3B1, CYP11A1 and CYP17A1), no statistical significance between the high and normal progesterone groups was identified in the distribution of genotypes and allele frequencies after multiple test correction to adjust the false discovery rate (PFDR > 0.05). When compared with the most common haplotypes of each gene, haplotype GAAG in CYP17A1 was associated with a 1.44-fold increased risk of progesterone elevation (95% confidence interval [CI] 1.22-1.69, PFDR < 0.001), while haplotypes of the following genes showed a decreased risk of progesterone elevation: haplotype CC in FSHR and LHCGR (0.66-fold, PFDR = 0.020, and 0.64-fold, PFDR < 0.001, respectively), CA in ESR1 (0.90-fold, PFDR < 0.001), TCTGG in ESR2 (0.92-fold, PFDR = 0.007) and GAACC in HSD3B1 (0.42-fold, PFDR < 0.001). CONCLUSIONS Polymorphism in genes involved in enzymes or hormone receptors in the progesterone synthesis pathway may have a role in modifying risk of serum progesterone elevation.
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Affiliation(s)
- Ping Cao
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Benyu Miao
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Yan Xu
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Qi Fan
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Qian Zhang
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Guirong Zhang
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Canquan Zhou
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Yanwen Xu
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China.
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21
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Lipiński P, Ciara E, Jurkiewicz D, Pollak A, Wypchło M, Płoski R, Cielecka-Kuszyk J, Socha P, Pawłowska J, Jankowska I. Targeted Next-Generation Sequencing in Diagnostic Approach to Monogenic Cholestatic Liver Disorders-Single-Center Experience. Front Pediatr 2020; 8:414. [PMID: 32793533 PMCID: PMC7393978 DOI: 10.3389/fped.2020.00414] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Objective: To evaluate the clinical utility of panel-based NGS in the diagnostic approach of monogenic cholestatic liver diseases. Study design: Patients with diagnosis of chronic cholestatic liver disease of an unknown etiology underwent NGS of targeted genes panel. Group 1 included five patients (prospectively recruited) hospitalized from January to December 2017 while group 2 included seventeen patients (retrospectively recruited) hospitalized from 2010 to 2017 presenting with low-GGT PFIC phenotype (group 2a, 11 patients) or indeterminant cholestatic liver cirrhosis (group 2b, 6 patients). Results: Among 22 patients enrolled into the study, 21 various pathogenic variants (including 11 novel) in 5 different genes (including ABCB11, ABCB4, TJP2, DGUOK, CYP27A1) were identified. The molecular confirmation was obtained in 15 out of 22 patients (68%). In group 1, two out of five patients presented with low-GGT cholestasis, and were diagnosed with BSEP deficiency. Out of three patients presenting with high-GGT cholestasis, one patient was diagnosed with PFIC-3, and the remaining two were not molecularly diagnosed. In group 2a, seven out of eleven patients, were diagnosed with BSEP deficiency and two with TJP-2 deficiency. In group 2b, three out of six patients were molecularly diagnosed; one with PFIC-3, one with CYP27A1 deficiency, and one with DGUOK deficiency. Conclusions: Panel-based NGS appears to be a very useful tool in diagnosis of monogenic cholestatic liver disorders in cases when extrahepatic causes have been primarily excluded. NGS presented the highest diagnosis rate to identify the molecular background of cholestatic liver diseases presenting with a low-GGT PFIC phenotype.
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Affiliation(s)
- Patryk Lipiński
- Department of Pediatrics, Nutrition and Metabolic Diseases, The Children's Memorial Health Institute, Warsaw, Poland.,Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Jurkiewicz
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Maria Wypchło
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Piotr Socha
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Joanna Pawłowska
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Irena Jankowska
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
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22
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Rosier M, Guedj M, Calvas P, Julia S, Garnier C, Cambon-Thomsen A, Muñoz Sastre MT. Attitudes of French populations towards the disclosure of unsolicited findings in medical genetics. J Health Psychol 2019; 26:1767-1779. [PMID: 31707852 DOI: 10.1177/1359105319886622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing techniques enable unsolicited findings to be detected. This discovery raises ethical questions concerning the return of these findings. Our study aimed to highlight the views of the general public, patients under supervision and health professionals concerning the acceptability of disclosing unsolicited results to patients. In total, 449 participants assessed scenarios, consisted of all combinations of three factors (patient's information and consent, prevention and treatment of the unsolicited disease and doctor's decision). The response profiles were grouped into six clusters. The participants took ethical aspects into account, but health professionals also considered the medical aspects to a greater extent.
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23
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Fischer-Hwang I, Ochoa I, Weissman T, Hernaez M. Denoising of Aligned Genomic Data. Sci Rep 2019; 9:15067. [PMID: 31636330 PMCID: PMC6803637 DOI: 10.1038/s41598-019-51418-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/25/2019] [Indexed: 12/30/2022] Open
Abstract
Noise in genomic sequencing data is known to have effects on various stages of genomic data analysis pipelines. Variant identification is an important step of many of these pipelines, and is increasingly being used in clinical settings to aid medical practices. We propose a denoising method, dubbed SAMDUDE, which operates on aligned genomic data in order to improve variant calling performance. Denoising human data with SAMDUDE resulted in improved variant identification in both individual chromosome as well as whole genome sequencing (WGS) data sets. In the WGS data set, denoising led to identification of almost 2,000 additional true variants, and elimination of over 1,500 erroneously identified variants. In contrast, we found that denoising with other state-of-the-art denoisers significantly worsens variant calling performance. SAMDUDE is written in Python and is freely available at https://github.com/ihwang/SAMDUDE .
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Affiliation(s)
- Irena Fischer-Hwang
- Stanford University, Department of Electrical Engineering, Stanford, 94305, USA.
| | - Idoia Ochoa
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, 61801, USA
| | - Tsachy Weissman
- Stanford University, Department of Electrical Engineering, Stanford, 94305, USA
| | - Mikel Hernaez
- University of Illinois Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, Urbana, 61801, USA.
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24
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De Franco E. From Biology to Genes and Back Again: Gene Discovery for Monogenic Forms of Beta-Cell Dysfunction in Diabetes. J Mol Biol 2019; 432:1535-1550. [PMID: 31479665 DOI: 10.1016/j.jmb.2019.08.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/14/2022]
Abstract
This review focuses on gene discovery strategies used to identify monogenic forms of diabetes caused by reduced pancreatic beta-cell number (due to destruction or defective development) or impaired beta-cell function. Gene discovery efforts in monogenic diabetes have identified 36 genes so far. These genetic causes have been identified using four main approaches: linkage analysis, candidate gene sequencing and most recently, exome and genome sequencing. The advent of next-generation sequencing has allowed researchers to move away from linkage analysis (relying on large pedigrees and/or multiple families with the same genetic condition) and candidate gene (relying on previous knowledge on the gene's role) strategies to use a gene agnostic approach, utilizing genetic evidence (such as variant frequency, predicted variant effect on protein function, and predicted mode of inheritance) to identify the causative mutation. This approach led to the identification of seven novel genetic causes of monogenic diabetes, six by exome sequencing and one by genome sequencing. In many of these cases, the disease-causing gene was not known to be important for beta-cell function prior to the gene discovery study. These novel findings highlight a new role for gene discovery studies in furthering our understanding of beta-cell function and dysfunction in diabetes. While many gene discovery studies in the past were led by knowledge in the field (through the candidate gene strategy), now they often lead the scientific advances in the field by identifying new important biological players to be further characterized by in vitro and in vivo studies.
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Affiliation(s)
- Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, EX2 5DW Exeter, UK; Institute of Biomedical and Clinical Science, Level 3, RILD Building, Barrack Road, EX2 5DW Exeter, United Kingdom.
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25
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Jayasinghe K, White SM, Kerr PG, MacGregor D, Stark Z, Wilkins E, Simons C, Mallett A, Quinlan C. Isolated proteinuria due to CUBN homozygous mutation - challenging the investigative paradigm. BMC Nephrol 2019; 20:330. [PMID: 31438875 PMCID: PMC6704575 DOI: 10.1186/s12882-019-1474-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/19/2019] [Indexed: 11/25/2022] Open
Abstract
Background Proteinuria is a common clinical presentation, the diagnostic workup for which involves many non-invasive and invasive investigations. We report on two siblings that highlight the clinically relevant functional role of cubulin for albumin resorption in the proximal tubule and supports the use of genomic sequencing early in the diagnostic work up of patients who present with proteinuria. Case presentation An 8-year-old boy was referred with an incidental finding of proteinuria. All preliminary investigations were unremarkable. Further assessment revealed consanguineous family history and a brother with isolated proteinuria. Renal biopsy demonstrated normal light microscopy and global glomerular basement membrane thinning on electron microscopy. Chromosomal microarray revealed long continuous stretches of homozygosity (LCSH) representing ~ 4.5% of the genome. Shared regions of LCSH between the brothers were identified and their further research genomic analysis implicated a homozygous stop-gain variant in CUBN (10p12.31). Conclusions CUBN mutations have been implicated as a hereditary cause of megaloblastic anaemia and variable proteinuria. This is the second reported family with isolated proteinuria due to biallelic CUBN variants in the absence of megaloblastic anaemia, demonstrating the ability of genomic testing to identify genetic causes of nephropathy within expanding associated phenotypic spectra. Genomic sequencing, undertaken earlier in the diagnostic trajectory, may reduce the need for invasive investigations and the time to definitive diagnosis for patients and families.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Australia.,Monash University, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia.,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia
| | - Susan M White
- The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Peter G Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Australia.,Monash University, Melbourne, Australia
| | - Duncan MacGregor
- Department of Pathology, Royal Children's Hospital, Melbourne, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, Australia.,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Ella Wilkins
- Murdoch Children's Research Institute, Melbourne, Australia.,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Australia.,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia
| | - Andrew Mallett
- Murdoch Children's Research Institute, Melbourne, Australia.,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia.,Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Catherine Quinlan
- Murdoch Children's Research Institute, Melbourne, Australia. .,The KidGen Collaborative, Australian Genomics Health Alliance, Victoria, Australia. .,Department of Paediatric Nephrology, Royal Children's Hospital, 50 Flemington Street, Parkville, Australia.
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26
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Zhang X, Wang Y, Yang F, Tang J, Xu X, Yang L, Yang XA, Wu D. Biallelic INTS1 Mutations Cause a Rare Neurodevelopmental Disorder in Two Chinese Siblings. J Mol Neurosci 2019; 70:1-8. [PMID: 31428919 DOI: 10.1007/s12031-019-01393-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/29/2019] [Indexed: 01/08/2023]
Abstract
This study presents two Chinese siblings with a rare neurodevelopmental disorder (NDD) caused by biallelic INTS1 mutations and investigates the clinical features of this disease by means of in silico analysis. Two siblings, an 11-year-old brother and a 5-year-old sister, visited our hospital due to physical retardation and profound intellectual disability. Whole-exome sequencing (WES) was performed for the girl, and Sanger sequencing was used to validate the identified variants. Phenotype correlation analysis and in silico genetic interaction network analysis were performed to investigate genes that could lead to diseases similar to the rare disease in the patients. Growth retardation, distinct intellectual disability, hypertelorism, mild cataract, uneven teeth, abnormal palmar and plantar creases, and dubious genitalia were noted in the sister. No neurological features related to neuropathy were found. The brother showed features and growth delay similar to his sister. Heterozygous novel variants of c.1645A>G,p.Met549Val and c.5881C>T,p.Gln1961* in INTS1 were considered a candidate etiology. Sanger sequencing demonstrated that the variants were inherited from the grandfather and (maternal) grandmother. Phenotype correlation analysis revealed that CTDP1 mutation-induced congenital cataracts-facial dysmorphism-neuropathy (CCFDN) mostly overlapped with the performance of our patients. In silico analysis of the genetic interaction network showed that INTS1 is highly associated with INTS8 and CTDP1. Our study further validated that biallelic INTS1 mutations could bring about the onset of a novel neurodevelopmental disorder.
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Affiliation(s)
- Xuemin Zhang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Yajian Wang
- Beijing Chigene Translational Medicine Research Center Co., Ltd., Beijing, 100875, People's Republic of China
| | - Fang Yang
- School of Basic Medical Science, Chengde Medical University, Anyuan Road, Chengde, 067000, People's Republic of China
| | - Jiulai Tang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Xiaoyan Xu
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Li Yang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Anyuan Road, Chengde, 067000, People's Republic of China.
| | - De Wu
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China.
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27
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Jayasinghe K, Stark Z, Patel C, Mallawaarachchi A, McCarthy H, Faull R, Chakera A, Sundaram M, Jose M, Kerr P, Wu Y, Wardrop L, Goranitis I, Best S, Martyn M, Quinlan C, Mallett AJ. Comprehensive evaluation of a prospective Australian patient cohort with suspected genetic kidney disease undergoing clinical genomic testing: a study protocol. BMJ Open 2019; 9:e029541. [PMID: 31383705 PMCID: PMC6687024 DOI: 10.1136/bmjopen-2019-029541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Recent advances in genomic technology have allowed better delineation of renal conditions, the identification of new kidney disease genes and subsequent targets for therapy. To date, however, the utility of genomic testing in a clinically ascertained, prospectively recruited kidney disease cohort remains unknown. The aim of this study is to explore the clinical utility and cost-effectiveness of genomic testing within a national cohort of patients with suspected genetic kidney disease who attend multidisciplinary renal genetics clinics. METHODS AND ANALYSIS This is a prospective observational cohort study performed at 16 centres throughout Australia. Patients will be included if they are referred to one of the multidisciplinary renal genetics clinics and are deemed likely to have a genetic basis to their kidney disease by the multidisciplinary renal genetics team. The expected cohort consists of 360 adult and paediatric patients recruited by December 2018 with ongoing validation cohort of 140 patients who will be recruited until June 2020. The primary outcome will be the proportion of patients who receive a molecular diagnosis via genomic testing (diagnostic rate) compared with usual care. Secondary outcomes will include change in clinical diagnosis following genomic testing, change in clinical management following genomic testing and the cost-effectiveness of genomic testing compared with usual care. ETHICS AND DISSEMINATION The project has received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. All participants will provide written informed consent for data collection and to undergo clinically relevant genetic/genomic testing. The results of this study will be published in peer-reviewed journals and will also be presented at national and international conferences.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia
- Monash University, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Amali Mallawaarachchi
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Department of Medical genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Hugh McCarthy
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Randall Faull
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Aron Chakera
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Madhivanan Sundaram
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Matthew Jose
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Peter Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia
- Monash University, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - You Wu
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise Wardrop
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Paediatric Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Andrew J Mallett
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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28
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van Dongen JJM, van der Burg M, Kalina T, Perez-Andres M, Mejstrikova E, Vlkova M, Lopez-Granados E, Wentink M, Kienzler AK, Philippé J, Sousa AE, van Zelm MC, Blanco E, Orfao A. EuroFlow-Based Flowcytometric Diagnostic Screening and Classification of Primary Immunodeficiencies of the Lymphoid System. Front Immunol 2019; 10:1271. [PMID: 31263462 PMCID: PMC6585843 DOI: 10.3389/fimmu.2019.01271] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Guidelines for screening for primary immunodeficiencies (PID) are well-defined and several consensus diagnostic strategies have been proposed. These consensus proposals have only partially been implemented due to lack of standardization in laboratory procedures, particularly in flow cytometry. The main objectives of the EuroFlow Consortium were to innovate and thoroughly standardize the flowcytometric techniques and strategies for reliable and reproducible diagnosis and classification of PID of the lymphoid system. The proposed EuroFlow antibody panels comprise one orientation tube and seven classification tubes and corresponding databases of normal and PID samples. The 8-color 12-antibody PID Orientation tube (PIDOT) aims at identification and enumeration of the main lymphocyte and leukocyte subsets; this includes naïve pre-germinal center (GC) and antigen-experienced post-GC memory B-cells and plasmablasts. The seven additional 8(-12)-color tubes can be used according to the EuroFlow PID algorithm in parallel or subsequently to the PIDOT for more detailed analysis of B-cell and T-cell subsets to further classify PID of the lymphoid system. The Pre-GC, Post-GC, and immunoglobulin heavy chain (IgH)-isotype B-cell tubes aim at identification and enumeration of B-cell subsets for evaluation of B-cell maturation blocks and specific defects in IgH-subclass production. The severe combined immunodeficiency (SCID) tube and T-cell memory/effector subset tube aim at identification and enumeration of T-cell subsets for assessment of T-cell defects, such as SCID. In case of suspicion of antibody deficiency, PIDOT is preferably directly combined with the IgH isotype tube(s) and in case of SCID suspicion (e.g., in newborn screening programs) the PIDOT is preferably directly combined with the SCID T-cell tube. The proposed ≥8-color antibody panels and corresponding reference databases combined with the EuroFlow PID algorithm are designed to provide fast, sensitive and cost-effective flowcytometric diagnosis of PID of the lymphoid system, easily applicable in multicenter diagnostic settings world-wide.
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Affiliation(s)
- Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, Rotterdam, Netherlands.,Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Tomas Kalina
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Charles University, Prague, Czechia
| | - Martin Perez-Andres
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
| | - Ester Mejstrikova
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Charles University, Prague, Czechia
| | - Marcela Vlkova
- Institute of Clinical Immunology and Allergology, St. Anne's University Hospital Brno, Masaryk University, Brno, Czechia
| | | | | | - Anne-Kathrin Kienzler
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jan Philippé
- Department of Laboratory Medicine, University Hospital Ghent, Ghent, Belgium
| | - Ana E Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, Rotterdam, Netherlands.,Department of Immunology and Pathology, Central Clinical School, Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
| | - Alberto Orfao
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
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29
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Bosio M, Drechsel O, Rahman R, Muyas F, Rabionet R, Bezdan D, Domenech Salgado L, Hor H, Schott JJ, Munell F, Colobran R, Macaya A, Estivill X, Ossowski S. eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics. Hum Mutat 2019; 40:865-878. [PMID: 31026367 PMCID: PMC6767450 DOI: 10.1002/humu.23772] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
Mendelian diseases have shown to be an and efficient model for connecting genotypes to phenotypes and for elucidating the function of genes. Whole‐exome sequencing (WES) accelerated the study of rare Mendelian diseases in families, allowing for directly pinpointing rare causal mutations in genic regions without the need for linkage analysis. However, the low diagnostic rates of 20–30% reported for multiple WES disease studies point to the need for improved variant pathogenicity classification and causal variant prioritization methods. Here, we present the exome Disease Variant Analysis (eDiVA; http://ediva.crg.eu), an automated computational framework for identification of causal genetic variants (coding/splicing single‐nucleotide variants and small insertions and deletions) for rare diseases using WES of families or parent–child trios. eDiVA combines next‐generation sequencing data analysis, comprehensive functional annotation, and causal variant prioritization optimized for familial genetic disease studies. eDiVA features a machine learning‐based variant pathogenicity predictor combining various genomic and evolutionary signatures. Clinical information, such as disease phenotype or mode of inheritance, is incorporated to improve the precision of the prioritization algorithm. Benchmarking against state‐of‐the‐art competitors demonstrates that eDiVA consistently performed as a good or better than existing approach in terms of detection rate and precision. Moreover, we applied eDiVA to several familial disease cases to demonstrate its clinical applicability.
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Affiliation(s)
- Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Oliver Drechsel
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut de Recerca Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Daniela Bezdan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura Domenech Salgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hyun Hor
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Jacques Schott
- L'Institut du Thorax, INSERM, CNRS, Univ Nantes, Nantes, France.,Service de Cardiologie, L'institut du thorax, CHU Nantes, Nantes, France
| | | | - Roger Colobran
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Alfons Macaya
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Xavier Estivill
- Sidra Medicine, Doha, Qatar.,Women's Health Dexeus, Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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30
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Bennett TD, Callahan TJ, Feinstein JA, Ghosh D, Lakhani SA, Spaeder MC, Szefler SJ, Kahn MG. Data Science for Child Health. J Pediatr 2019; 208:12-22. [PMID: 30686480 PMCID: PMC6486872 DOI: 10.1016/j.jpeds.2018.12.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Tellen D Bennett
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; CU Data Science to Patient Value (D2V), University of Colorado School of Medicine, Aurora, CO; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO.
| | - Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - James A Feinstein
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Debashis Ghosh
- CU Data Science to Patient Value (D2V), University of Colorado School of Medicine, Aurora, CO; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Michael C Spaeder
- Pediatric Critical Care, University of Virginia School of Medicine, Charlottesville, VA
| | - Stanley J Szefler
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Michael G Kahn
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
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31
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Integrated Analysis of Whole Exome Sequencing and Copy Number Evaluation in Parkinson's Disease. Sci Rep 2019; 9:3344. [PMID: 30833663 PMCID: PMC6399448 DOI: 10.1038/s41598-019-40102-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
Genetic studies of the familial forms of Parkinson’s disease (PD) have identified a number of causative genes with an established role in its pathogenesis. These genes only explain a fraction of the diagnosed cases. The emergence of Next Generation Sequencing (NGS) expanded the scope of rare variants identification in novel PD related genes. In this study we describe whole exome sequencing (WES) genetic findings of 60 PD patients with 125 variants validated in 51 of these cases. We used strict criteria for variant categorization that generated a list of variants in 20 genes. These variants included loss of function and missense changes in 18 genes that were never previously linked to PD (NOTCH4, BCOR, ITM2B, HRH4, CELSR1, SNAP91, FAM174A, BSN, SPG7, MAGI2, HEPHL1, EPRS, PUM1, CLSTN1, PLCB3, CLSTN3, DNAJB9 and NEFH) and 2 genes that were previously associated with PD (EIF4G1 and ATP13A2). These genes either play a critical role in neuronal function and/or have mouse models with disease related phenotypes. We highlight NOTCH4 as an interesting candidate in which we identified a deleterious truncating and a splice variant in 2 patients. Our combined molecular approach provides a comprehensive strategy applicable for complex genetic disorders.
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32
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Yang T, Guo L, Wang L, Yu X. Diagnosis, Intervention, and Prevention of Genetic Hearing Loss. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1130:73-92. [PMID: 30915702 DOI: 10.1007/978-981-13-6123-4_5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is estimated that at least 50% of congenital or childhood hearing loss is attributable to genetic causes. In non-syndromic hearing loss, which accounts for 70% of genetic hearing loss, approximately 80% of cases are autosomal recessive, 15% autosomal dominant, and 1-2% mitochondrial or X-linked. In addition, 30% of genetic hearing loss is syndromic. The genetic causes of hearing loss are highly heterogeneous. So far, more than 140 deafness-related genes have been discovered. Studies on those genes tremendously increased our understanding of the inner ear functions at the molecular level. It also offers important information for the patients and allows personalized and accurate genetic counseling. In many cases, genetic diagnosis of hearing loss can help to avoid unnecessary and costly clinical testing, offer prognostic information, and guide future medical management. On the other hand, a variety of gene therapeutic approaches have been developed aiming to relieve or converse the hearing loss due to genetic causes. Prevention of genetic hearing loss is feasible through prepregnancy and prenatal genetic diagnosis and counseling.
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Affiliation(s)
- Tao Yang
- Department of Otorhinolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
| | - Luo Guo
- Key Laboratory of Hearing Medicine of NHFPC, ENT Institute and Otorhinolaryngology Department, Shanghai Engineering Research Centre of Cochlear Implant, Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China
| | - Longhao Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Xiaoyu Yu
- Department of Otorhinolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
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33
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Ogasawara D, Ichu TA, Vartabedian VF, Benthuysen J, Jing H, Reed A, Ulanovskaya OA, Hulce JJ, Roberts A, Brown S, Rosen H, Teijaro JR, Cravatt BF. Selective blockade of the lyso-PS lipase ABHD12 stimulates immune responses in vivo. Nat Chem Biol 2018; 14:1099-1108. [PMID: 30420694 PMCID: PMC6263940 DOI: 10.1038/s41589-018-0155-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022]
Abstract
ABHD12 metabolizes bioactive lysophospholipids, including lysophosphatidylserine (lyso-PS). Deleterious mutations in human ABHD12 cause the neurological disease PHARC, and ABHD12-/- mice display PHARC-like phenotypes, including hearing loss, along with elevated brain lyso-PS and features of stimulated innate immune cell function. Here, we develop a selective and in vivo-active inhibitor of ABHD12 termed DO264 and show that this compound elevates lyso-PS in mouse brain and primary human macrophages. Unlike ABHD12-/- mice, adult mice treated with DO264 exhibited minimal perturbations in auditory function. On the other hand, both DO264-treated and ABHD12-/- mice displayed heightened immunological responses to lymphocytic choriomeningitis virus (LCMV) clone 13 infection that manifested as severe lung pathology with elevated proinflammatory chemokines. These results reveal similarities and differences in the phenotypic impact of pharmacological versus genetic blockade of ABHD12 and point to a key role for this enzyme in regulating immunostimulatory lipid pathways in vivo.
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Affiliation(s)
- Daisuke Ogasawara
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Taka-Aki Ichu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Vincent F Vartabedian
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Hui Jing
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Alex Reed
- Abide Therapeutics, San Diego, CA, USA
| | | | - Jonathan J Hulce
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Amanda Roberts
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven Brown
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Hugh Rosen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Teijaro
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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34
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Jayasinghe K, Quinlan C, Stark Z, Patel C, Mallawaarachchi A, Wardrop L, Kerr PG, Trnka P, Mallett AJ. Renal genetics in Australia: Kidney medicine in the genomic age. Nephrology (Carlton) 2018; 24:279-286. [PMID: 30239064 PMCID: PMC6587832 DOI: 10.1111/nep.13494] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Abstract
There have been few new therapies for patients with chronic kidney disease in the last decade. However, the management of patients affected by genetic kidney disease is rapidly evolving. Inherited or genetic kidney disease affects around 10% of adults with end‐stage kidney disease and up to 70% of children with early onset kidney disease. Advances in next‐generation sequencing have enabled rapid and cost‐effective sequencing of large amounts of DNA. Next‐generation sequencing‐based diagnostic tests now enable identification of a monogenic cause in around 20% of patients with early‐onset chronic kidney disease. A definitive diagnosis through genomic testing may negate the need for prolonged diagnostic investigations and surveillance, facilitate reproductive planning and provide accurate counselling for at‐risk relatives. Genomics has allowed the better understanding of disease pathogenesis, providing prognostic information and facilitating development of targeted treatments for patients with inherited or genetic kidney disease. Although genomic testing is becoming more readily available, there are many challenges to implementation in clinical practice. Multidisciplinary renal genetics clinics serve as a model of how some of these challenges may be overcome. Such clinics are already well established in most parts of Australia, with more to follow in future. With the rapid pace of new technology and gene discovery, collaboration between expert clinicians, laboratory and research scientists is of increasing importance to maximize benefits to patients and health‐care systems. The authors reckoned the importance of genomic testing as it allows better understanding of disease pathogenesis, provides prognostic information and facilitates development of targeted treatment, particularly for patients with inherited or genetic kidney disease.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia.,KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatric Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Zornitza Stark
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Amali Mallawaarachchi
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Louise Wardrop
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Peter G Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia
| | - Peter Trnka
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Queensland Child and Adolescent Renal Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Andrew J Mallett
- KidGen Renal Genetics Flagship, Australian Genomic Health Alliance, Melbourne, Victoria, Australia.,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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35
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Hashmi JA, Safar RA, Afzal S, Albalawi AM, Abdu-Samad F, Iqbal Z, Basit S. Whole exome sequencing identification of a novel insertion mutation in the phospholipase C ε‑1 gene in a family with steroid resistant inherited nephrotic syndrome. Mol Med Rep 2018; 18:5095-5100. [PMID: 30280192 DOI: 10.3892/mmr.2018.9528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/27/2018] [Indexed: 11/05/2022] Open
Abstract
Nephrotic syndrome (NS) represents a heterogeneous group of kidney disorders characterized by excessive proteinuria, hypoalbuminemia and edema. Defects in the filtration barrier of the glomeruli results in the development of NS. The genetic cause of NS remains to be fully elucidated. However, previous studies based on positional cloning of genes mutated in NS have provided limited insight into the pathogenesis of this disease. Mutations in phospholipase C ε‑1 (PLCE1) have been reported as a cause of early onset NS characterized by histology of diffuse mesangial sclerosis. In the present study, the underlying cause of NS in a consanguineous family was identified. Clinical and molecular aspects of a consanguineous Saudi family comprised of five individuals with steroid resistant NS were examined. Seven healthy individuals from the same family were also studied. Whole exome sequencing (WES) was performed to detect the genetic defect underlying NS. WES identified a homozygous novel insertion mutation (c.6272_6273insT) in the PLCE1 gene. Pedigree and segregation analysis confirmed an autosomal recessive inheritance pattern. This mutation may result in a bi‑allelic loss of the C‑terminal Ras‑associating domain in PLCE1 that results in NS. The present study expanded the mutational spectrum of PLCE1 in NS. In addition, the present study provided further evidence that supports the important involvement of PLCE1 in the physiological function of the glomerular filtration barrier.
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Affiliation(s)
- Jamil Amjad Hashmi
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Ramziah Ahmed Safar
- Department of Nephrology, Madinah Maternity and Children Hospital, Medina 42319, Kingdom of Saudi Arabia
| | - Sibtain Afzal
- Prince Naif Centre for Immunology Research, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh 12372, Kingdom of Saudi Arabia
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Feroz Abdu-Samad
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
| | - Zafar Iqbal
- College of Applied Medical Sciences, National Guard Health Affairs, Al‑Ahsa 36428, Kingdom of Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Medina 42318, Kingdom of Saudi Arabia
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36
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Lin H, Hu N, Zhang Y, Wang Y, Macdonald RL. Whole exome sequencing reveals novel NOV and DCAF13 variants in a Chinese pedigree with familial cortical myoclonic tremor with epilepsy. Neurosci Lett 2018; 684:115-120. [PMID: 30003937 DOI: 10.1016/j.neulet.2018.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022]
Abstract
OBJECTIVE We report a large new family of familial cortical myoclonic tremor with epilepsy(FCMTE) from China and identify the possible causative gene(s) for the family. METHOD Whole exome sequencing of blood genomic DNA from 4 patients and 2 unaffected family members were performed. Detected variants and their cosegregation were confirmed by Sanger sequencing. RESULTS We identified c.20 G > C variant in the DCAF13 gene and c.983 T > C variant in the NOV gene cosegregating in the family. There was no additional cross-over in the family to narrow to one gene. The two DCAF13 and NOV gene variants are located on 8q23.3 and 8q24.12, which is consistent with the location 8q23.3-q24.13 reported previously for a group of Japanese families. The DCAF13 variant is located in alternative transcription start site(TSS) and the function of alternative TSS is unknown. The missense NOV variant is near the C terminus in a site that is highly conserved across species. It was predicted to be deleterious on protein function. CONCLUSIONS In this study, we identify two novel variants in the DCAF13 and NOV genes associated with FCMTE in Asian populations. The interval between two variants is 15.6Mb, which is very close to each other. Future studies of additional families with this phenotype are warranted to confirm whether it is rare bigenic or monogenic inheritance.
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Affiliation(s)
- Hua Lin
- Department of Neurology, XuanWu Hospital, Capital Medical University, Beijing, China.
| | - Ningning Hu
- Departments of Neurology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Yanfeng Zhang
- Division of Epidemiology, Departments of Medicine, Vanderbilt University Medical Center Nashville, TN USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yuping Wang
- Department of Neurology, XuanWu Hospital, Capital Medical University, Beijing, China.
| | - Robert L Macdonald
- Departments of Neurology, Vanderbilt University Medical Center, Nashville, TN USA; Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN USA; Pharmacology, Vanderbilt University Medical Center, Nashville, TN USA.
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37
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Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. High-throughput mouse phenomics for characterizing mammalian gene function. Nat Rev Genet 2018; 19:357-370. [PMID: 29626206 PMCID: PMC6582361 DOI: 10.1038/s41576-018-0005-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We are entering a new era of mouse phenomics, driven by large-scale and economical generation of mouse mutants coupled with increasingly sophisticated and comprehensive phenotyping. These studies are generating large, multidimensional gene-phenotype data sets, which are shedding new light on the mammalian genome landscape and revealing many hitherto unknown features of mammalian gene function. Moreover, these phenome resources provide a wealth of disease models and can be integrated with human genomics data as a powerful approach for the interpretation of human genetic variation and its relationship to disease. In the future, the development of novel phenotyping platforms allied to improved computational approaches, including machine learning, for the analysis of phenotype data will continue to enhance our ability to develop a comprehensive and powerful model of mammalian gene-phenotype space.
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Affiliation(s)
| | - Chris C Holmes
- Nuffield Department of Medicine and Department of Statistics, University of Oxford, Oxford, UK.
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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38
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Trubiroha A, Gillotay P, Giusti N, Gacquer D, Libert F, Lefort A, Haerlingen B, De Deken X, Opitz R, Costagliola S. A Rapid CRISPR/Cas-based Mutagenesis Assay in Zebrafish for Identification of Genes Involved in Thyroid Morphogenesis and Function. Sci Rep 2018; 8:5647. [PMID: 29618800 PMCID: PMC5884836 DOI: 10.1038/s41598-018-24036-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 03/26/2018] [Indexed: 02/06/2023] Open
Abstract
The foregut endoderm gives rise to several organs including liver, pancreas, lung and thyroid with important roles in human physiology. Understanding which genes and signalling pathways regulate their development is crucial for understanding developmental disorders as well as diseases in adulthood. We exploited unique advantages of the zebrafish model to develop a rapid and scalable CRISPR/Cas-based mutagenesis strategy aiming at the identification of genes involved in morphogenesis and function of the thyroid. Core elements of the mutagenesis assay comprise bi-allelic gene invalidation in somatic mutants, a non-invasive monitoring of thyroid development in live transgenic fish, complementary analyses of thyroid function in fixed specimens and quantitative analyses of mutagenesis efficiency by Illumina sequencing of individual fish. We successfully validated our mutagenesis-phenotyping strategy in experiments targeting genes with known functions in early thyroid morphogenesis (pax2a, nkx2.4b) and thyroid functional differentiation (duox, duoxa, tshr). We also demonstrate that duox and duoxa crispants phenocopy thyroid phenotypes previously observed in human patients with bi-allelic DUOX2 and DUOXA2 mutations. The proposed combination of efficient mutagenesis protocols, rapid non-invasive phenotyping and sensitive genotyping holds great potential to systematically characterize the function of larger candidate gene panels during thyroid development and is applicable to other organs and tissues.
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Affiliation(s)
- A Trubiroha
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium.,German Federal Institute for Risk Assessment (BfR), Department Chemicals and Product Safety, Max-Dohrn-Strasse 8-10, 10589, Berlin, Germany
| | - P Gillotay
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - N Giusti
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - D Gacquer
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - F Libert
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - A Lefort
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - B Haerlingen
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - X De Deken
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - R Opitz
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium. .,Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - S Costagliola
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium.
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39
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Ewans LJ, Schofield D, Shrestha R, Zhu Y, Gayevskiy V, Ying K, Walsh C, Lee E, Kirk EP, Colley A, Ellaway C, Turner A, Mowat D, Worgan L, Freckmann ML, Lipke M, Sachdev R, Miller D, Field M, Dinger ME, Buckley MF, Cowley MJ, Roscioli T. Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genet Med 2018; 20:1564-1574. [PMID: 29595814 DOI: 10.1038/gim.2018.39] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/31/2018] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) has revolutionized Mendelian diagnostics, however, there is no consensus on the timing of data review in undiagnosed individuals and only preliminary data on the cost-effectiveness of this technology. We aimed to assess the utility of WES data reanalysis for diagnosis in Mendelian disorders and to analyze the cost-effectiveness of this technology compared with a traditional diagnostic pathway. METHODS WES was applied to a cohort of 54 patients from 37 families with a variety of Mendelian disorders to identify the genetic etiology. Reanalysis was performed after 12 months with an improved WES diagnostic pipeline. A comparison was made between costs of a modeled WES pathway and a traditional diagnostic pathway in a cohort with intellectual disability (ID). RESULTS Reanalysis of WES data at 12 months improved diagnostic success from 30 to 41% due to interim publication of disease genes, expanded phenotype data from referrer, and an improved bioinformatics pipeline. Cost analysis on the ID cohort showed average cost savings of US$586 (AU$782) for each additional diagnosis. CONCLUSION Early application of WES in Mendelian disorders is cost-effective and reanalysis of an undiagnosed individual at a 12-month time point increases total diagnoses by 11%.
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Affiliation(s)
- Lisa J Ewans
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia. .,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
| | - Deborah Schofield
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,Faculty of Pharmacy, Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Rupendra Shrestha
- Faculty of Pharmacy, Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Ying Zhu
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia.,Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Corrina Walsh
- Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Eric Lee
- Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Edwin P Kirk
- Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Alison Colley
- Clinical Genetics Department, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Carolyn Ellaway
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, New South Wales, Australia
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Lisa Worgan
- Clinical Genetics Department, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Mary-Louise Freckmann
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Michelle Lipke
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - David Miller
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Michael Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - Marcel E Dinger
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Michael F Buckley
- Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Mark J Cowley
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Tony Roscioli
- Randwick Genetics, NSW Health Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,NeuRA and Prince of Wales Clinical School, University of New South Wales, Kensington, Australia, New South Wales
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40
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Bradshaw G, Lualhati RR, Albury CL, Maksemous N, Roos-Araujo D, Smith RA, Benton MC, Eccles DA, Lea RA, Sutherland HG, Haupt LM, Griffiths LR. Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case. Front Immunol 2018; 9:420. [PMID: 29556235 PMCID: PMC5845094 DOI: 10.3389/fimmu.2018.00420] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background We investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood. Aim To identify causative functional genetic variants related to an undiagnosed primary immunodeficiency. Method Whole genome microarray copy number variant (CNV) analysis was performed on the proband followed by whole exome sequencing (WES) and trio analysis of the proband and family members. A >4 kbp deletion identified by repeated CNV analysis of exome sequencing data along with three damaging missense single nucleotide variants were validated by Sanger sequencing in all family members. Confirmation of the causative role of the candidate gene was performed by qPCR and Western Blot analyses on the proband, family members and a healthy control. Results CNV identified our previously reported interleukin 25 amplification in the proband; however, the variant was not validated to be a candidate gene for immunodeficiency. WES trio analysis, data filtering and in silico prediction identified a novel, damaging (SIFT: 0; Polyphen 1; Grantham score: 101) and disease-causing (MutationTaster) single base mutation in the X chromosome (c.511C > T p.Arg171Trp) MSN gene not identified in the UCSC Genome Browser database. The mutation was validated by Sanger sequencing, confirming the proband was hemizygous X-linked recessive (–/T) at this locus and inherited the affected T allele from his non-symptomatic carrier mother (C/T), with other family members (father, sister) confirmed to be wild type (C/C). Western Blot analysis demonstrated an absence of moesin protein in lymphocytes derived from the proband, compared with normal expression in lymphocytes derived from the healthy control, father and mother. qPCR identified significantly lower MSN mRNA transcript expression in the proband compared to an age- and sex-matched healthy control subject in whole blood (p = 0.02), and lymphocytes (p = 0.01). These results confirmed moesin deficiency in the proband, directly causative of his immunodeficient phenotype. Conclusion These findings confirm X-linked moesin-associated immunodeficiency in a proband previously undiagnosed up to 24 years of age. This study also highlights the utility of WES for the diagnosis of rare or novel forms of primary immunodeficiency disease.
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Affiliation(s)
- Gabrielle Bradshaw
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robbie R Lualhati
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Deidre Roos-Araujo
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - David A Eccles
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rod A Lea
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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41
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Kalayinia S, Goodarzynejad H, Maleki M, Mahdieh N. Next generation sequencing applications for cardiovascular disease. Ann Med 2018; 50:91-109. [PMID: 29027470 DOI: 10.1080/07853890.2017.1392595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs). Finding new variants may contribute to establishing a risk profile for the pathology process of diseases. Here, recent applications of NGS in cardiovascular medicine are discussed; both Mendelian disorders of the cardiovascular system and complex genetic CVDs including inherited cardiomyopathy, channelopathies, stroke, coronary artery disease (CAD) and are considered. We also state some future use of NGS in clinical practice for increasing our information about the CVDs genetics and the limitations of this new technology. Key messages Traditional Sanger's method was the mainstay for Human Genome Project (HGP); Sanger sequencing has high fidelity but is slow and costly as compared to next generation methods. Within cardiovascular medicine, NGS has been shown to be successful in identifying novel causative mutations and in the diagnosis of Mendelian diseases which are caused by a single variant in a single gene. NGS has provided the opportunity to perform parallel analysis of a great number of genes in an unbiased approach (i.e. without knowing the underlying biological mechanism) which probably contribute to advance our knowledge regarding the pathology of complex diseases such as CVD.
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Affiliation(s)
- Samira Kalayinia
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | | | - Majid Maleki
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | - Nejat Mahdieh
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
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42
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Guacci A, Cordella A, Rocco T, Giurato G, Nassa G, Rizzo F, Carlomagno C, Pepe S, Tarallo R, Weisz A. Identification of a novel truncating mutation in PALB2 gene by a multigene sequencing panel for mutational screening of breast cancer risk-associated and related genes. J Clin Lab Anal 2018; 32:e22418. [PMID: 29484706 DOI: 10.1002/jcla.22418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/04/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common neoplasm in women, with 5%-10% patients showing a familial predisposition, where germline mutations in BRCA1/BRCA2 genes are found in -20% of cases. Next-generation sequencing (NGS) is among the best available options for genetic screening, providing several benefits that include enhanced sensitivity and unbiased mutation detection. PALB2 (partner and localizer of BRCA2) is a cancer predisposing gene recently described that encodes a protein partner of BRCA2 involved in DNA double-strand break repair and cell cycle control. The DNA damage response represents a key cellular event, targeted by innovative anticancer therapies, including those based on poly (ADP-ribose) polymerase (PARP) inhibitors targeting PARP1 and PARP2 enzymes, activated by DNA damage and involved in single-strand break and base excision repair. METHODS Genomic DNA was isolated from 34 patient samples and four BC cell lines, as controls, and 27 breast cancer predisposing genes belonging to the BRCA1/BRCA2 and PARP pathways were sequenced by NGS. RESULTS The panel described here allowed identification of several sequence variations in most investigated genes, among which we found a novel truncating mutation in PALB2. CONCLUSIONS The NGS-based strategy designed here for molecular analysis of a customized panel of BC predisposing and related genes was found to perform effectively, providing a comprehensive exploration of all genomic sequences of the investigated genes. It is thus useful for BC molecular diagnosis, in particular for familiar cases where alterations in routinely investigated genes, such as BRCAs, result to be absent.
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Affiliation(s)
- Anna Guacci
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Angela Cordella
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Teresa Rocco
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Giorgio Giurato
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy.,Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy.,Medical Genomics Program, 'SS. Giovanni di Dio e Ruggi d'Aragona' Hospital, University of Salerno, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy.,Medical Genomics Program, 'SS. Giovanni di Dio e Ruggi d'Aragona' Hospital, University of Salerno, Salerno, Italy
| | - Chiara Carlomagno
- Department of Clinical Medicine and Surgery, University of Napoli 'Federico II', Napoli, Italy
| | - Stefano Pepe
- Division of Oncology, 'SS. Giovanni di Dio e Ruggi d'Aragona' Hospital, University of Salerno, Salerno, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy.,Medical Genomics Program, 'SS. Giovanni di Dio e Ruggi d'Aragona' Hospital, University of Salerno, Salerno, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy.,Medical Genomics Program, 'SS. Giovanni di Dio e Ruggi d'Aragona' Hospital, University of Salerno, Salerno, Italy
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Nicastro E, D'Antiga L. Next generation sequencing in pediatric hepatology and liver transplantation. Liver Transpl 2018; 24:282-293. [PMID: 29080241 DOI: 10.1002/lt.24964] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/04/2017] [Accepted: 10/18/2017] [Indexed: 02/07/2023]
Abstract
Next generation sequencing (NGS) has revolutionized the analysis of human genetic variations, offering a highly cost-effective way to diagnose monogenic diseases (MDs). Because nearly half of the children with chronic liver disorders have a genetic cause and approximately 20% of pediatric liver transplantations are performed in children with MDs, NGS offers the opportunity to significantly improve the diagnostic yield in this field. Among the NGS strategies, the use of targeted gene panels has proven useful to rapidly and reliably confirm a clinical suspicion, whereas the whole exome sequencing (WES) with variants filtering has been adopted to assist the diagnostic workup in unclear clinical scenarios. WES is powerful but challenging because it detects a great number of variants of unknown significance that can be misinterpreted and lead to an incorrect diagnosis. In pediatric hepatology, targeted NGS can be very valuable to discriminate neonatal/infantile cholestatic disorders, disclose genetic causes of acute liver failure, and diagnose the subtype of inborn errors of metabolism presenting with a similar phenotype (such as glycogen storage disorders, mitochondrial cytopathies, or nonalcoholic fatty liver disease). The inclusion of NGS in diagnostic processes will lead to a paradigm shift in medicine, changing our approach to the patient as well as our understanding of factors affecting genotype-phenotype match. In this review, we discuss the opportunities and the challenges offered nowadays by NGS, and we propose a novel algorithm for cholestasis of infancy adopted in our center, including targeted NGS as a pivotal tool for the diagnosis of liver-based MDs. Liver Transplantation 24 282-293 2018 AASLD.
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Affiliation(s)
- Emanuele Nicastro
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
| | - Lorenzo D'Antiga
- Pediatric Hepatology, Gastroenterology and Transplantation, Hospital Papa Giovanni XXIII, Bergamo, Italy
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44
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Normand EA, Alaimo JT, Van den Veyver IB. Exome and genome sequencing in reproductive medicine. Fertil Steril 2018; 109:213-220. [PMID: 29395096 DOI: 10.1016/j.fertnstert.2017.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/07/2017] [Indexed: 12/15/2022]
Abstract
The advent of next-generation sequencing has enabled clinicians to assess many genes simultaneously and at high resolution. This is advantageous for diagnosing patients in whom a genetic disorder is suspected but who have a nonspecific or atypical phenotype or when the disorder has significant genetic heterogeneity. Herein, we describe common clinical applications of next-generation sequencing technology, as well as their respective benefits and limitations. We then discuss key considerations of variant interpretation and reporting, clinical utility, pre- and posttest genetic counseling, and ethical challenges. We will present these topics with an emphasis on their applicability to the reproductive medicine setting.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.
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45
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Verkerk AJMH, Zeidler S, Breedveld G, Overbeek L, Huigh D, Koster L, van der Linde H, de Esch C, Severijnen LA, de Vries BBA, Swagemakers SMA, Willemsen R, Hoogeboom AJM, van der Spek PJ, Oostra BA. CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability. Eur J Hum Genet 2018; 26:552-560. [PMID: 29374277 DOI: 10.1038/s41431-017-0051-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.
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Affiliation(s)
- Annemieke J M H Verkerk
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. .,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lydia Overbeek
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Koster
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Celine de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies-Anne Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter J van der Spek
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Shin S, Jang W, Kim M, Kim Y, Park SY, Park J, Yang YJ. Targeted next-generation sequencing identifies a novel nonsense mutation in SPTB for hereditary spherocytosis: A case report of a Korean family. Medicine (Baltimore) 2018; 97:e9677. [PMID: 29505016 PMCID: PMC5779785 DOI: 10.1097/md.0000000000009677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RATIONALE Hereditary spherocytosis (HS) is an inherited disorder characterized by the presence of spherical-shaped red blood cells (RBCs) on the peripheral blood (PB) smear. To date, a number of mutations in 5 genes have been identified and the mutations in SPTB gene account for about 20% patients. PATIENT CONCERNS A 65-year-old female had been diagnosed as hemolytic anemia 30 years ago, based on a history of persistent anemia and hyperbilirubinemia for several years. She received RBC transfusion several times and a cholecystectomy roughly 20 years ago before. Round, densely staining spherical-shaped erythrocytes (spherocytes) were frequently found on the PB smear. Numerous spherocytes were frequently found in the PB smears of symptomatic family members, her 3rd son and his 2 grandchildren. DIAGNOSIS One heterozygous mutation of SPTB was identified by targeted next-generation sequencing (NGS). The nonsense mutation, c.1956G>A (p.Trp652*), in exon 13 was confirmed by Sanger sequencing and thus the proband was diagnosed with HS. INTERVENTIONS The proband underwent a splenectomy due to transfusion-refractory anemia and splenomegaly. OUTCOMES After the splenectomy, her hemoglobin level improved to normal range (14.1 g/dL) and her bilirubin levels decreased dramatically (total bilirubin 1.9 mg/dL; direct bilirubin 0.6 mg/dL). LESSONS We suggest that NGS of causative genes could be a useful diagnostic tool for the genetically heterogeneous RBC membrane disorders, especially in cases with a mild or atypical clinical manifestation.
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Affiliation(s)
- Soyoung Shin
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
| | - Suk Young Park
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
| | - Young Jun Yang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Feng C, Wang Q, Wang J, Liu F, Shen H, Fu H, Mao J. Coenzyme Q10 supplementation therapy for 2 children with proteinuria renal disease and ADCK4 mutation: Case reports and literature review. Medicine (Baltimore) 2017; 96:e8880. [PMID: 29382012 PMCID: PMC5709011 DOI: 10.1097/md.0000000000008880] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
RATIONALE Mitochondrial nephropathy has a poor prognosis and often progresses to the end-stage renal disease. Renal pathology often is focal segmental glomerulosclerosis (FSGS) and does not respond to steroid therapy or immunosuppressive therapy. Some patients are benefited from the therapy of coenzyme Q10, which affect the synthesis pathway of coenzyme Q10. PATIENT CONCERNS Herein, we report 2 cases of children with proteinuria renal disease with ADCK4 mutation. DIAGNOSES Proteinuria renal disease with ADCK4 mutation. INTERVENTIONS Compound heterozygous mutation in ADCK4 gene were detected with next-generation sequencing and confirmed by Sanger sequencing. Both of the patients were given coenzyme Q10 supplementation therapy. OUTCOMES The first patient showed a decreased proteinuria after coenzyme Q10 supplementation therapy, while the other was not improved. LESSONS Based on the cases we reported and from the literature, recognition of ADCK4 mutation through early and accurate genetic screening could be helpful in avoiding unnecessary toxicities and in preventing complications arising in mitochondrial nephropathy.
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Affiliation(s)
- Chunyue Feng
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
| | - Qiong Wang
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
- Department of Nephrology, The Second Hospital of Jiaxing Municipal, Jiaxing, Zhejiang Province, China
| | - Jingjing Wang
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
| | - Fei Liu
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
| | - Huijun Shen
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
| | - Haidong Fu
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
| | - Jianhua Mao
- Department of Nephrology, The Children Hospital of Zhejiang University School of Medicine, Hangzhou
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48
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Wang Z, Sadovnick AD, Traboulsee AL, Ross JP, Bernales CQ, Encarnacion M, Yee IM, de Lemos M, Greenwood T, Lee JD, Wright G, Ross CJ, Zhang S, Song W, Vilariño-Güell C. Case-Control Studies Are Not Familial Studies. Neuron 2017; 92:339-341. [PMID: 27764669 DOI: 10.1016/j.neuron.2016.09.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/04/2016] [Accepted: 09/25/2016] [Indexed: 01/22/2023]
Abstract
Identifying rare genetic variants that drive the onset of disease is challenging, even before considering the additional genetic and environmental influences that likely exist in complex diseases. We recently published a study proposing a rare variant in the NR1H3 gene (p.R415Q, rs61731956) as responsible for the onset of multiple sclerosis (MS) in two multi-incident families (Wang et al., 2016). This publication has generated much discussion, and fortunately the possibility to validate a finding or prove it spurious can occur rapidly in genetic studies. All novel discoveries must be replicated, and best efforts should be made to ensure that these replications use the appropriate samples and approach, and provide the correct interpretation of the results. This Matters Arising Response paper addresses the Minikel and MacArthur (2016) and The International Multiple Sclerosis Genetics Consortium (2016) Matters Arising papers, published concurrently in Neuron.
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Affiliation(s)
- Zhe Wang
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - A Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anthony L Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jay P Ross
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Cecily Q Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Irene M Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Madonna de Lemos
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Talitha Greenwood
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joshua D Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Galen Wright
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Colin J Ross
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Si Zhang
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carles Vilariño-Güell
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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49
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Nestor JG, Groopman EE, Gharavi AG. Towards precision nephrology: the opportunities and challenges of genomic medicine. J Nephrol 2017; 31:47-60. [PMID: 29043570 DOI: 10.1007/s40620-017-0448-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/10/2017] [Indexed: 12/28/2022]
Abstract
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice. In addition, it will discuss some of the challenges associated with the expansion of genetic testing into the clinical setting, including clinical variant interpretation and return of genetic results.
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Affiliation(s)
- Jordan G Nestor
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Emily E Groopman
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA.
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Cristofoli F, De Keersmaecker B, De Catte L, Vermeesch JR, Van Esch H. Novel STIL Compound Heterozygous Mutations Cause Severe Fetal Microcephaly and Centriolar Lengthening. Mol Syndromol 2017; 8:282-293. [PMID: 29230157 DOI: 10.1159/000479666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2017] [Indexed: 01/20/2023] Open
Abstract
STIL (SCL/TAL1 interrupting locus) is a core component of the centriole duplication process. STIL mutations have been associated with both autosomal recessive primary microcephaly (MCPH) and holoprosencephaly. In this report, we describe a family with multiple miscarriages and 2 terminations of pregnancy due to marked fetal microcephaly, delayed cortical gyrification, and dysgenesis of the corpus callosum. Whole exome sequencing allowed us to identify novel compound heterozygous mutations in STIL. The mutations lie, respectively, in the CPAP/CENPJ and the hsSAS6 interacting domains of STIL. M-phase synchronized amniocytes from both affected fetuses did not display an aberrant number of centrioles, as shown previously for either STIL-depleted or overexpressing cells. However, we observed an elongation of at least 1 centriole for each duplicated centrosome. These preliminary results may point to a novel mechanism causing MCPH and embryonic lethality in humans.
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Affiliation(s)
| | - Bart De Keersmaecker
- Laboratories for Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - Luc De Catte
- Laboratories for Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - Joris R Vermeesch
- Laboratories for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.,Laboratories for Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Van Esch
- Laboratories for Genetics of Cognition, Center for Human Genetics, KU Leuven, Leuven, Belgium.,Laboratories for Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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