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Ferreira T, Polavarapu K, Olimpio C, Paramonov I, Lochmüller H, Horvath R. Variants in mitochondrial disease genes are common causes of inherited peripheral neuropathies. J Neurol 2024; 271:3546-3553. [PMID: 38549004 PMCID: PMC11136726 DOI: 10.1007/s00415-024-12319-y] [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: 02/13/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Peripheral neuropathies in mitochondrial disease are caused by mutations in nuclear genes encoding mitochondrial proteins, or in the mitochondrial genome. Whole exome or genome sequencing enable parallel testing of nuclear and mtDNA genes, and it has significantly advanced the genetic diagnosis of inherited diseases. Despite this, approximately 40% of all Charcot-Marie-Tooth (CMT) cases remain undiagnosed. METHODS The genome-phenome analysis platform (GPAP) in RD-Connect was utilised to create a cohort of 2087 patients with at least one Human Phenotype Ontology (HPO) term suggestive of a peripheral neuropathy, from a total of 10,935 patients. These patients' genetic data were then analysed and searched for variants in known mitochondrial disease genes. RESULTS A total of 1,379 rare variants were identified, 44 of which were included in this study as either reported pathogenic or likely causative in 42 patients from 36 families. The most common genes found to be likely causative for an autosomal dominant neuropathy were GDAP1 and GARS1. We also detected heterozygous likely pathogenic variants in DNA2, MFN2, DNM2, PDHA1, SDHA, and UCHL1. Biallelic variants in SACS, SPG7, GDAP1, C12orf65, UCHL1, NDUFS6, ETFDH and DARS2 and variants in the mitochondrial DNA (mtDNA)-encoded MT-ATP6 and MT-TK were also causative for mitochondrial CMT. Only 50% of these variants were already reported as solved in GPAP. CONCLUSION Variants in mitochondrial disease genes are frequent in patients with inherited peripheral neuropathies. Due to the clinical overlap between mitochondrial disease and CMT, agnostic exome or genome sequencing have better diagnostic yields than targeted gene panels.
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Affiliation(s)
- Tomas Ferreira
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Catarina Olimpio
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ida Paramonov
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Centro Nacional de Análisis Genómico, Barcelona, Spain
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK.
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Pucel J, Briere LC, Reuter C, Gochyyev P, LeBlanc K. Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med 2024; 26:101115. [PMID: 38436216 PMCID: PMC11161308 DOI: 10.1016/j.gim.2024.101115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases. METHODS In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS. RESULTS Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively). CONCLUSION We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.
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Affiliation(s)
- Jenna Pucel
- MGH Institute of Health Professions, Boston, MA.
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Cardiovascular Medicine, Stanford University, Palo Alto, CA
| | | | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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Ciancia S, Madeo SF, Calabrese O, Iughetti L. The Approach to a Child with Dysmorphic Features: What the Pediatrician Should Know. CHILDREN (BASEL, SWITZERLAND) 2024; 11:578. [PMID: 38790573 PMCID: PMC11120268 DOI: 10.3390/children11050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
The advancement of genetic knowledge and the discovery of an increasing number of genetic disorders has made the role of the geneticist progressively more complex and fundamental. However, most genetic disorders present during childhood; thus, their early recognition is a challenge for the pediatrician, who will be also involved in the follow-up of these children, often establishing a close relationship with them and their families and becoming a referral figure. In this review, we aim to provide the pediatrician with a general knowledge of the approach to treating a child with a genetic syndrome associated with dysmorphic features. We will discuss the red flags, the most common manifestations, the analytic collection of the family and personal medical history, and the signs that should alert the pediatrician during the physical examination. We will offer an overview of the physical malformations most commonly associated with genetic defects and the way to describe dysmorphic facial features. We will provide hints about some tools that can support the pediatrician in clinical practice and that also represent a useful educational resource, either online or through apps downloaded on a smartphone. Eventually, we will offer an overview of genetic testing, the ethical considerations, the consequences of incidental findings, and the main indications and limitations of the principal technologies.
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Affiliation(s)
- Silvia Ciancia
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
| | - Simona Filomena Madeo
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
| | - Olga Calabrese
- Medical Genetics Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Lorenzo Iughetti
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124 Modena, Italy
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van der Geest MA, Maeckelberghe ELM, van Gijn ME, Lucassen AM, Swertz MA, van Langen IM, Plantinga M. Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications. Eur J Hum Genet 2024; 32:489-497. [PMID: 38480795 PMCID: PMC11061183 DOI: 10.1038/s41431-023-01529-z] [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: 07/26/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 05/02/2024] Open
Abstract
With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.
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Affiliation(s)
- Marije A van der Geest
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Els L M Maeckelberghe
- Institute for Medical Education, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Faculty of Medicine, Clinical Ethics and Law, University of Southampton, Southampton, UK
- Centre for Personalised Medicine, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Ferrer A, Duffy P, Olson RJ, Meiners MA, Schultz-Rogers L, Macke EL, Safgren S, Morales-Rosado JA, Cousin MA, Oliver GR, Rider D, Williams M, Pichurin PN, Deyle DR, Morava E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Kaiwar C, Vitek CR, McAllister TM, Wick MJ, Schimmenti LA, Lazaridis KN, Vairo FPE, Klee EW. Semiautomated approach focused on new genomic information results in time and effort-efficient reannotation of negative exome data. Hum Genet 2024; 143:649-666. [PMID: 38538918 DOI: 10.1007/s00439-024-02664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/25/2024] [Indexed: 05/18/2024]
Abstract
Most rare disease patients (75-50%) undergoing genomic sequencing remain unsolved, often due to lack of information about variants identified. Data review over time can leverage novel information regarding disease-causing variants and genes, increasing this diagnostic yield. However, time and resource constraints have limited reanalysis of genetic data in clinical laboratories setting. We developed RENEW, (REannotation of NEgative WES/WGS) an automated reannotation procedure that uses relevant new information in on-line genomic databases to enable rapid review of genomic findings. We tested RENEW in an unselected cohort of 1066 undiagnosed cases with a broad spectrum of phenotypes from the Mayo Clinic Center for Individualized Medicine using new information in ClinVar, HGMD and OMIM between the date of previous analysis/testing and April of 2022. 5741 variants prioritized by RENEW were rapidly reviewed by variant interpretation specialists. Mean analysis time was approximately 20 s per variant (32 h total time). Reviewed cases were classified as: 879 (93.0%) undiagnosed, 63 (6.6%) putatively diagnosed, and 4 (0.4%) definitively diagnosed. New strategies are needed to enable efficient review of genomic findings in unsolved cases. We report on a fast and practical approach to address this need and improve overall diagnostic success in patient testing through a recurrent reannotation process.
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Affiliation(s)
- Alejandro Ferrer
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick Duffy
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael A Meiners
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica L Macke
- The Institute of Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Joel A Morales-Rosado
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Rider
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Megan Williams
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Klass J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Myra J Wick
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Departments of Otorhinolaryngology, Head and Neck Surgery, Ophthalmology, and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [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: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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7
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [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: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Gerik-Celebi HB, Unsel-Bolat G, Bolat H. Association of ABCA13 Gene Variants with Autism Spectrum Disorder and Other Neuropsychiatric Disorders. Mol Syndromol 2024; 15:22-29. [PMID: 38357255 PMCID: PMC10862315 DOI: 10.1159/000534123] [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: 07/16/2023] [Accepted: 09/08/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a neuropsychiatric disorder characterized by impaired social skills and limited or repetitive behaviors. In this study, we investigated the role of the ABCA13 gene in the etiopathogenesis of ASD. Methods Single-nucleotide variants were evaluated in 79 ASD patients (59 males +20 females) with no established genetic etiology associated with ASD using whole-exome sequencing/clinical exome sequencing method. Family segregation analysis was performed using Sanger sequencing. We presented the clinical and genetic findings of these cases and their parents in detail. Results We presented 10 different ABCA13 gene variants in cases with ASD and 10 parents carrying the same ABCA13 gene variant. There of these variants were likely pathogenic and seven variants were classified as variant of uncertain significance. Our cases had a comorbidity rate for attention deficit hyperactivity disorder (ADHD) as 70%. Various types of neuropsychiatric symptoms and diagnoses were detected including ADHD, anxiety disorder, intellectual disability, delay in speech, and febrile convulsion among the parents. Conclusion To date, very few variants have been reported in the ABCA13 gene. Our findings enrich the role of ABCA13 gene may play a common role in the landscape of neuropsychiatric disorders.
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Affiliation(s)
| | - Gul Unsel-Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
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Vaseghi P, Habibi L, Neidich JA, Cao Y, Fattahi N, Rashidi-Nezhad R, Salehnezhad T, Dalili H, Rahimi Sharbaf F, Zarkesh MR, Malekian M, Mokhberdezfuli M, Mehrtash A, Ardeshirdavani A, Kariminejad R, Ghorbansabagh V, Sadeghimoghadam P, Naddaf A, Esmaeilnia Shirvany T, Mosayebi Z, Sahebdel B, Golshahi F, Shirazi M, Shamel S, Moeini R, Heidari A, Daneshmand MA, Ghasemi R, Akrami SM, Rashidi-Nezhad A. Towards solving the genetic diagnosis odyssey in Iranian patients with congenital anomalies. Eur J Hum Genet 2024:10.1038/s41431-024-01533-x. [PMID: 38278869 DOI: 10.1038/s41431-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
Understanding the underlying causes of congenital anomalies (CAs) can be a complex diagnostic journey. We aimed to assess the efficiency of exome sequencing (ES) and chromosomal microarray analysis (CMA) in patients with CAs among a population with a high fraction of consanguineous marriage. Depending on the patient's symptoms and family history, karyotype/Quantitative Fluorescence- Polymerase Chain Reaction (QF-PCR) (n = 84), CMA (n = 81), ES (n = 79) or combined CMA and ES (n = 24) were performed on 168 probands (66 prenatal and 102 postnatal) with CAs. Twelve (14.28%) probands were diagnosed by karyotype/QF-PCR and seven (8.64%) others were diagnosed by CMA. ES findings were conclusive in 39 (49.36%) families, and 61.90% of them were novel variants. Also, 64.28% of these variants were identified in genes that follow recessive inheritance in CAs. The diagnostic rate (DR) of ES was significantly higher than that of CMA in children from consanguineous families (P = 0·0001). The highest DR by CMA was obtained in the non-consanguineous postnatal subgroup and by ES in the consanguineous prenatal subgroup. In a population that is highly consanguineous, our results suggest that ES may have a higher diagnostic yield than CMA and should be considered as the first-tier test in the evaluation of patients with congenital anomalies.
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Affiliation(s)
- Parisa Vaseghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Laleh Habibi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | - Julie A Neidich
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Cao
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Neda Fattahi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | | | | | - Hossein Dalili
- Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahimi Sharbaf
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zarkesh
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | - Mahdieh Mokhberdezfuli
- Ronash Medical Genetics Laboratory, Tehran, Iran
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Vafa Ghorbansabagh
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvane Sadeghimoghadam
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Naddaf
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Esmaeilnia Shirvany
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Mosayebi
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrokh Sahebdel
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golshahi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboobeh Shirazi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Shamel
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | - Roksana Moeini
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | | | - Reza Ghasemi
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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10
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Cheung C, Berger SM, Ross M, Kramer T, Li Y, Andrews C, Dergham KR, Spitz E, Florido ME, Ahimaz P. Assessing management practices for variants of uncertain significance among genetic counselors in pediatrics. J Genet Couns 2024. [PMID: 38217320 DOI: 10.1002/jgc4.1860] [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: 02/14/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/15/2024]
Abstract
Increased utilization of genomic sequencing in pediatric medicine has increased the detection of variants of uncertain significance (VUS). Periodic VUS reinterpretation can clarify clinical significance and increase diagnostic yield, highlighting the importance of systematic VUS tracking and reinterpretation. There are currently no standardized guidelines or established best practices for VUS management, and our understanding of how genetic counselors (GCs) track and manage VUS results for pediatric patients is limited. In this exploratory study, GCs in pediatric clinics in North America were surveyed about their VUS management practices. A total of 124 responses were included in the analysis. The majority (n = 115, 92.7%) of GCs reported that VUS management workflows were at the discretion of each individual provider in their workplace. Approximately half (n = 65, 52%) kept track of patient VUS results over time, and GCs with lower patient volumes were more likely to do so (p = 0.04). While 95% (n = 114) of GCs had requested VUS reinterpretation at least once, only 5% (n = 6) requested it routinely. Most (n = 80, 86%) GCs notified patients when a VUS was reclassified, although methods of recontact differed when the reclassification was an upgrade versus a downgrade. GCs who asked patients to stay in touch through periodic recontact or follow-up appointments were more likely to request VUS reinterpretation (p = 0.01). The most frequently reported barriers to requesting reinterpretation regularly were patients being lost to follow-up (n = 39, 33.1%), insufficient bandwidth (n = 27, 22.9%), and lack of standardized guidelines (n = 25, 21.2%). GCs had consistent overall practices around VUS management around investigation, disclosure, reinterpretation, and recontact, but specific methods used differed and were at the discretion of each provider. These results showcase the current landscape of VUS management workflows in pediatrics and the challenges associated with adopting more uniform practices. The study findings can help inform future strategies to develop standardized guidelines surrounding VUS management.
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Affiliation(s)
- Chloe Cheung
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Clinical Trials Office, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sara M Berger
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Meredith Ross
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tamar Kramer
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yuhuan Li
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Carli Andrews
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Katia R Dergham
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- School of Pharmacy and Health Sciences, Keck Graduate Insititute, Claremont, California, USA
| | - Elana Spitz
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Hematology Oncology, University of Carlifornia, Los Angeles Health, Los Angeles, California, USA
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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11
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van Slobbe M, van Haeringen A, Vissers LELM, Bijlsma EK, Rutten JW, Suerink M, Nibbeling EAR, Ruivenkamp CAL, Koene S. Reanalysis of whole-exome sequencing (WES) data of children with neurodevelopmental disorders in a standard patient care context. Eur J Pediatr 2024; 183:345-355. [PMID: 37889289 PMCID: PMC10858114 DOI: 10.1007/s00431-023-05279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
This study aims to inform future genetic reanalysis management by evaluating the yield of whole-exome sequencing (WES) reanalysis in standard patient care in the Netherlands. Single-center data of 159 patients with a neurodevelopmental disorder (NDD), in which WES analysis and reanalysis were performed between January 1, 2014, and December 31, 2021, was retrospectively collected. Patients were included if they were under the age of 18 years at initial analysis and if this initial analysis did not result in a diagnosis. Demographic, phenotypic, and genotypic characteristics of patients were collected and analyzed. The primary outcomes of our study were (i) diagnostic yield at reanalysis, (ii) reasons for detecting a new possibly causal variant at reanalysis, (iii) unsolicited findings, and (iv) factors associated with positive result of reanalysis. In addition, we conducted a questionnaire study amongst the 7 genetic department in the Netherlands creating an overview of used techniques, yield, and organization of WES reanalysis. The single-center data show that in most cases, WES reanalysis was initiated by the clinical geneticist (65%) or treating physician (30%). The mean time between initial WES analysis and reanalysis was 3.7 years. A new (likely) pathogenic variant or VUS with a clear link to the phenotype was found in 20 initially negative cases, resulting in a diagnostic yield of 12.6%. In 75% of these patients, the diagnosis had clinical consequences, as for example, a screening plan for associated signs and symptoms could be devised. Most (32%) of the (likely) causal variants identified at WES reanalysis were discovered due to a newly described gene-disease association. In addition to the 12.6% diagnostic yield based on new diagnoses, reclassification of a variant of uncertain significance found at initial analysis led to a definite diagnosis in three patients. Diagnostic yield was higher in patients with dysmorphic features compared to patients without clear dysmorphic features (yield 27% vs. 6%; p = 0.001). CONCLUSIONS Our results show that WES reanalysis in patients with NDD in standard patient care leads to a substantial increase in genetic diagnoses. In the majority of newly diagnosed patients, the diagnosis had clinical consequences. Knowledge about the clinical impact of WES reanalysis, clinical characteristics associated with higher yield, and the yield per year after a negative WES in larger clinical cohorts is warranted to inform guidelines for genetic reanalysis. These guidelines will be of great value for pediatricians, pediatric rehabilitation specialists, and pediatric neurologists in daily care of patients with NDD. WHAT IS KNOWN • Whole exome sequencing can cost-effectively identify a genetic cause of intellectual disability in about 30-40% of patients. • WES reanalysis in a research setting can lead to a definitive diagnosis in 10-20% of previously exome negative cases. WHAT IS NEW • WES reanalysis in standard patient care resulted in a diagnostic yield of 13% in previously exome negative children with NDD. • The presence of dysmorphic features is associated with an increased diagnostic yield of WES reanalysis.
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Affiliation(s)
- Michelle van Slobbe
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
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12
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Racine C, Denommé-Pichon AS, Engel C, Tran Mau-Them F, Bruel AL, Vitobello A, Safraou H, Sorlin A, Nambot S, Delanne J, Garde A, Colin E, Moutton S, Thevenon J, Jean-Marçais N, Willems M, Geneviève D, Pinson L, Perrin L, Laffargue F, Lespinasse J, Lacaze E, Molin A, Gerard M, Lambert L, Benigni C, Patat O, Bourgeois V, Poe C, Chevarin M, Couturier V, Garret P, Philippe C, Duffourd Y, Faivre L, Thauvin-Robinet C. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet 2023; 61:36-46. [PMID: 37586840 DOI: 10.1136/jmg-2023-109170] [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: 01/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Wide access to clinical exome/genome sequencing (ES/GS) enables the identification of multiple molecular diagnoses (MMDs), being a long-standing but underestimated concept, defined by two or more causal loci implicated in the phenotype of an individual with a rare disease. Only few series report MMDs rates (1.8% to 7.1%). This study highlights the increasing role of MMDs in a large cohort of individuals addressed for congenital anomalies/intellectual disability (CA/ID). METHODS From 2014 to 2021, our diagnostic laboratory rendered 880/2658 positive ES diagnoses for CA/ID aetiology. Exhaustive search on MMDs from ES data was performed prospectively (January 2019 to December 2021) and retrospectively (March 2014 to December 2018). RESULTS MMDs were identified in 31/880 individuals (3.5%), responsible for distinct (9/31) or overlapping (22/31) phenotypes, and potential MMDs in 39/880 additional individuals (4.4%). CONCLUSION MMDs are frequent in CA/ID and remain a strong challenge. Reanalysis of positive ES data appears essential when phenotypes are partially explained by the initial diagnosis or atypically enriched overtime. Up-to-date clinical data, clinical expertise from the referring physician, strong interactions between clinicians and biologists, and increasing gene discoveries and improved ES bioinformatics tools appear all the more fundamental to enhance chances of identifying MMDs. It is essential to provide appropriate patient care and genetic counselling.
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Affiliation(s)
- Caroline Racine
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Camille Engel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Frederic Tran Mau-Them
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Hana Safraou
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Estelle Colin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Marjolaine Willems
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - David Geneviève
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
- INSERM U1183, Université de Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Laurence Perrin
- Genetic Department, Robert-Debré Hospital Department of Genetics, Paris, France
| | - Fanny Laffargue
- Service de Génétique médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - James Lespinasse
- Unité de Génétique médicale, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Elodie Lacaze
- Department of Medical Genetics, Hospital Group Le Havre, Le Havre, France
| | - Arnaud Molin
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | - Marion Gerard
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | | | | | - Olivier Patat
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, France
| | - Valentin Bourgeois
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Charlotte Poe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Martin Chevarin
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Victor Couturier
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Philippine Garret
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christophe Philippe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Yannis Duffourd
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
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13
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Yoon E, Lee JK, Park TK, Chang SA, Huh J, Kim JW, Kim DK, Jang JH. Experience of reassessing FBN1 variants of uncertain significance by gene-specific guidelines. J Med Genet 2023; 61:57-60. [PMID: 37558401 DOI: 10.1136/jmg-2023-109433] [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: 05/30/2023] [Accepted: 07/22/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Despite the 2015 American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) guideline, many variants of FBN1 gene remain inconclusive. In line with publication of the FBN1-specific variant interpretation guideline by ClinGen in 2022, we reassessed variants of uncertain significance (VUS) in FBN1 gene found in our institution. METHODS VUS found in the course of FBN1 sequencing between December 2015 and April 2022 were reassessed based on FBN1-specific variant interpretation guideline, review of updated literatures and additional genetic tests including family study and/or RNA study if available. RESULTS Out of 695 patients who underwent FBN1 sequencing, 61 VUS were found in 69 patients. Among them, 38 VUS in 43 patients (62.3%) were reclassified as pathogenic and likely pathogenic variant ((L)PV), including 20 novel (L)PV. Major causes of reclassification were: (1) gene-specific modification of ACMG/AMP criteria, (2) updated literatures and (3) additional genetic tests. The most important evidence for reclassification was clarification of critical amino acid residues. CONCLUSIONS After reassessing FBN1 variants according to FBN1-specific guideline and up-to-date database, a significant number of VUS was reclassified. Clinical laboratories are encouraged to perform variant reassessment at regular intervals or when there is a major change in the principle of variant interpretation.
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Affiliation(s)
- Eungjun Yoon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Kwon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Taek Kyu Park
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sung-A Chang
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - June Huh
- Division of Cardiology, Department of Pediatrics, Adult Congenital Heart Disease Clinic, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Duk-Kyung Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Division of Cardiology, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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14
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Meyer AP, Ma J, Brock G, Hashimoto S, Cottrell CE, Mathew M, Hunter JM, Leung ML, Corsmeier D, Jayaraman V, Waldrop MA, Flanigan KM. Exome sequencing in the pediatric neuromuscular clinic leads to more frequent diagnosis of both neuromuscular and neurodevelopmental conditions. Muscle Nerve 2023; 68:833-840. [PMID: 37789688 DOI: 10.1002/mus.27976] [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: 01/06/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION/AIMS Exome sequencing (ES) has proven to be a valuable diagnostic tool for neuromuscular disorders, which often pose a diagnostic challenge. The aims of this study were to investigate the clinical outcomes associated with utilization of ES in the pediatric neuromuscular clinic and to determine if specific phenotypic features or abnormal neurodiagnostic tests were predictive of a diagnostic result. METHODS This was a retrospective medical record review of 76 pediatric neuromuscular clinic patients who underwent ES. Based upon clinical assessment prior to ES, patients were divided into two groups: affected by neuromuscular (n = 53) or non-neuromuscular (n = 23) syndromes. RESULTS A diagnosis was made in 28/76 (36.8%), with 29 unique disorders identified. In the neuromuscular group, a neuromuscular condition was confirmed in 78% of those receiving a genetic diagnosis. Early age of symptom onset was associated with a significantly higher diagnostic yield. The most common reason neuromuscular diagnoses were not detected on prior testing was due to causative genes not being present on disease-specific panels. Changes to medical care were made in 57% of individuals receiving a diagnosis on ES. DISCUSSION These data further support ES as a powerful diagnostic tool in the pediatric neuromuscular clinic and highlight the advantages of ES over gene panels, including the ability to identify diagnoses regardless of etiology, identify genes newly associated with disease, and identify multiple confounding diagnoses. Rapid and accurate diagnosis by ES can not only end the patient's diagnostic odyssey, but often impacts patients' medical management and genetic counseling of families.
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Affiliation(s)
- Alayne P Meyer
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jianing Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Guy Brock
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Mariam Mathew
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Jesse M Hunter
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Marco L Leung
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Don Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Megan A Waldrop
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kevin M Flanigan
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
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15
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Viora-Dupont E, Denommé-Pichon A, Chevarin M, Patat O, Willems M, Bourgon N, Bruel A, Aubert-Mucca M, Galinier M, Itier R, Decramer S, Piton A, Gerard B, Billon C, Jeunemaitre X, Duffourd Y, Callier P, Thauvin C, Philippe C, Faivre L, Albuisson J, Vitobello A. Identification of the first homozygous intragenic deletion in the YY1AP1 gene in a consanguineous family: New insights into the phenotypic variability associated with Grange syndrome. Am J Med Genet A 2023; 191:2728-2735. [PMID: 37698238 DOI: 10.1002/ajmg.a.63394] [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: 03/09/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023]
Abstract
Grange syndrome (GRNG-MIM#135580) is a rare recessive disorder associating variable features including diffuse vascular stenosis, brachysyndactyly, osteopenia with increased bone fragility, cardiac malformations, and variable developmental delay. Since its first description in 1998, only 15 individuals from 10 families have been reported, carrying homozygous or compound heterozygous frameshift or nonsense variants in YY1AP1. In a patient with cutaneous and bone syndactyly and a hemorrhagic stroke at the age of 16 months, consistent with a clinical diagnosis of GRNG, we performed exome sequencing after negative array-CGH and congenital limb malformation panel results. Copy number variant analysis from exome data identified a homozygous intragenic out-of-frame deletion of 1.84 kb encompassing exons seven and eight of YY1AP1, confirming a molecular diagnosis of GRNG. Genetic counseling led to the identification of additional family members compatible with GRNG. Here, we provide new insights into the phenotypic variability associated with GRNG and highlight the utility of the detection of small copy number variants to identify the molecular causes of heterogeneous malformative genetic disorders.
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Affiliation(s)
- E Viora-Dupont
- Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, Dijon Bourgogne University Hospital, Dijon, France
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
| | - A Denommé-Pichon
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
| | - M Chevarin
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
| | - O Patat
- Service de Génétique Médicale, CHU Toulouse, France, Toulouse, France
| | - M Willems
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Université de Montpellier, CHU de Montpellier, CLAD ASOOR Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier, Université de Montpellier, INSERM, Montpellier, France
| | - N Bourgon
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
| | - A Bruel
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
| | - M Aubert-Mucca
- Service de Génétique Médicale, CHU Toulouse, France, Toulouse, France
| | - M Galinier
- Fédération des Services de Cardiologie, CHU Toulouse-Rangueil, Toulouse, France
- UMR UT3 CNRS 5288 Evolutionary Medicine, Obesity and Heart Failure: Molecular and Clinical Investigations, INI-CRCT F-CRIN, GREAT Networks, Toulouse, France
- Université Paul Sabatier-Toulouse III, Faculté de Médecine, Toulouse, France
| | - R Itier
- UMR UT3 CNRS 5288 Evolutionary Medicine, Obesity and Heart Failure: Molecular and Clinical Investigations, INI-CRCT F-CRIN, GREAT Networks, Toulouse, France
| | - S Decramer
- Centre Hospitalier Universitaire de Toulouse, Service de Nephrologie Pediatrique, Hopital des Enfants, Centre De Reference des Maladies Rénales Rares du Sud-Ouest, Toulouse, France
| | - A Piton
- Unité de Génétique Moléculaire, Strasbourg University Hospital, Strasbourg, France
| | - B Gerard
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - C Billon
- Centre de Référence des Maladies Vasculaires Rares et Département de génétique, Hôpital Européen Georges Pompidou, Paris, France
| | - X Jeunemaitre
- Centre de Référence des Maladies Vasculaires Rares et Département de génétique, Hôpital Européen Georges Pompidou, Paris, France
| | - Y Duffourd
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
| | - P Callier
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
| | - C Thauvin
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital d'Enfants, Dijon, France
| | - C Philippe
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
| | - L Faivre
- Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, Dijon Bourgogne University Hospital, Dijon, France
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
| | - J Albuisson
- Centre de Référence des Maladies Vasculaires Rares et Département de génétique, Hôpital Européen Georges Pompidou, Paris, France
| | - A Vitobello
- UMR1231 GAD "Génétique des Anomalies du Développement", FHU-TRANSLAD, UFR des Sciences de Santé, INSERM-University of Burgundy, Dijon, France
- Unité Fonctionnelle d'Innovation diagnostique des maladies rares, Dijon Bourgogne University Hospital, Dijon, France
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Outram SM, Rego S, Norstad M, Ackerman S. The Need to Standardize the Reanalysis of Genomic Sequencing Results: Findings from Interviews with Underserved Families in Genomic Research. JOURNAL OF BIOETHICAL INQUIRY 2023:10.1007/s11673-023-10267-2. [PMID: 37624546 DOI: 10.1007/s11673-023-10267-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/06/2023] [Indexed: 08/26/2023]
Abstract
The reanalysis of genomic sequencing results has the potential to provide results that are of considerable medical and personal importance to recipients. Employing interviews with forty-seven predominantly medically underserved families and ethnographic observations we argue that there is pressing need to standardize the approach taken to reanalysis. Our findings highlight that study participants were unclear as to the likelihood of reanalysis happening, the process of initiating reanalysis, and whether they would receive revised results. Their reflections mirror the lack a specific focus upon reanalysis within consent and results sessions as observed in clinical settings. Mechanisms need to be put into place that standardize the approach to reanalysis in research and in clinical contexts. This would enable clinicians and genetic counsellors to communicate clearly with research participants with respect to potential for reanalysis of results and the process of reanalysis. We argue that that the role of reanalysis is too important to be referred to in an ad-hoc manner. Furthermore, the ad-hoc nature of the current process may increase health inequities given the likelihood that only those families who have the means to press for reanalysis are likely to receive it.
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Affiliation(s)
- Simon M Outram
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA.
| | - Shannon Rego
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Matthew Norstad
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA
| | - Sara Ackerman
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA
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18
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Barili V, Ambrosini E, Uliana V, Bellini M, Vitetta G, Martorana D, Cannizzaro IR, Taiani A, De Sensi E, Caggiati P, Hilton S, Banka S, Percesepe A. Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond. Genes (Basel) 2023; 14:1241. [PMID: 37372421 DOI: 10.3390/genes14061241] [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: 04/30/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.
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Affiliation(s)
- Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Melissa Bellini
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy
| | - Giulia Vitetta
- Medical Genetics, University of Bologna, 40138 Bologna, Italy
| | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Ilenia Rita Cannizzaro
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Antonietta Taiani
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Sarah Hilton
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Antonio Percesepe
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
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19
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Gerik-Celebi HB, Aydin H, Bolat H, Unsel-Bolat G. Clinical and Genetic Characteristics of Patients with Unexplained Intellectual Disability/Developmental Delay without Epilepsy. Mol Syndromol 2023; 14:208-218. [PMID: 37323201 PMCID: PMC10267527 DOI: 10.1159/000529018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/05/2023] [Indexed: 10/21/2023] Open
Abstract
Introduction Global developmental delay (DD), intellectual disability (ID), and autism spectrum disorder (ASD) are mainly evaluated under the neurodevelopmental disorder framework. In this study, we aimed to determine the genetic diagnosis yield using step-by-step genetic analysis in 38 patients with unexplained ID/DD and/or ASD. Methods In 38 cases (27 male, 11 female) with unexplained ID/DD and/or ASD, chromosomal microarray (CMA) analysis, clinical exome sequencing (CES), and whole-exome sequencing (WES) analysis were applied, respectively. Results We found a diagnostic rate of only CMA analysis as 21% (8/38) presenting 8 pathogenic and likely pathogenic CNVs. The rate of patients diagnosed with CES/WES methods was 32.2% (10/31). When all pathogenic and likely pathogenic variants were evaluated, the diagnosis rate was 44.7% (17/38). A dual diagnosis was obtained in a case with 16p11.2 microduplication and de novo SNV. We identified eight novel variants: TUBA1A (c.787C>G), TMEM63A (c.334-2A>G), YY1AP1 (c.2051_2052del), ABCA13 (c.12064C>T), ABCA13 (c.13187G>A), USP9X (c.1189T>C), ANKRD17 (c.328_330dup), and GRIA4 (c.17G>A). Conclusion We present diagnostic rates of a complementary approach to genetic analysis (CMA, CES, and WES). The combined use of genetic analysis methods in unexplained ID/DD and/or ASD cases has contributed significantly to diagnosis rates. Also, we present detailed clinical characteristics to improve genotype-phenotype correlation in the literature for rare and novel variants.
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Affiliation(s)
| | - Hilal Aydin
- Department of Pediatrics, Division of Child Neurology, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Gul Unsel-Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
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20
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Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Tran Mau-Them F, Wentzensen IM, Au KS, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LW, Brasch-Andersen C, Maxel Juul T, El It F, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MD, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet 2023; 110:790-808. [PMID: 37071997 PMCID: PMC10183470 DOI: 10.1016/j.ajhg.2023.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.
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Affiliation(s)
- Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Aurore Garde
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Thierry Gautier
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Emma van Reempts
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | | | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kate Richardson
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, USA; Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, CHU Montpellier, Montpellier, France
| | - David Geneviève
- Montpellier University, Inserm U1183, Montpellier, France; Reference center for rare disease developmental anomaly malformative syndrome, Department of Medical Genetics, Montpellier Hospital, Montpellier, France
| | | | | | | | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark; Human Genetics, Department of Clinical Research, Health Faculty, University of Southern Denmark, 5000 Odense, Denmark
| | - Trine Maxel Juul
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Fatima El It
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Laboratoire de Génétique Chromosomique et Moléculaire, Pôle de Biologie, CHU de Dijon, Dijon, France
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | | | - Sophie Naudion
- Medical Genetics Department, CHU Bordeaux, Bordeaux, France
| | | | | | - Aurelien Trimouille
- INSERM U1211, Laboratoire MRGM, Bordeaux University, Bordeaux, France; Pathology Department, CHU Bordeaux, Bordeaux, France
| | - Martine Doco Fenzy
- Service de génétique, CHU de Reims, Reims, France; Service de génétique médicale, CHU de Nantes, Nantes, France; L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU de Nantes, Nantes, France
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kimberly Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hagith Yonath
- Internal Medicine A, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Montanari
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Sartor
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Marco Seri
- UO Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Claude Besmond
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Karine Poirier
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Laurence Hubert
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Arnold Munnich
- Université Paris Cité, Imagine Institute, INSERM UMR1163, Paris 75015, France
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France; Centre de Référence Maladies Rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs", Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jérôme Govin
- University Grenoble Alpes, Inserm U1209, CNRS UMR 5309, Institute for Advanced Biosciences (IAB), 38000 Grenoble, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France.
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21
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Denommé-Pichon AS, Matalonga L, de Boer E, Jackson A, Benetti E, Banka S, Bruel AL, Ciolfi A, Clayton-Smith J, Dallapiccola B, Duffourd Y, Ellwanger K, Fallerini C, Gilissen C, Graessner H, Haack TB, Havlovicova M, Hoischen A, Jean-Marçais N, Kleefstra T, López-Martín E, Macek M, Mencarelli MA, Moutton S, Pfundt R, Pizzi S, Posada M, Radio FC, Renieri A, Rooryck C, Ryba L, Safraou H, Schwarz M, Tartaglia M, Thauvin-Robinet C, Thevenon J, Tran Mau-Them F, Trimouille A, Votypka P, de Vries BBA, Willemsen MH, Zurek B, Verloes A, Philippe C, Vitobello A, Vissers LELM, Faivre L. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing. Genet Med 2023; 25:100018. [PMID: 36681873 DOI: 10.1016/j.gim.2023.100018] [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: 03/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. METHODS Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. RESULTS We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). CONCLUSION The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock.
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Affiliation(s)
- Anne-Sophie Denommé-Pichon
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France.
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation," The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Elisa Benetti
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Ange-Line Bruel
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Yannis Duffourd
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Kornelia Ellwanger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Chiara Fallerini
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy
| | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radbound University, Nijmegen, The Netherlands
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Alexander Hoischen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radbound University, Nijmegen, The Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Nolwenn Jean-Marçais
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
| | - Estrella López-Martín
- Institute of Rare Diseases Research, Spanish Undiagnosed Rare Diseases Cases Program (SpainUDP) & Undiagnosed Diseases Network International, Instituto de Salud Carlos III, Madrid, Spain
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Sébastien Moutton
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Manuel Posada
- Institute of Rare Diseases Research, Spanish Undiagnosed Rare Diseases Cases Program (SpainUDP) & Undiagnosed Diseases Network International, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Alessandra Renieri
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy; Medical Genetics, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Caroline Rooryck
- MRGM INSERM U1211, University of Bordeaux, Medical Genetics Department, Bordeaux University Hospital, Bordeaux, France
| | - Lukas Ryba
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Hana Safraou
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Martin Schwarz
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Christel Thauvin-Robinet
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Julien Thevenon
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Frédéric Tran Mau-Them
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Aurélien Trimouille
- Molecular Genetics Laboratory, Medical Genetics Department, Bordeaux University Hospital - Hôpital Pellegrin, Bordeaux, France
| | - Pavel Votypka
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Alain Verloes
- Department of Genetics, Assistance Publique-Hôpitaux de Paris - Université de Paris, Paris, France; INSERM UMR 1141 "NeuroDiderot," Hôpital Robert Debré, Paris, France
| | - Christophe Philippe
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Laurence Faivre
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France.
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22
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Oleari R, Lettieri A, Manzini S, Paganoni A, André V, Grazioli P, Busnelli M, Duminuco P, Vitobello A, Philippe C, Bizaoui V, Storr HL, Amoruso F, Memi F, Vezzoli V, Massa V, Scheiffele P, Howard SR, Cariboni A. Autism-linked NLGN3 is a key regulator of gonadotropin-releasing hormone deficiency. Dis Model Mech 2023; 16:dmm049996. [PMID: 36810932 PMCID: PMC10110398 DOI: 10.1242/dmm.049996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
Gonadotropin-releasing hormone (GnRH) deficiency (GD) is a disorder characterized by absent or delayed puberty, with largely unknown genetic causes. The purpose of this study was to obtain and exploit gene expression profiles of GnRH neurons during development to unveil novel biological mechanisms and genetic determinants underlying GD. Here, we combined bioinformatic analyses of immortalized and primary embryonic GnRH neuron transcriptomes with exome sequencing from GD patients to identify candidate genes implicated in the pathogenesis of GD. Among differentially expressed and filtered transcripts, we found loss-of-function (LoF) variants of the autism-linked neuroligin 3 (NLGN3) gene in two unrelated patients co-presenting with GD and neurodevelopmental traits. We demonstrated that NLGN3 is upregulated in maturing GnRH neurons and that NLGN3 wild-type, but not mutant, protein promotes neuritogenesis when overexpressed in developing GnRH cells. Our data represent proof of principle that this complementary approach can identify new candidate GD genes and demonstrate that LoF NLGN3 variants can contribute to GD. This novel genotype-phenotype correlation implies common genetic mechanisms underlying neurodevelopmental disorders, such as GD and autistic spectrum disorder.
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Affiliation(s)
- Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Antonella Lettieri
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan, Milan 20142, Italy
- Department of Health Sciences, University of Milan, Milan 20142, Italy
| | - Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Alyssa Paganoni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Valentina André
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Paolo Grazioli
- Department of Health Sciences, University of Milan, Milan 20142, Italy
| | - Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Paolo Duminuco
- Laboratory of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Cusano Milanino 20095, Italy
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire (FHU) TRANSLAD, CHU Dijon Bourgogne, Dijon 21079, France
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon 21070, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire (FHU) TRANSLAD, CHU Dijon Bourgogne, Dijon 21079, France
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon 21070, France
| | - Varoona Bizaoui
- Genetics and Neurodevelopment, Centre Hospitalier de l'Estran, Pontorson 50170, France
| | - Helen L. Storr
- Centre for Endocrinology William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Royal London Children's Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Federica Amoruso
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Fani Memi
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Valeria Vezzoli
- Laboratory of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Cusano Milanino 20095, Italy
| | - Valentina Massa
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan, Milan 20142, Italy
- Department of Health Sciences, University of Milan, Milan 20142, Italy
| | | | - Sasha R. Howard
- Centre for Endocrinology William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Royal London Children's Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
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23
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Akbari M, Ebrahimi Tapeh Z, Zaersabet M, Rahimi H, Ganji M. Novel pyrroline-5-carboxylate reductase 2 (PYCR2) mutation in an Iranian patient with hypomyelinating leukodystrophy: findings of molecular and in silico investigations. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-023-00393-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Background
Hypomyelinating leukodystrophy (HLD) is a specific group of leukodystrophies and is characterized by progressive postnatal growth delay that represents a type of clinically overlapping but genetically heterogeneous diseases with autosomal recessive inheritance. Loss-of-function mutations in PYCR2 are one of the main causes of HLD type 10 (HLD10), which is identified by cerebral hypomyelination, inadequate growth, brain atrophy, and movement abnormality. This study aimed to investigate the molecular etiology of HLD10 disorder in an Iranian patient from a consanguineous marriage family.
Results
The DNA samples were extracted from the patient, a 9-year-old girl, and her parents. Whole-exome sequencing was conducted for these samples and the results were eventually confirmed and segregated via Sanger sequencing. Our findings demonstrated a novel homozygous frameshift mutation in PYCR2 gene, c.135dup (NM_013328.4). The heterozygous state of this variant was confirmed in parents. Additionally, this mutation was predicted to exhibit damaging effects through protein sequence alteration.
Conclusions
Such findings are of importance for understanding the underlying pathogenicity mechanisms and for improving genetic counseling knowledge of HLD patients for families.
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24
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Tran Mau-Them F, Overs A, Bruel AL, Duquet R, Thareau M, Denommé-Pichon AS, Vitobello A, Sorlin A, Safraou H, Nambot S, Delanne J, Moutton S, Racine C, Engel C, De Giraud d’Agay M, Lehalle D, Goldenberg A, Willems M, Coubes C, Genevieve D, Verloes A, Capri Y, Perrin L, Jacquemont ML, Lambert L, Lacaze E, Thevenon J, Hana N, Van-Gils J, Dubucs C, Bizaoui V, Gerard-Blanluet M, Lespinasse J, Mercier S, Guerrot AM, Maystadt I, Tisserant E, Faivre L, Philippe C, Duffourd Y, Thauvin-Robinet C. Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis. Front Genet 2023; 14:1122985. [PMID: 37152996 PMCID: PMC10157399 DOI: 10.3389/fgene.2023.1122985] [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: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. Patients and methods: We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. Results: After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Alexis Overs
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Romain Duquet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Mylene Thareau
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Arthur Sorlin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Camille Engel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | | | - Daphne Lehalle
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Marjolaine Willems
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Christine Coubes
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - David Genevieve
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Alain Verloes
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Department of Medical Genetics, AP-HPNord- Université de Paris, Hôpital Robert Debré, Paris, France
- INSERM UMR 1141, Paris, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Laurence Perrin
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Elodie Lacaze
- Unité de Génétique Médicale, Groupe Hospitalier du Havre, Le Havre, France
| | - Julien Thevenon
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nadine Hana
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
- INSERM U1148, Laboratory for Vascular Translational Science, Université Paris de Paris, Hôpital Bichat, Paris, France
| | - Julien Van-Gils
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Charlotte Dubucs
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Varoona Bizaoui
- Service de Génétique, Centre Hospitalier Universitaire Caen Normandie, Caen, France
| | | | | | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Rouen, France
- Inserm U1245, FHU G4 Génomique, Rouen, France
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Emilie Tisserant
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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25
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Mazel B, Mallet D, Roucher-Boulez F, Signor CB, Bournez M, Darmency V, Bourgeois V, Poe C, El Khabbaz F, Vitobello A, Philippe C, Duffourd Y, Thauvin-Robinet C, Faivre L, Nambot S. Epileptic encephalopathy as a new feature of the sudden infant death with dysgenesis of the testes syndrome caused by TSPYL1 variants. Am J Med Genet A 2022; 188:3540-3545. [PMID: 36082874 DOI: 10.1002/ajmg.a.62966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Sudden infant death with dysgenesis of the testes syndrome (SIDDT) is a rare autosomal recessive disorder associating developmental sex disorder (DSD) in patients with 46,XY karyotype and visceroautonomic dysfunction responsible for sudden infant death. First described in 2004, very few patients have since been reported. We describe here a new patient with SIDDT and epileptic encephalopathy (EE). We provide the phenotypic description and genetic results of a boy carrying biallelic TSPYL1 deleterious variants. We also reviewed the data of the 26 previously described patients with SIDDT. Our patient presented gonadal dysgenesis, cardio-respiratory dysfunction, and repeated seizures, leading in 1 month to severe intractable EE. He died at age 10 months of cardiorespiratory arrest. Four other reported patients from two families presented with progressive epilepsy, including one with severe EE. No similar phenotype was described in the 22 other patients and the recurrent variant p.Val242Glufs*52 appears to be more frequently associated with seizures. To note, our patient is the first case with compound heterozygous TSPYL1 variants. These findings expand the phenotypic spectrum of SIDDT by reporting progressive epilepsy and severe EE as a possible outcome. This information may help in managing patients with SIDDT.
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Affiliation(s)
- Benoit Mazel
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHUTRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France.,Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Delphine Mallet
- Hospices Civils de Lyon, Groupement Hospitalier Est, Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes et Mucoviscidose, Bron, France.,Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
| | - Florence Roucher-Boulez
- Hospices Civils de Lyon, Groupement Hospitalier Est, Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes et Mucoviscidose, Bron, France.,Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France.,Université de Lyon, Université Claude-Bernard Lyon 1, Lyon, France
| | - Candace Ben Signor
- Department of Endocrino-Pediatry, Dijon University Hospital, Dijon, France
| | - Marie Bournez
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France
| | - Véronique Darmency
- Service de Neurophysiologie Clinique, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Valentin Bourgeois
- Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Charlotte Poe
- Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Fares El Khabbaz
- Service de Soins Intensifs Néonataux, Centre Hospitalier d'Auxerre, Auxerre, France
| | - Antonio Vitobello
- Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Christophe Philippe
- Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Yannis Duffourd
- Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHUTRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHUTRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHUTRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France.,Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
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26
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Al-Ali S, Jeffries L, Faustino EVS, Ji W, Mis E, Konstantino M, Zerillo C, Jiang YH, Spencer-Manzon M, Bale A, Zhang H, McGlynn J, McGrath JM, Tremblay T, Brodsky NN, Lucas CL, Pierce R, Deniz E, Khokha MK, Lakhani SA. A retrospective cohort analysis of the Yale pediatric genomics discovery program. Am J Med Genet A 2022; 188:2869-2878. [PMID: 35899841 PMCID: PMC9474639 DOI: 10.1002/ajmg.a.62918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/29/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
The Pediatric Genomics Discovery Program (PGDP) at Yale uses next-generation sequencing (NGS) and translational research to evaluate complex patients with a wide range of phenotypes suspected to have rare genetic diseases. We conducted a retrospective cohort analysis of 356 PGDP probands evaluated between June 2015 and July 2020, querying our database for participant demographics, clinical characteristics, NGS results, and diagnostic and research findings. The three most common phenotypes among the entire studied cohort (n = 356) were immune system abnormalities (n = 105, 29%), syndromic or multisystem disease (n = 103, 29%), and cardiovascular system abnormalities (n = 62, 17%). Of 216 patients with final classifications, 77 (36%) received new diagnoses and 139 (64%) were undiagnosed; the remaining 140 patients were still actively being investigated. Monogenetic diagnoses were found in 67 (89%); the largest group had variants in known disease genes but with new contributions such as novel variants (n = 31, 40%) or expanded phenotypes (n = 14, 18%). Finally, five PGDP diagnoses (8%) were suggestive of novel gene-to-phenotype relationships. A broad range of patients can benefit from single subject studies combining NGS and functional molecular analyses. All pediatric providers should consider further genetics evaluations for patients lacking precise molecular diagnoses.
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Affiliation(s)
- Samir Al-Ali
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - E. Vincent S. Faustino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cynthia Zerillo
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yong-hui Jiang
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Michele Spencer-Manzon
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Julie McGlynn
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - James M. McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | | | - Nina N. Brodsky
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carrie L. Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard Pierce
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Saquib A. Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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27
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ADGRL1 haploinsufficiency causes a variable spectrum of neurodevelopmental disorders in humans and alters synaptic activity and behavior in a mouse model. Am J Hum Genet 2022; 109:1436-1457. [PMID: 35907405 PMCID: PMC9388395 DOI: 10.1016/j.ajhg.2022.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/22/2022] [Indexed: 02/06/2023] Open
Abstract
ADGRL1 (latrophilin 1), a well-characterized adhesion G protein-coupled receptor, has been implicated in synaptic development, maturation, and activity. However, the role of ADGRL1 in human disease has been elusive. Here, we describe ten individuals with variable neurodevelopmental features including developmental delay, intellectual disability, attention deficit hyperactivity and autism spectrum disorders, and epilepsy, all heterozygous for variants in ADGRL1. In vitro, human ADGRL1 variants expressed in neuroblastoma cells showed faulty ligand-induced regulation of intracellular Ca2+ influx, consistent with haploinsufficiency. In vivo, Adgrl1 was knocked out in mice and studied on two genetic backgrounds. On a non-permissive background, mice carrying a heterozygous Adgrl1 null allele exhibited neurological and developmental abnormalities, while homozygous mice were non-viable. On a permissive background, knockout animals were also born at sub-Mendelian ratios, but many Adgrl1 null mice survived gestation and reached adulthood. Adgrl1-/- mice demonstrated stereotypic behaviors, sexual dysfunction, bimodal extremes of locomotion, augmented startle reflex, and attenuated pre-pulse inhibition, which responded to risperidone. Ex vivo synaptic preparations displayed increased spontaneous exocytosis of dopamine, acetylcholine, and glutamate, but Adgrl1-/- neurons formed synapses in vitro poorly. Overall, our findings demonstrate that ADGRL1 haploinsufficiency leads to consistent developmental, neurological, and behavioral abnormalities in mice and humans.
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28
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Baker EK, Ulm EA, Belonis A, Brightman DS, Hallinan BE, Leslie ND, Miethke AG, Vawter-Lee M, Wu Y, Pena LDM. Clinically available testing options resulting in diagnosis in post-exome clinic at one medical center. Front Genet 2022; 13:887698. [PMID: 35937981 PMCID: PMC9355124 DOI: 10.3389/fgene.2022.887698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/28/2022] [Indexed: 11/27/2022] Open
Abstract
Exome sequencing (ES) became clinically available in 2011 and promised an agnostic, unbiased next-generation sequencing (NGS) platform for patients with symptoms believed to have a genetic etiology. The diagnostic yield of ES has been estimated to be between 25–40% and may be higher in specific clinical scenarios. Those who remain undiagnosed may have no molecular findings of interest on ES, variants of uncertain significance in genes that are linked to human disease, or variants of uncertain significance in candidate genes that are not definitively tied to human disease. Recent evidence suggests that a post-exome evaluation consisting of clinical re-phenotyping, functional studies of candidate variants in known genes, and variant reevaluation can lead to a diagnosis in 5–15% of additional cases. In this brief research study, we present our experience on post-exome evaluations in a cohort of patients who are believed to have a genetic etiology for their symptoms. We have reached a full or partial diagnosis in approximately 18% (6/33) of cases that have completed evaluations to date. We accomplished this by utilizing NGS-based methods that are available on a clinical basis. A sample of these cases highlights the utility of ES reanalysis with updated phenotyping allowing for the discovery of new genes, re-adjudication of known variants, incorporating updated phenotypic information, utilizing functional testing such as targeted RNA sequencing, and deploying other NGS-based testing methods such as gene panels and genome sequencing to reach a diagnosis.
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Affiliation(s)
- Elizabeth K. Baker
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Elizabeth A. Ulm
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Alyce Belonis
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Diana S. Brightman
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Barbara E. Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Nancy D. Leslie
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alexander G. Miethke
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Marissa Vawter-Lee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Yaning Wu
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Loren D. M. Pena
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Loren D. M. Pena,
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29
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Lesca G, Baumgartner T, Monin P, De Dominicis A, Kunz WS, Specchio N. Genetic causes of rare and common epilepsies: What should the epileptologist know? Eur J Med Genet 2022; 65:104570. [PMID: 35850153 DOI: 10.1016/j.ejmg.2022.104570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
In past decades, the identification of genes involved in epileptic disorders has grown exponentially. The pace of gene identification in epileptic disorders began to accelerate in the late 2000s, driven by new technologies such as molecular cytogenetics and next-generation sequencing (NGS). These technologies have also been applied to genetic diagnostics, with different configurations, such as gene panels, whole-exome sequencing and whole-genome sequencing. The clinician must be aware that any technology has its limitations and complementary techniques must still be used to establish a diagnosis for specific diseases. In addition, increasing the amount of genetic information available in a larger patient sample also increases the need for rigorous interpretation steps, when taking into account the clinical, electroclinical, and when available, functional data. Local, multidisciplinary discussions have proven valuable in difficult diagnostic situations, especially in cases where precision medicine is being considered. They also serve to improve genetic counseling in complex situations. In this article, we will briefly review the genetic basis of rare and common epilepsies, the current strategies used for molecular diagnosis, including their limitations, and some pitfalls for data interpretation, in the context of etiological diagnosis and genetic counseling.
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Affiliation(s)
- Gaetan Lesca
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France.
| | - Tobias Baumgartner
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Pauline Monin
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France
| | - Angela De Dominicis
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Wolfram S Kunz
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Full Member of European Reference Network EpiCARE, Rome, Italy
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30
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Yauy K, Lecoquierre F, Baert-Desurmont S, Trost D, Boughalem A, Luscan A, Costa JM, Geromel V, Raymond L, Richard P, Coutant S, Broutin M, Lanos R, Fort Q, Cackowski S, Testard Q, Diallo A, Soirat N, Holder JM, Duforet-Frebourg N, Bouge AL, Beaumeunier S, Bertrand D, Audoux J, Genevieve D, Mesnard L, Nicolas G, Thevenon J, Philippe N. Genome Alert!: A standardized procedure for genomic variant reinterpretation and automated gene-phenotype reassessment in clinical routine. Genet Med 2022; 24:1316-1327. [PMID: 35311657 DOI: 10.1016/j.gim.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Retrospective interpretation of sequenced data in light of the current literature is a major concern of the field. Such reinterpretation is manual and both human resources and variable operating procedures are the main bottlenecks. METHODS Genome Alert! method automatically reports changes with potential clinical significance in variant classification between releases of the ClinVar database. Using ClinVar submissions across time, this method assigns validity category to gene-disease associations. RESULTS Between July 2017 and December 2019, the retrospective analysis of ClinVar submissions revealed a monthly median of 1247 changes in variant classification with potential clinical significance and 23 new gene-disease associations. Re-examination of 4929 targeted sequencing files highlighted 45 changes in variant classification, and of these classifications, 89% were expert validated, leading to 4 additional diagnoses. Genome Alert! gene-disease association catalog provided 75 high-confidence associations not available in the OMIM morbid list; of which, 20% became available in OMIM morbid list For more than 356 negative exome sequencing data that were reannotated for variants in these 75 genes, this elective approach led to a new diagnosis. CONCLUSION Genome Alert! (https://genomealert.univ-grenoble-alpes.fr/) enables systematic and reproducible reinterpretation of acquired sequencing data in a clinical routine with limited human resource effect.
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Affiliation(s)
- Kevin Yauy
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; SeqOne Genomics, Montpellier, France.
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | | | | | | | - Pascale Richard
- Unité Fonctionnelle de Cardiogénétique et Myogénétique, Centre de Génétique, Hôpitaux Universitaire Pitié Salpêtrière-Charles Foix, Paris, France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | - Stenzel Cackowski
- Grenoble Institut Neurosciences, GIN, Inserm U1216, Université de Grenoble Alpes, Grenoble, France
| | - Quentin Testard
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; Laboratoire Eurofins Biomnis, Lyon, France
| | | | | | | | | | | | | | | | | | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu, Hôpital Tenon, Assistance Publique des Hôpitaux de Paris, Paris, France; UMR_S1155, INSERM, Sorbonne Université, Paris, France
| | - Gael Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Julien Thevenon
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [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: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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Dai P, Honda A, Ewans L, McGaughran J, Burnett L, Law M, Phan TG. Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis. Genet Med 2022; 24:1618-1629. [PMID: 35550369 DOI: 10.1016/j.gim.2022.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The study aimed to determine the diagnostic yield, optimal timing, and methodology of next generation sequencing data reanalysis in suspected Mendelian disorders. METHODS We conducted a systematic review and meta-analysis of studies that conducted data reanalysis in patients with suspected Mendelian disorders. Random effects model was used to pool the estimated outcome with subgroup analysis stratified by timing, sequencing methodology, sample size, segregation, use of research validation, and artificial intelligence (AI) variant curation tools. RESULTS A search of PubMed, Embase, Scopus, and Web of Science between 2007 and 2021 yielded 9327 articles, of which 29 were selected. Significant heterogeneity was noted between studies. Reanalysis had an overall diagnostic yield of 0.10 (95% CI = 0.06-0.13). Literature updates accounted for most new diagnoses. Diagnostic yield was higher after 24 months, although this was not statistically significant. Increased diagnoses were obtained with research validation and data sharing. AI-based tools did not adversely affect reanalysis diagnostic rate. CONCLUSION Next generation sequencing data reanalysis can improve diagnostic yield. Owing to the heterogeneity of the studies, the optimal time to reanalysis and the impact of AI-based tools could not be determined with confidence. We propose standardized guidelines for future studies to reduce heterogeneity and improve the quality of the conclusions.
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Affiliation(s)
- Pei Dai
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andrew Honda
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Clinical Genetics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Leslie Burnett
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Genetic Medicine Program, Northern Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew Law
- Biostatistics and Databases Program, The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tri Giang Phan
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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33
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Wang Q, Tang X, Yang K, Huo X, Zhang H, Ding K, Liao S. Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders. Mol Genet Genomic Med 2022; 10:e1918. [PMID: 35266334 PMCID: PMC9034680 DOI: 10.1002/mgg3.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Background Neurodevelopmental disorders, a group of early‐onset neurological disorders with significant clinical and genetic heterogeneity, remain a diagnostic challenge for clinical genetic evaluation. Therefore, we assessed the diagnostic yield by combining standard phenotypes and whole‐exome sequencing in families with these disorders that were “not yet diagnosed” by the traditional testing methods. Methods Using a standardized vocabulary of phenotypic abnormalities from human phenotype ontology (HPO), we performed deep phenotyping for 45 “not yet diagnosed” pedigrees to characterize multiple clinical features extracted from Chinese electronic medical records (EMRs). By matching HPO terms with known human diseases and phenotypes from model organisms, together with whole‐exome sequencing data, we prioritized candidate mutations/genes. We made probable genetic diagnoses for the families. Results We obtained a diagnostic yield of 29% (13 out of 45) with probably genetic diagnosis, of which compound heterozygosity and de novo mutations accounted for 77% (10/13) of the diagnosis. Of note, these pedigrees are accompanied by a more significant number of non‐neurological features. Conclusions Deep phenotyping and whole‐exome sequencing improve the etiological evaluation for neurodevelopmental disorders in the clinical setting.
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Affiliation(s)
- Qingqing Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xia Tang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Ke Yang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xiaodong Huo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Hui Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
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Bullich G, Matalonga L, Pujadas M, Papakonstantinou A, Piscia D, Tonda R, Artuch R, Gallano P, Garrabou G, González JR, Grinberg D, Guitart M, Laurie S, Lázaro C, Luengo C, Martí R, Milà M, Ovelleiro D, Parra G, Pujol A, Tizzano E, Macaya A, Palau F, Ribes A, Pérez-Jurado LA, Beltran S. Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases. J Mol Diagn 2022; 24:529-542. [PMID: 35569879 DOI: 10.1016/j.jmoldx.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/26/2022] Open
Abstract
Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).
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Affiliation(s)
- Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Pujadas
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anastasios Papakonstantinou
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Davide Piscia
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Tonda
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Pia Gallano
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Genetics Department, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Glòria Garrabou
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Internal Medicine Department, Hospital Clinic of Barcelona, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Grinberg
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Institute of Biomedicine of the University of Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Míriam Guitart
- Genetics Laboratory, Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Steven Laurie
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Conxi Lázaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Catalan Institute of Oncology, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Luengo
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ramon Martí
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Milà
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Institut d'Investigació Biomèdica August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - David Ovelleiro
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Genís Parra
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aurora Pujol
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)-Hospital Duran i Reynals, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eduardo Tizzano
- Department of Clinical and Molecular Genetics, Medicine Genetics Group Vall d'Hebron Institut de Recerca (VHIR), European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Universitat Autònoma de Barcelona, Hospital Vall d´Hebron, Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Palau
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetic and Molecular Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Clinic Institute of Medicine and Dermatology, Hospital Clínic de Barcelona and Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Antònia Ribes
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Secció d'Errors Congènits del Metabolisme-Institute of Clinical Biochemistry (IBC), Servei de Bioquímica i Genètìca Molecular, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute and The University of Adelaide, Adelaide, South Australia, Australia
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Sloboda N, Lambert L, Ciorna V, Bruel AL, Tran Mau-Them F, Gomola V, Lemelle JL, Klein O, Camoin-Schweitzer MC, Magnavacca M, Legagneur C, Ezsto ML, Bonnet C, Philippe C, Leheup B. Atypical phenotype of a patient with Bardet-Biedl syndrome type 4. Mol Genet Genomic Med 2022; 10:e1869. [PMID: 35318824 PMCID: PMC9034675 DOI: 10.1002/mgg3.1869] [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: 06/06/2020] [Revised: 06/16/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Background Bardet–Biedl syndrome (BBS) is a multisystemic disorder characterized by rod–cone dystrophy, truncal obesity, postaxial polydactyly, cognitive impairment, male hypogonadotropic hypogonadism, complex female genitourinary malformations, and renal abnormalities. There is a large clinical and also genetic heterogeneity in BBS. Here, we report a patient with polydactyly, hyperechogenic kidneys increased in size with normal corticomedullary differentiation, anal imperforation, and malformation of genitals with presence of a genital tubercle with ventral urethral meatus associated with two unfused lateral genital swelling and absent urethral folds, in the context of 46, XY karyotype. Methods Karyotype and solo exome sequencing were performed to look for a genetic etiology for the features described in our patient. Results We identified a homozygous in‐frame deletion of exons 4 to 6 in the BBS4 gene (NM‐033028 (BBS4‐i001): c.[(157‐?)_(405 +?)del] p.(Ala53‐Trp135del), which is classified as pathogenic variant. This analysis allowed the molecular diagnosis of BBS type 4 in this patient. Conclusion Complex genital malformations are only reported in female BBS6 patients yet, and genital abnormalities and anal imperforation are not reported in male BBS4 patients to date. We discuss the possible hypotheses for this phenotype, including the phenotypic overlap between ciliopathies.
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Affiliation(s)
| | | | | | - Ange-Line Bruel
- Laboratoire de génétique, Innovation en diagnostic génomique des maladies rares UF6254, Plate-forme de Biologie Hospitalo-Universitaire, CHU Dijon, Dijon, France
| | - Frédéric Tran Mau-Them
- Laboratoire de génétique, Innovation en diagnostic génomique des maladies rares UF6254, Plate-forme de Biologie Hospitalo-Universitaire, CHU Dijon, Dijon, France.,INSERM U1231, LNC UMR1231 GAD, Université de Bourgogne, Dijon, France
| | - Vladimir Gomola
- Service de Chirurgie Viscérale Infantile, CHRU Nancy, Nancy, France
| | | | - Olivier Klein
- Service de Neurochirurgie Pédiatrique, CHRU Nancy, Nancy, France
| | | | - Marie Magnavacca
- Service de néphrologie pédiatrique, dialyse, transplantation rénale, CHRU Nancy, Nancy, France
| | - Carole Legagneur
- Unité d'Endocrinologie Pédiatrique et Diabétologie, CHRU Nancy, Nancy, France
| | | | | | - Christophe Philippe
- Laboratoire de génétique, Innovation en diagnostic génomique des maladies rares UF6254, Plate-forme de Biologie Hospitalo-Universitaire, CHU Dijon, Dijon, France.,INSERM U1231, LNC UMR1231 GAD, Université de Bourgogne, Dijon, France
| | - Bruno Leheup
- Service de Génétique Clinique, CHRU Nancy, Nancy, France
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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The Genetic Diagnosis of Ultrarare DEEs: An Ongoing Challenge. Genes (Basel) 2022; 13:genes13030500. [PMID: 35328054 PMCID: PMC8953579 DOI: 10.3390/genes13030500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Epileptic encephalopathies (EEs) and developmental and epileptic encephalopathies (DEEs) are a group of severe early-onset neurodevelopmental disorders (NDDs). In recent years, next-generation equencing (NGS) technologies enabled the discovery of numerous genes involved in these conditions. However, more than 50% of patients remained undiagnosed. A major obstacle lies in the high degree of genetic heterogeneity and the wide phenotypic variability that has characterized these disorders. Interpreting a large amount of NGS data is also a crucial challenge. This study describes a dynamic diagnostic procedure used to investigate 17 patients with DEE or EE with previous negative or inconclusive genetic testing by whole-exome sequencing (WES), leading to a definite diagnosis in about 59% of participants. Biallelic mutations caused most of the diagnosed cases (50%), and a pathogenic somatic mutation resulted in 10% of the subjects. The high diagnostic yield reached highlights the relevance of the scientific approach, the importance of the reverse phenotyping strategy, and the involvement of a dedicated multidisciplinary team. The study emphasizes the role of recessive and somatic variants, new genetic mechanisms, and the complexity of genotype–phenotype associations. In older patients, WES results could end invasive diagnostic procedures and allow a more accurate transition. Finally, an early pursued diagnosis is essential for comprehensive care of patients, precision approach, knowledge of prognosis, patient and family planning, and quality of life.
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Tisserant E, Vitobello A, Callegarin D, Verdez S, Bruel AL, Aho Glele LS, Sorlin A, Viora-Dupont E, Konyukh M, Marle N, Nambot S, Moutton S, Racine C, Garde A, Delanne J, Tran-Mau-Them F, Philippe C, Kuentz P, Poulleau M, Payet M, Poe C, Thauvin-Robinet C, Faivre L, Mosca-Boidron AL, Thevenon J, Duffourd Y, Callier P. Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array-CGH. Ann Hum Genet 2022; 86:171-180. [PMID: 35141892 DOI: 10.1111/ahg.12459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/14/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
It has been estimated that Copy Number Variants (CNVs) account for 10%-20% of patients affected by Developmental Disorder (DD)/Intellectual Disability (ID). Although array comparative genomic hybridization (array-CGH) represents the gold-standard for the detection of genomic imbalances, common Agilent array-CGH 4 × 180 kb arrays fail to detect CNVs smaller than 30 kb. Whole Exome sequencing (WES) is becoming the reference application for the detection of gene variants and makes it possible also to infer genomic imbalances at single exon resolution. However, the contribution of small CNVs in DD/ID is still underinvestigated. We made use of the eXome Hidden Markov Model (XHMM) software, a tool utilized by the ExAC consortium, to detect CNVs from whole exome sequencing data, in a cohort of 200 unsolved DD/DI patients after array-CGH and WES-based single nucleotide/indel variant analyses. In five out of 200 patients (2.5%), we identified pathogenic CNV(s) smaller than 30 kb, ranging from one to six exons. They included two heterozygous deletions in TCF4 and STXBP1 and three homozygous deletions in PPT1, CLCN2, and PIGN. After reverse phenotyping, all variants were reported as causative. This study shows the interest in applying sequencing-based CNV detection, from available WES data, to reduce the diagnostic odyssey of additional patients unsolved DD/DI patients and compare the CNV-detection yield of Agilent array-CGH 4 × 180kb versus whole exome sequencing.
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Affiliation(s)
- Emilie Tisserant
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Davide Callegarin
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Simon Verdez
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | | | - Arthur Sorlin
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Eleonore Viora-Dupont
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Marina Konyukh
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Nathalie Marle
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Sophie Nambot
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Hospital Hygiene and Epidemiology Unit, Dijon University Hospital, Dijon Cedex, France
| | - Sébastien Moutton
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France.,Reference Center for Intellectual Disorders, Dijon University Hospital, Dijon, France
| | - Caroline Racine
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France.,Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, FHU TRANSLAD, Dijon University Hospital, Dijon, France
| | - Aurore Garde
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Julian Delanne
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, FHU TRANSLAD, Dijon University Hospital, Dijon, France
| | - Frédéric Tran-Mau-Them
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | - Christophe Philippe
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Paul Kuentz
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | - Marlène Poulleau
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Muriel Payet
- Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Charlotte Poe
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, FHU TRANSLAD, Dijon University Hospital, Dijon, France.,Reference Center for Intellectual Disorders, Dijon University Hospital, Dijon, France
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, FHU TRANSLAD, Dijon University Hospital, Dijon, France.,Reference Center for Intellectual Disorders, Dijon University Hospital, Dijon, France
| | - Anne-Laure Mosca-Boidron
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Department and Reference Center for Developmental Disorders and Malformative Syndromes for East France, FHU TRANSLAD, Dijon University Hospital, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD, Faculty of Health Sciences, University of Burgundy and Franche-Comté, Dijon, France.,Molecular and chromosomal genetics laboratory, Biology Transfer Platform, Dijon University Hospital, Dijon, France
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39
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Leung ML, Ji J, Baker S, Buchan JG, Sivakumaran TA, Krock BL, Hutchins R, Bayrak-Toydemir P, Pfeifer J, Cremona ML, Funke B, Santani AB. A Framework of Critical Considerations in Clinical Exome Reanalyses by Clinical and Laboratory Standards Institute. J Mol Diagn 2022; 24:177-188. [PMID: 35074075 DOI: 10.1016/j.jmoldx.2021.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
Exome reanalysis is useful for providing molecular diagnoses for previously uninformative samples. However, challenges exist in implementing a practical solution for clinicians and laboratories. This study complements the current literature by providing practical considerations for patient-level and cohort-level reanalyses. The Clinical and Laboratory Standards Institute assembled the Document Development Committee and an interpretation working group that developed the framework for reevaluation of exome-based data. We describe two distinct but complementary approaches toward exome reanalyses: clinician-initiated patient-level reanalysis, and laboratory-initiated cohort-level reanalysis. We highlight the advantages and constraints for both approaches, and provide a high-level conceptual guide for ordering clinicians and laboratories through the critical decision pathways. Because clinical exome sequencing continues to be the standard of care in genetics, exome reanalysis would be critical in increasing the overall diagnostic yield. A systematic guide will facilitate the efficient adoption of reevaluation of exome data for laboratories, health care professionals, genetic counselors, and clinicians.
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Affiliation(s)
- Marco L Leung
- Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Jianling Ji
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California; Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Samuel Baker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jillian G Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Theru A Sivakumaran
- Division of Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, Arizona
| | | | | | - Pinar Bayrak-Toydemir
- Department of Pathology, The University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - John Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | | | | | - Avni B Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania; Veritas Genetics, Boston, Massachusetts.
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40
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Bae S, Yang A, Kim J, Lee HJ, Park HK. Identification of a novel KAT6A variant in an infant presenting with facial dysmorphism and developmental delay: a case report and literature review. BMC Med Genomics 2021; 14:297. [PMID: 34930245 PMCID: PMC8686292 DOI: 10.1186/s12920-021-01148-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/13/2021] [Indexed: 11/27/2022] Open
Abstract
Background Arboleda-Tham syndrome (ARTHS), caused by a pathogenic variant of KAT6A, is an autosomal dominant inherited genetic disorder characterized by various degrees of developmental delay, dysmorphic facial appearance, cardiac anomalies, and gastrointestinal problems.
Case presentation A baby presented multiple facial deformities including a high arched and cleft palate, with philtral ridge and vermilion indentation, a prominent nasal bridge, a thin upper lip, low-set ears, an epicanthal fold, and cardiac malformations. Whole exome sequencing (WES) revealed a heterozygous nonsense mutation in exon 8 of the KAT6A gene (c.1312C>T, p.[Arg438*]) at 2 months of age. After a diagnosis of ARTHS, an expressive language delay was observed during serial assessments of developmental milestones. Conclusions In this study, we describe a case with a novel KAT6A variant first identified in Korea. This case broadens the scope of clinical features of ARTHS and emphasizes that WES is necessary for early diagnosis in patients with dysmorphic facial appearances, developmental delay, and other congenital abnormalities. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01148-x.
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Affiliation(s)
- Soyoung Bae
- Department of Pediatrics, Hanyang University Medical Center, Hanyang University College of Medicine, 222-1, Wangshimri-ro, Sungdong-gu, Seoul, 04763, Republic of Korea
| | - Aram Yang
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinsup Kim
- Department of Pediatrics, Hanyang University Medical Center, Hanyang University College of Medicine, 222-1, Wangshimri-ro, Sungdong-gu, Seoul, 04763, Republic of Korea.
| | - Hyun Ju Lee
- Department of Pediatrics, Hanyang University Medical Center, Hanyang University College of Medicine, 222-1, Wangshimri-ro, Sungdong-gu, Seoul, 04763, Republic of Korea
| | - Hyun Kyung Park
- Department of Pediatrics, Hanyang University Medical Center, Hanyang University College of Medicine, 222-1, Wangshimri-ro, Sungdong-gu, Seoul, 04763, Republic of Korea
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41
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Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 2021; 43:328-346. [PMID: 34918412 PMCID: PMC9069542 DOI: 10.1002/humu.24314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ2, p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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42
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Al-Saady ML, Kaiser CS, Wakasuqui F, Korenke GC, Waisfisz Q, Polstra A, Pouwels PJW, Bugiani M, van der Knaap MS, Lunsing RJ, Liebau E, Wolf NI. Homozygous UBA5 Variant Leads to Hypomyelination with Thalamic Involvement and Axonal Neuropathy. Neuropediatrics 2021; 52:489-494. [PMID: 33853163 DOI: 10.1055/s-0041-1724130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The enzyme ubiquitin-like modifier activating enzyme 5 (UBA5) plays an important role in activating ubiquitin-fold modifier 1 (UFM1) and its associated cascade. UFM1 is widely expressed and known to facilitate the post-translational modification of proteins. Variants in UBA5 and UFM1 are involved in neurodevelopmental disorders with early-onset epileptic encephalopathy as a frequently seen disease manifestation. Using whole exome sequencing, we detected a homozygous UBA5 variant (c.895C > T p. [Pro299Ser]) in a patient with severe global developmental delay and epilepsy, the latter from the age of 4 years. Magnetic resonance imaging showed hypomyelination with atrophy and T2 hyperintensity of the thalamus. Histology of the sural nerve showed axonal neuropathy with decreased myelin. Functional analyses confirmed the effect of the Pro299Ser variant on UBA5 protein function, showing 58% residual protein activity. Our findings indicate that the epilepsy currently associated with UBA5 variants may present later in life than previously thought, and that radiological signs include hypomyelination and thalamic involvement. The data also reinforce recently reported associations between UBA5 variants and peripheral neuropathy.
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Affiliation(s)
- Murtadha L Al-Saady
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Charlotte S Kaiser
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Felipe Wakasuqui
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | | | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Abeltje Polstra
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Petra J W Pouwels
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - Marianna Bugiani
- Department of Pathology, Amsterdam Leukodystrophy Center, VU University Medical Center and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Roelineke J Lunsing
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Liebau
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
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43
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Cloney T, Gallacher L, Pais LS, Tan NB, Yeung A, Stark Z, Brown NJ, McGillivray G, Delatycki MB, de Silva MG, Downie L, Stutterd CA, Elliott J, Compton AG, Lovgren A, Oertel R, Francis D, Bell KM, Sadedin S, Lim SC, Helman G, Simons C, Macarthur DG, Thorburn DR, O'Donnell-Luria AH, Christodoulou J, White SM, Tan TY. Lessons learnt from multifaceted diagnostic approaches to the first 150 families in Victoria's Undiagnosed Diseases Program. J Med Genet 2021; 59:748-758. [PMID: 34740920 DOI: 10.1136/jmedgenet-2021-107902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Clinical exome sequencing typically achieves diagnostic yields of 30%-57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals. AIM We share the lessons learnt from the first 3 years of the Undiagnosed Diseases Program-Victoria, an Australian programme embedded within a clinical genetics service in the state of Victoria with a focus on paediatric rare diseases. METHODS We enrolled families who remained without a diagnosis after clinical genomic (panel, exome or genome) sequencing between 2016 and 2018. We used family-based exome sequencing (family ES), family-based genome sequencing (family GS), RNA sequencing (RNA-seq) and high-resolution chromosomal microarray (CMA) with research-based analysis. RESULTS In 150 families, we achieved a diagnosis or strong candidate in 64 (42.7%) (37 in known genes with a consistent phenotype, 3 in known genes with a novel phenotype and 24 in novel disease genes). Fifty-four diagnoses or strong candidates were made by family ES, six by family GS with RNA-seq, two by high-resolution CMA and two by data reanalysis. CONCLUSION We share our lessons learnt from the programme. Flexible implementation of multiple strategies allowed for scalability and response to the availability of new technologies. Broad implementation of family ES with research-based analysis showed promising yields post a negative clinical singleton ES. RNA-seq offered multiple benefits in family ES-negative populations. International data sharing strategies were critical in facilitating collaborations to establish novel disease-gene associations. Finally, the integrated approach of a multiskilled, multidisciplinary team was fundamental to having diverse perspectives and strategic decision-making.
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Affiliation(s)
- Thomas Cloney
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lynn S Pais
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lilian Downie
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alysia Lovgren
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Analytic and Translational Genomics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ralph Oertel
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sze Chern Lim
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Guy Helman
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Translational Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Daniel G Macarthur
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anne H O'Donnell-Luria
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Neurodevelopmental Genomics Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia .,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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44
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Mensah NE, Sabir AH, Bond A, Roworth W, Irving M, Davies AC, Ahn JW. Automated reanalysis application to assist in detecting novel gene–disease associations after genome sequencing. Genet Med 2021; 24:811-820. [DOI: 10.1016/j.gim.2021.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/31/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
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45
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Delanne J, Bruel AL, Huet F, Moutton S, Nambot S, Grisval M, Houcinat N, Kuentz P, Sorlin A, Callier P, Jean-Marcais N, Mosca-Boidron AL, Mau-Them FT, Denommé-Pichon AS, Vitobello A, Lehalle D, El Chehadeh S, Francannet C, Lebrun M, Lambert L, Jacquemont ML, Gerard-Blanluet M, Alessandri JL, Willems M, Thevenon J, Chouchane M, Darmency V, Fatus-Fauconnier C, Gay S, Bournez M, Masurel A, Leguy V, Duffourd Y, Philippe C, Feillet F, Faivre L, Thauvin-Robinet C. The diagnostic rate of inherited metabolic disorders by exome sequencing in a cohort of 547 individuals with developmental disorders. Mol Genet Metab Rep 2021; 29:100812. [PMID: 34712575 PMCID: PMC8528787 DOI: 10.1016/j.ymgmr.2021.100812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 11/24/2022] Open
Abstract
Considering that some Inherited Metabolic Disorders (IMDs) can be diagnosed in patients with no distinctive clinical features of IMDs, we aimed to evaluate the power of exome sequencing (ES) to diagnose IMDs within a cohort of 547 patients with unspecific developmental disorders (DD). IMDs were diagnosed in 12% of individuals with causative diagnosis (177/547). There are clear benefits of using ES in DD to diagnose IMD, particularly in cases where biochemical studies are unavailable. Synopsis Exome sequencing and diagnostic rate of Inherited Metabolic Disorders in individuals with developmental disorders.
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Affiliation(s)
- Julian Delanne
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Ange-Line Bruel
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Frédéric Huet
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Sébastien Moutton
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Sophie Nambot
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Margot Grisval
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Nada Houcinat
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Paul Kuentz
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France.,Biologie moléculaire, CHU Besançon, Besançon, France
| | - Arthur Sorlin
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Patrick Callier
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Laboratoire de cytogénétique et génétique moléculaire, CHU Dijon Bourgogne, France
| | - Nolwenn Jean-Marcais
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | | | - Frédéric Tran Mau-Them
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Anne-Sophie Denommé-Pichon
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Antonio Vitobello
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Daphné Lehalle
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Salima El Chehadeh
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Christine Francannet
- Service de Génétique Médicale, Centre de Référence Déficiences Intellectuelles de causes rares, CHU Clermont Ferrand, France
| | - Marine Lebrun
- Laboratoire de génétique, CHU de Saint-Etienne, Saint-Etienne, France
| | | | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Jean-Luc Alessandri
- Service de Réanimation Néonatale, Pole Femme-Mère-Enfant, CH Felix Guyon, CHU de La Réunion, Saint-Denis, La Réunion, France
| | - Marjolaine Willems
- Department of Medical Genetics, Reference Center for Rare Diseases, Developmental Disorders and Multiple Congenital Anomalies, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Julien Thevenon
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Mondher Chouchane
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Véronique Darmency
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | | | - Sébastien Gay
- Service de Pédiatrie, CH William Morey, Chalon-Sur-Saône, France
| | - Marie Bournez
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Alice Masurel
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Vanessa Leguy
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Yannis Duffourd
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Christophe Philippe
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - François Feillet
- Department of Medical Genetics, Reference Center for Rare Diseases, Developmental Disorders and Multiple Congenital Anomalies, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Laurence Faivre
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Christel Thauvin-Robinet
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France.,Centre de référence maladies rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
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46
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Tran Mau-Them F, Duffourd Y, Vitobello A, Bruel AL, Denommé-Pichon AS, Nambot S, Delanne J, Moutton S, Sorlin A, Couturier V, Bourgeois V, Chevarin M, Poe C, Mosca-Boidron AL, Callier P, Safraou H, Faivre L, Philippe C, Thauvin-Robinet C. Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases. Mol Genet Genomic Med 2021; 9:e1836. [PMID: 34716697 PMCID: PMC8683640 DOI: 10.1002/mgg3.1836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders. Conclusions Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
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Affiliation(s)
- Frederic Tran Mau-Them
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | -
- FHU-TRANSLAD, Dijon, France
| | - Victor Couturier
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Valentin Bourgeois
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Martin Chevarin
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Charlotte Poe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | | | - Patrick Callier
- Laboratoire de Génétique Chromosomique et Moléculaire, CHU de Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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47
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Salinas V, Martínez N, Maturo JP, Rodriguez-Quiroga SA, Zavala L, Medina N, Amartino H, Sfaello I, Agosta G, Serafín EM, Morón DG, Kauffman MA, Vega P. Clinical next generation sequencing in developmental and epileptic encephalopathies: Diagnostic relevance of data re-analysis and variants re-interpretation. Eur J Med Genet 2021; 64:104363. [PMID: 34673242 DOI: 10.1016/j.ejmg.2021.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 09/24/2021] [Accepted: 10/08/2021] [Indexed: 11/26/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) are complex pediatric epilepsies, in which heterogeneous pathogenic factors play an important role. Next-generation-sequencing based tools have shown excellent effectiveness. The constant increase in the number of new genotype-phenotype associations suggests the periodic need for re-interpretation and re-analysis of genetic studies without positive results. In this study, we report the diagnostic utility of targeted gene panel sequencing and whole exome sequencing in 55 Argentine subjects with DEE, focusing on the utility of re-interpretation and re-analysis of undetermined and negative genetic diagnoses. The new information in biomedical literature and databases was used for the re-interpretation. For re-analysis, sequencing data processing was repeated using updated bioinformatics tools. Initially, pathogenic variants were detected in 21 subjects (38%). After an average time of 29 months, 25% of the subjects without a genetic diagnosis were re-categorized as diagnosed. Finally, the overall diagnostic yield increased to 53% (29 subjects). In consequence of the re-interpretation and re-analysis, we identified novel variants in the genes: CHD2, COL4A1, FOXG1, GABRA1, GRIN2B, HNRNPU, KCNQ2, MECP2, PCDH19, SCN1A, SCN2A, SCN8A, SLC6A1, STXBP1 and WWOX. Our results expand the diagnostic yield of this subgroup of infantile and childhood seizures and demonstrate the importance of re-evaluation of genetic tests in subjects without an identified causative etiology.
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Affiliation(s)
- Valeria Salinas
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Nerina Martínez
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Josefina Pérez Maturo
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | | | - Lucia Zavala
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Nancy Medina
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Hernán Amartino
- Paediatric Neurology Unit, Hospital Universitario Austral, Buenos Aires, Argentina.
| | - Ignacio Sfaello
- CETES, Instituto de Neurología Infanto-Juvenil, Córdoba, Argentina.
| | - Guillermo Agosta
- Paediatric Neurology Unit, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.
| | | | | | - Marcelo A Kauffman
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Patricia Vega
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
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48
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Liu Y, Teng Y, Li Z, Cui J, Liang D, Wu L. Increase in diagnostic yield achieved for 174 whole-exome sequencing cases reanalyzed 1-2 years after initial analysis. Clin Chim Acta 2021; 523:163-168. [PMID: 34560057 DOI: 10.1016/j.cca.2021.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Some missed diagnoses have been presented in whole-exome sequencing (WES) analysis for cases with possible Mendelian diseases. To assess how much contributions of WES reanalysis might improve diagnostic yield, we reviewed the WES data of 174 undiagnosed cases. METHODS We performed reanalysis with an updated bioinformatics pipeline involving better algorithms and updated databases so that CNVs and SNVs in intron regions and InDels within 10-50 bp can be detected. Upgraded variant interpretation processes, including updated software packages, databases and literature, expanded knowledge of genes and diseases, extended filtering conditions and phenotype reevaluation, were also implemented for reanalysis. Candidate variants were classified by ACMG guidelines and certified by Sanger sequencing, qPCR or MLPA. RESULTS Fourteen additional cases received new diagnosis in the reanalysis. The results which became positive were sorted according to the following aspects: detection of CNVs; diagnosis by SNVs in intron regions or InDels within 10-50 bp; reclassification due to new reports of variants or gene-disease relationships; digenic inheritance leading to disease; disease caused by frequent variations in the general population; and accurate phenotype assessment enabling the establishment of the molecular diagnosis. CONCLUSION Our study improved diagnosis yield through an optimized bioinformatics pipeline and variant interpretation strategy of WES and provided analysis experience learned from the WES reanalysis to reduce missed diagnoses.
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Affiliation(s)
- Yingdi Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Yanling Teng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jingyi Cui
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China.
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49
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Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Application of full-genome analysis to diagnose rare monogenic disorders. NPJ Genom Med 2021; 6:77. [PMID: 34556655 PMCID: PMC8460793 DOI: 10.1038/s41525-021-00241-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022] Open
Abstract
Current genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
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Affiliation(s)
- Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.
| | - Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Karen H Y Wong
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Verghese
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anne Slavotinek
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Renata C Gallagher
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Daniah Beleford
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Hazel Perry
- Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew G Sharo
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA, USA.,Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - David Martin
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
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50
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Kritioti E, Theodosiou A, Parpaite T, Alexandrou A, Nicolaou N, Papaevripidou I, Séjourné N, Coste B, Christophidou-Anastasiadou V, Tanteles GA, Sismani C. Unravelling the genetic causes of multiple malformation syndromes: A whole exome sequencing study of the Cypriot population. PLoS One 2021; 16:e0253562. [PMID: 34324503 PMCID: PMC8320927 DOI: 10.1371/journal.pone.0253562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Multiple malformation syndromes (MMS) belong to a group of genetic disorders characterised by neurodevelopmental anomalies and congenital malformations. Here we explore for the first time the genetic aetiology of MMS using whole-exome sequencing (WES) in undiagnosed patients from the Greek-Cypriot population after prior extensive diagnostics workup including karyotype and array-CGH. A total of 100 individuals (37 affected), from 32 families were recruited and family-based WES was applied to detect causative single-nucleotide variants (SNVs) and indels. A genetic diagnosis was reported for 16 MMS patients (43.2%), with 10/17 (58.8%) of the findings being novel. All autosomal dominant findings occurred de novo. Functional studies were also performed to elucidate the molecular mechanism relevant to the abnormal phenotypes, in cases where the clinical significance of the findings was unclear. The 17 variants identified in our cohort were located in 14 genes (PCNT, UBE3A, KAT6A, SPR, POMGNT1, PIEZO2, PXDN, KDM6A, PHIP, HECW2, TFAP2A, CNOT3, AGTPBP1 and GAMT). This study has highlighted the efficacy of WES through the high detection rate (43.2%) achieved for a challenging category of undiagnosed patients with MMS compared to other conventional diagnostic testing methods (10-20% for array-CGH and ~3% for G-banding karyotype analysis). As a result, family-based WES could potentially be considered as a first-tier cost effective diagnostic test for patients with MMS that facilitates better patient management, prognosis and offer accurate recurrence risks to the families.
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Affiliation(s)
- Evie Kritioti
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Athina Theodosiou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nayia Nicolaou
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nina Séjourné
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | - Bertrand Coste
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | | | - George A. Tanteles
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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