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Wallis M, Bodek SD, Munro J, Rafehi H, Bennett MF, Ye Z, Schneider A, Gardiner F, Valente G, Murdoch E, Uebergang E, Hunter J, Stutterd C, Huq A, Salmon L, Scheffer I, Eratne D, Meyn S, Fong CY, John T, Mullen S, White SM, Brown NJ, McGillivray G, Chen J, Richmond C, Hughes A, Krzesinski E, Fennell A, Chambers B, Santoreneos R, Le Fevre A, Hildebrand MS, Bahlo M, Christodoulou J, Delatycki M, Berkovic SF. Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless. Orphanet J Rare Dis 2024; 19:288. [PMID: 39095811 PMCID: PMC11297648 DOI: 10.1186/s13023-024-03297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. METHODS Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. RESULTS In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. CONCLUSION AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.
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Affiliation(s)
- Mathew Wallis
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Simon D Bodek
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia.
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia.
| | - Jacob Munro
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Haloom Rafehi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mark F Bennett
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Zimeng Ye
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Amy Schneider
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Fiona Gardiner
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Giulia Valente
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Emma Murdoch
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Eloise Uebergang
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
| | - Jacquie Hunter
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Chloe Stutterd
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Aamira Huq
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetic Medicine Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Lucinda Salmon
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetics Service, Royal Prince Alfred Hospital, Melbourne, Australia
| | - Ingrid Scheffer
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Department of Paediatrics, Austin Health, Melbourne, Australia
| | - Dhamidhu Eratne
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Neuropsychiatry, The Royal Melbourne Hospital, Melbourne, Australia
| | - Stephen Meyn
- Centre for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Chun Y Fong
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Tom John
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Saul Mullen
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Susan M White
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Melbourne, Australia
- Genetics Service, Mercy Hospital for Women, Melbourne, Australia
| | - Jesse Chen
- Neurology Service, Austin Health, Melbourne, Australia
| | - Chris Richmond
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Hughes
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | | | - Andrew Fennell
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Monash Health Genetics Clinic, Melbourne, Australia
| | - Brian Chambers
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | - Renee Santoreneos
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Anna Le Fevre
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Martin Delatycki
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Samuel F Berkovic
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
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Chen R, Zhou C, Peng Y, Huang P, Yu Y, Zhu M, Zhou M, Hong D, Tan D. Whole Exome Sequencing Indicating GGCCTG Hexanucleotide Repeat in Patients with Spinocerebellar Ataxia Type 36. NEURODEGENER DIS 2024:1-9. [PMID: 38934198 DOI: 10.1159/000540006] [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: 12/10/2023] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION Spinocerebellar ataxia type 36 (SCA36) is caused by large GGCCTG repeat expansion in the NOP56 gene. The genetic diagnosis based on Southern blot is expensive and time-consuming. This study aimed to evaluate the reliability and effectiveness of whole exome sequencing (WES) for routine genetic diagnosis of suspected SCA36 patients. METHODS Pathogenic repeat expansions for SCAs including SCA36 were first analyzed based on WES data using ExpansionHunter in five probands from SCA families, then the results were confirmed by triplet repeat primed polymerase chain reaction (TP-PCR) and Southern blot. RESULTS GGCCTG repeat expansion in NOP56 was indicated in all five probands by WES, then it was found in 11 SCA patients and three asymptomatic individuals by TP-PCR. The sizes of GGCCTG repeat expansions were confirmed to be 1,390-1,556 by Southern blot. The mean age at onset of the patients was 51.0 ± 9.3 (ranging from 41 to 71), and they presented slowly progressive cerebellar ataxia, atrophy and fasciculation in tongue or limb muscles. CONCLUSION The patients were clinically and genetically diagnosed as SCA36. This study proposed that WES could be a rapid, reliable, and cost-effective routine test for the preliminarily detection of SCA36 and other ataxia diseases.
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Affiliation(s)
- Ran Chen
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Chao Zhou
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yun Peng
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Pengcheng Huang
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanyan Yu
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Min Zhu
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Meihong Zhou
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Dandan Tan
- Department of Neurology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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Xiong J, He Z, Wang L, Fan C, Chao J. DNA Origami-Enabled Gene Localization of Repetitive Sequences. J Am Chem Soc 2024; 146:6317-6325. [PMID: 38391280 DOI: 10.1021/jacs.4c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.
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Affiliation(s)
- Jinxin Xiong
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zhimei He
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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Rafehi H, Bennett MF, Bahlo M. Detection and discovery of repeat expansions in ataxia enabled by next-generation sequencing: present and future. Emerg Top Life Sci 2023; 7:349-359. [PMID: 37733280 PMCID: PMC10754322 DOI: 10.1042/etls20230018] [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: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Hereditary cerebellar ataxias are a heterogenous group of progressive neurological disorders that are disproportionately caused by repeat expansions (REs) of short tandem repeats (STRs). Genetic diagnosis for RE disorders such as ataxias are difficult as the current gold standard for diagnosis is repeat-primed PCR assays or Southern blots, neither of which are scalable nor readily available for all STR loci. In the last five years, significant advances have been made in our ability to detect STRs and REs in short-read sequencing data, especially whole-genome sequencing. Given the increasing reliance of genomics in diagnosis of rare diseases, the use of established RE detection pipelines for RE disorders is now a highly feasible and practical first-step alternative to molecular testing methods. In addition, many new pathogenic REs have been discovered in recent years by utilising WGS data. Collectively, genomes are an important resource/platform for further advancements in both the discovery and diagnosis of REs that cause ataxia and will lead to much needed improvement in diagnostic rates for patients with hereditary ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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Read JL, Davies KC, Thompson GC, Delatycki MB, Lockhart PJ. Challenges facing repeat expansion identification, characterisation, and the pathway to discovery. Emerg Top Life Sci 2023; 7:339-348. [PMID: 37888797 PMCID: PMC10754332 DOI: 10.1042/etls20230019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Tandem repeat DNA sequences constitute a significant proportion of the human genome. While previously considered to be functionally inert, these sequences are now broadly accepted as important contributors to genetic diversity. However, the polymorphic nature of these sequences can lead to expansion beyond a gene-specific threshold, causing disease. More than 50 pathogenic repeat expansions have been identified to date, many of which have been discovered in the last decade as a result of advances in sequencing technologies and associated bioinformatic tools. Commonly utilised diagnostic platforms including Sanger sequencing, capillary array electrophoresis, and Southern blot are generally low throughput and are often unable to accurately determine repeat size, composition, and epigenetic signature, which are important when characterising repeat expansions. The rapid advances in bioinformatic tools designed specifically to interrogate short-read sequencing and the development of long-read single molecule sequencing is enabling a new generation of high throughput testing for repeat expansion disorders. In this review, we discuss some of the challenges surrounding the identification and characterisation of disease-causing repeat expansions and the technological advances that are poised to translate the promise of genomic medicine to individuals and families affected by these disorders.
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Affiliation(s)
- Justin L Read
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Genevieve C Thompson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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Méreaux JL, Davoine CS, Coutelier M, Guillot-Noël L, Castrioto A, Charles P, Coarelli G, Ewenczyk C, Klebe S, Heinzmann A, Méneret A, Fauret-Amsellem AL, de Sainte Agathe JM, Brice A, Durr A. Fast and reliable detection of repeat expansions in spinocerebellar ataxia using exomes. J Med Genet 2023:jmg-2022-108924. [PMID: 36599645 DOI: 10.1136/jmg-2022-108924] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/20/2022] [Indexed: 01/06/2023]
Abstract
Usually, molecular diagnosis of spinocerebellar ataxia is based on a step-by-step approach with targeted sizing of four repeat expansions accounting for most dominant cases, then targeted sequencing of other genes. Nowadays, genome sequencing allows detection of most pathogenic variants in a single step. The ExpansionHunter tool can detect expansions in short-read genome sequencing data. Recent studies have shown that ExpansionHunter can also be used to identify repeat expansions in exome sequencing data. We tested ExpansionHunter on spinocerebellar ataxia exomes in a research context as a second-line analysis, after exclusion of main CAG repeat expansions in half of the probands. First, we confirmed the detection of expansions in seven known expansion carriers and then, after targeted analysis of ATXN1, 2, 3 and 7, CACNA1A, TBP, ATN1, NOP56, AR and HTT in 498 exomes, we found 22 additional pathogenic expansions. Comparison with capillary migration sizing in 247 individuals and confirmation of all expanded alleles detected by ExpansionHunter demonstrated that for these loci, sensitivity and specificity reached 100%. ExpansionHunter detected but underestimated the repeat size for larger expansions, and the normal alleles distribution at each locus should be taken into account to detect expansions. Exome combined with ExpansionHunter is reliable to detect repeat expansions in selected loci as first-line analysis in spinocerebellar ataxia.
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Affiliation(s)
- Jean-Loup Méreaux
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire-Sophie Davoine
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marie Coutelier
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Léna Guillot-Noël
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anna Castrioto
- Department of Neurology, University Hospital Centre Grenoble Alpes, Grenoble, France
| | - Perrine Charles
- Genetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Giulia Coarelli
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Claire Ewenczyk
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Anna Heinzmann
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Méneret
- Neurology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Anne-Laure Fauret-Amsellem
- Molecular and Cellular Neurogenetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Madeleine de Sainte Agathe
- Molecular and Cellular Neurogenetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alexis Brice
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alexandra Durr
- Sorbonne University, Paris Brain Institute (ICM - Institut du Cerveau), INSERM, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
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Unexpected diagnosis of myotonic dystrophy type 2 repeat expansion by genome sequencing. Eur J Hum Genet 2023; 31:122-124. [PMID: 35945246 PMCID: PMC9823003 DOI: 10.1038/s41431-022-01166-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/29/2022] [Accepted: 07/21/2022] [Indexed: 02/08/2023] Open
Abstract
Several neurological disorders, such as myotonic dystrophy are caused by expansions of short tandem repeats (STRs) which can be difficult to detect by molecular tools. Methodological advances have made repeat expansion (RE) detection with whole genome sequencing (WGS) feasible. We recruited a multi-generational family (family A) ascertained for genetic studies of autism spectrum disorder. WGS was performed on seven children from four nuclear families from family A and analyzed for REs of STRs known to cause neurological disorders. We detected an expansion of a heterozygous intronic CCTG STR in CNBP in two siblings. This STR causes myotonic dystrophy type 2 (DM2). The expansion did not segregate with the ASD phenotype. Repeat-primed PCR showed that the DM2 CCTG motif was expanded above the pathogenic threshold in both children and their mother. On subsequent examination, the mother had mild features of DM2. We show that screening of STRs in WGS datasets has diagnostic utility, both in the clinical and research domain, with potential management and genetic counseling implications.
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Rosenbohm A, Pott H, Thomsen M, Rafehi H, Kaya S, Szymczak S, Volk AE, Mueller K, Silveira I, Weishaupt JH, Tönnies H, Seibler P, Zschiedrich K, Schaake S, Westenberger A, Zühlke C, Depienne C, Trinh J, Ludolph AC, Klein C, Bahlo M, Lohmann K. Familial Cerebellar Ataxia and Amyotrophic Lateral Sclerosis/Frontotemporal Dementia with DAB1 and C9ORF72 Repeat Expansions: An 18-Year Study. Mov Disord 2022; 37:2427-2439. [PMID: 36148898 PMCID: PMC10900262 DOI: 10.1002/mds.29221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Coding and noncoding repeat expansions are an important cause of neurodegenerative diseases. OBJECTIVE This study determined the clinical and genetic features of a large German family that has been followed for almost 2 decades with an autosomal dominantly inherited spinocerebellar ataxia (SCA) and independent co-occurrence of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). METHODS We carried out clinical examinations and telephone interviews, reviewed medical records, and performed magnetic resonance imaging and positron emission tomography scans of all available family members. Comprehensive genetic investigations included linkage analysis, short-read genome sequencing, long-read sequencing, repeat-primed polymerase chain reaction, and Southern blotting. RESULTS The family comprises 118 members across seven generations, 30 of whom were definitely and five possibly affected. In this family, two different pathogenic mutations were found, a heterozygous repeat expansion in C9ORF72 in four patients with ALS/FTD and a heterozygous repeat expansion in DAB1 in at least nine patients with SCA, leading to a diagnosis of DAB1-related ataxia (ATX-DAB1; SCA37). One patient was affected by ALS and SCA and carried both repeat expansions. The repeat in DAB1 had the same configuration but was larger than those previously described ([ATTTT]≈75 [ATTTC]≈40-100 [ATTTT]≈415 ). Clinical features in patients with SCA included spinocerebellar symptoms, sometimes accompanied by additional ophthalmoplegia, vertical nystagmus, tremor, sensory deficits, and dystonia. After several decades, some of these patients suffered from cognitive decline and one from additional nonprogressive lower motor neuron affection. CONCLUSION We demonstrate genetic and clinical findings during an 18-year period in a unique family carrying two different pathogenic repeat expansions, providing novel insights into their genotypic and phenotypic spectrums. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Hendrik Pott
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Mirja Thomsen
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Haloom Rafehi
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Sabine Kaya
- Institute of Human GeneticsUniversity Hospital EssenEssenGermany
| | - Silke Szymczak
- Insitute of Medical Biometry and StatisticsUniversity of LübeckLübeckGermany
| | - Alexander E. Volk
- Institute of Human GeneticsUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | | | - Isabel Silveira
- i3S‐Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
| | - Jochen H. Weishaupt
- Division of Neurodegeneration, Neurology DepartmentUniversity Medicine Mannheim, Heidelberg UniversityMannheimGermany
| | - Holger Tönnies
- Institute of Human GeneticsChristian‐Albrechts‐UniversityKielGermany
| | - Philip Seibler
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Susen Schaake
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | | | | | - Joanne Trinh
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Albert C. Ludolph
- Department of NeurologyUniversity of UlmUlmGermany
- German Center for Neurodegenerative Diseases, Site UlmUlmGermany
| | | | - Melanie Bahlo
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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9
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Watanabe K, Nakashima M, Wakatsuki R, Bunai T, Ouchi Y, Nakamura T, Miyajima H, Saitsu H. Cognitive Impairment in a Complex Family With AAGGG and ACAGG Repeat Expansions in RFC1 Detected by ExpansionHunter Denovo. NEUROLOGY GENETICS 2022; 8:e682. [PMID: 36381255 PMCID: PMC9641967 DOI: 10.1212/nxg.0000000000000682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/07/2022] [Indexed: 11/25/2022]
Abstract
Background and Objectives We investigated the genetic basis and brain metabolism and blood flow of a Japanese family with spinocerebellar degeneration (SCD), with multiple affected members for 3 generations. Methods After excluding DNA repeat expansion (RE) of common SCD genes by fragment analysis, we performed whole-exome sequencing (WES) and whole-genome sequencing (WGS). Homozygosity mapping was performed using these data. REs were investigated with WGS data using ExpansionHunter Denovo and Expansion Hunter. Results WES and WGS were unable to identify likely pathogenic variants, and homozygosity mapping failed to narrow down the locus. However, ExpansionHunter Denovo detected REs in intron 2 of the RFC1 gene and led us to the diagnosis of RFC1-related disorders. Subsequent repeat-primed PCR and Southern blot hybridization analyses revealed that 3 of 6 patients and 1 suspected individual had expansions of AAGGG ((AAGGG)exp) and (ACAGG)exp repeats in a compound heterozygous state and 3 had a homozygous (ACAGG)exp. The patients showed a variety of clinical features, including adult-onset ataxia, sensorimotor neuropathy, head tremor, parkinsonism, dystonia, and cognitive impairment. A comparison of previous reports with those of the family in study suggested that motor neuropathy could be a feature of compound heterozygous patients and biallelic (ACAGG)exp patients. Cognitive function tests showed cognitive impairment with a predominance of frontal lobe dysfunction. Examination of MRI, SPECT, and 18F-fluorodeoxyglucose-PET showed clear cortical damage with frontal lobe predominance in 1 case, but no cerebral damage was evident in the other 2 cases. Discussion Our report shows the usefulness of WGS and RE detection tools for SCD of unknown cause. The studied family with RFC1-related disorders included patients with (ACAGG)exp and (AAGGG)exp in a compound heterozygous state and was characterized by motor neuropathy. Based on the results of cognitive function tests and imaging studies, 1 patient presented with cognitive impairment due to frontal lobe metabolic changes, but there were also patients who presented with cognitive impairment without apparent cerebral metabolic or blood flow, suggesting that other factors are also associated with cognitive impairment.
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10
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Ibañez K, Polke J, Hagelstrom RT, Dolzhenko E, Pasko D, Thomas ERA, Daugherty LC, Kasperaviciute D, Smith KR, Deans ZC, Hill S, Fowler T, Scott RH, Hardy J, Chinnery PF, Houlden H, Rendon A, Caulfield MJ, Eberle MA, Taft RJ, Tucci A. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study. Lancet Neurol 2022; 21:234-245. [PMID: 35182509 PMCID: PMC8850201 DOI: 10.1016/s1474-4422(21)00462-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders. METHODS We retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013-17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result. FINDINGS The diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2-99·0) and 99·6% specificity (99·1-99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate). INTERPRETATION In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder. FUNDING Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.
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Affiliation(s)
- Kristina Ibañez
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | | | | | - Dorota Pasko
- Genomics England, Queen Mary University of London, London, UK
| | | | - Louise C Daugherty
- Genomics England, Queen Mary University of London, London, UK; Healx, Cambridge, UK
| | - Dalia Kasperaviciute
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Katherine R Smith
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Zandra C Deans
- Genomics Quality Assessment, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK; NHS England and NHS Improvement, London, UK
| | - Sue Hill
- NHS England and NHS Improvement, London, UK
| | - Tom Fowler
- Genomics England, Queen Mary University of London, London, UK
| | - Richard H Scott
- Genomics England, Queen Mary University of London, London, UK; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - John Hardy
- Department of Neurodegenerative Disorders, Institute of Neurology, University College London, London, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit and Department of ClinicalNeurosciences, University of Cambridge, Cambridge, UK
| | - Henry Houlden
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | | | - Arianna Tucci
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK.
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11
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Yau WY, Vandrovcova J, Sullivan R, Chen Z, Zecchinelli A, Cilia R, Duga S, Murray M, Carmona S, Chelban V, Ishiura H, Tsuji S, Jaunmuktane Z, Turner C, Wood NW, Houlden H. Low Prevalence of NOTCH2NLC GGC Repeat Expansion in White Patients with Movement Disorders. Mov Disord 2020; 36:251-255. [PMID: 33026126 PMCID: PMC8436747 DOI: 10.1002/mds.28302] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/27/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The objective of this study was to determine the prevalence of the GGC-repeat expansion in NOTCH2NLC in whites presenting with movement disorders. METHODS We searched for the GGC-repeat expansion in NOTCH2NLC using repeat-primed polymerase chain reaction in 203 patients with essential tremor, 825 patients with PD, 194 patients with spinocerebellar ataxia, 207 patients with "possible" or "probable" MSA, and 336 patients with pathologically confirmed MSA. We also screened 30,008 patients enrolled in the 100,000 Genomes Project for the same mutation using ExpansionHunter, followed by repeat-primed polymerase chain reaction. All possible expansions were confirmed by Southern blotting and/or long-read sequencing. RESULTS We identified 1 patient who carried the NOTCH2NLC mutation in the essential tremor cohort, and 1 patient presenting with recurrent encephalopathy and postural tremor/parkinsonism in the 100,000 Genomes Project. CONCLUSIONS GGC-repeat expansion in NOTCH2NLC is rare in whites presenting with movement disorders. In addition, existing whole-genome sequencing data are useful in case ascertainment. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Wai Yan Yau
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Zhongbo Chen
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.,Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Anna Zecchinelli
- Biobank Centro Parkinson e Parkinsonismi ASST Pini CTO, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Istituto Clinico Humanitas, Rozzano, Milan, Italy
| | - Malgorzata Murray
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Susana Carmona
- UK Dementia Research Institute (UK DRI) at UCL, London, United Kingdom
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- Genomics England, London, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | | | - Shoji Tsuji
- Department of Molecular Neurology, The University of Tokyo, Tokyo, Japan.,Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Zane Jaunmuktane
- Divison of Neuropathology, National Hospital for Neurology and Neurosurgery, London, United Kingdom.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Chris Turner
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom.,Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.,Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
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