1
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Austin ED, Aldred MA, Alotaibi M, Gräf S, Nichols WC, Trembath RC, Chung WK. Genetics and precision genomics approaches to pulmonary hypertension. Eur Respir J 2024:2401370. [PMID: 39209481 DOI: 10.1183/13993003.01370-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
Considerable progress has been made in the genomics of pulmonary arterial hypertension (PAH) since the 6th World Symposium on Pulmonary Hypertension, with the identification of rare variants in several novel genes, as well as common variants that confer a modest increase in PAH risk. Gene and variant curation by an expert panel now provides a robust framework for knowing which genes to test and how to interpret variants in clinical practice. We recommend that genetic testing be offered to specific subgroups of symptomatic patients with PAH, and to children with certain types of group 3 pulmonary hypertension (PH). Testing of asymptomatic family members and the use of genetics in reproductive decision-making require the involvement of genetics experts. Large cohorts of PAH patients with biospecimens now exist and extension to non-group 1 PH has begun. However, these cohorts are largely of European origin; greater diversity will be essential to characterise the full extent of genomic variation contributing to PH risk and treatment responses. Other types of omics data are also being incorporated. Furthermore, to advance gene- and pathway-specific care and targeted therapies, gene-specific registries will be essential to support patients and their families and to lay the foundation for genetically informed clinical trials. This will require international outreach and collaboration between patients/families, clinicians and researchers. Ultimately, harmonisation of patient-derived biospecimens, clinical and omic information, and analytic approaches will advance the field.
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Affiliation(s)
- Eric D Austin
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Mona Alotaibi
- University of California San Diego, San Diego, CA, USA
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Victor Phillip Dahdaleh Heart and Lung Research Institute, Cambridge, UK
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Richard C Trembath
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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2
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Bozkurt B, Bağcı O, Üzüm S, Çora T. A novel LTBP2 gene variant in a Turkish family with juvenile-onset open-angle glaucoma. Ophthalmic Genet 2024; 45:384-389. [PMID: 38557215 DOI: 10.1080/13816810.2024.2331540] [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: 10/17/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Juvenile-onset open-angle glaucoma (JOAG) is a rare form of primary open-angle glaucoma (POAG) with an early age of onset before 40 years. Latent transforming growth factor-beta binding protein 2 (LTBP-2) is an extracellular matrix protein with a multi-domain structure and homology to fibrillins. LTBP2 gene variants have been associated with JOAG in a small number of patients. Herein, we report a novel missense variant in the LTBP2 gene in a Turkish family with JOAG. MATERIALS AND METHODS Blood samples were obtained from three siblings (a 20-year-old woman with JOAG, 26-year-old man with JOAG, and 15-year-old girl with posterior embryotoxon) for genetic analysis. Their father had moderate-severe POAG and the 24-year-old brother had JOAG. The mother and 32-year-old sister were healthy. Although the parents reported no consanguinity, they come from the same village. RESULTS Clinical exome sequencing analysis of the two siblings with JOAG revealed a novel c.607C>T p.(R203C) (rs777450651) homozygous LTBP2 variant, while the variant was heterozygous in their 15-year-old sister. There were no mutations in the MYOC, CYP1B1, or FBN1 genes. CONCLUSION We documented a novel missense mutation in the LTBP2 gene leading to a severe form of JOAG with refractory IOP and progressive optic nerve damage, which seems to show autosomal recessive inheritance.
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Affiliation(s)
- Banu Bozkurt
- Department of Ophthalmology, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Ozkan Bağcı
- Department of Medical Genetics, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Sema Üzüm
- Department of Ophthalmology, Selçuk University Faculty of Medicine, Konya, Türkiye
| | - Tülin Çora
- Department of Medical Genetics, Selçuk University Faculty of Medicine, Konya, Türkiye
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3
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Houge G, Bratland E, Aukrust I, Tveten K, Žukauskaitė G, Sansovic I, Brea-Fernández AJ, Mayer K, Paakkola T, McKenna C, Wright W, Markovic MK, Lildballe DL, Konecny M, Smol T, Alhopuro P, Gouttenoire EA, Obeid K, Todorova A, Jankovic M, Lubieniecka JM, Stojiljkovic M, Buisine MP, Haukanes BI, Lorans M, Roomere H, Petit FM, Haanpää MK, Beneteau C, Pérez B, Plaseska-Karanfilska D, Rath M, Fuhrmann N, Ferreira BI, Stephanou C, Sjursen W, Maver A, Rouzier C, Chirita-Emandi A, Gonçalves J, Kuek WCD, Broly M, Haer-Wigman L, Thong MK, Tae SK, Hyblova M, den Dunnen JT, Laner A. Comparison of the ABC and ACMG systems for variant classification. Eur J Hum Genet 2024; 32:858-863. [PMID: 38778080 PMCID: PMC11219933 DOI: 10.1038/s41431-024-01617-8] [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: 12/19/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
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Affiliation(s)
- Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Eirik Bratland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Gabrielė Žukauskaitė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ivona Sansovic
- Department of Medical and Laboratory Genetics, Endocrinology and Diabetology, Childrens' Hospital Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBERER), Santiago de Compostela, Spain
| | - Karin Mayer
- Center for Human Genetics and Laboratory Diagnostics, MVZ Martinsried GmbH, Martinsried, Germany
| | - Teija Paakkola
- Nordlab Wellbeing Service Group, Genetics Laboratory, Oulu, Finland
| | - Caoimhe McKenna
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - William Wright
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - Milica Keckarevic Markovic
- Center for Applied and Forensic Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dorte L Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Konecny
- Laboratory of Genomic Medicine, GHC GENETICS SK, Bratislava, Slovakia
- Department of Biology, Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Thomas Smol
- Institut de Genetique Medicale-CHU Lille, Lille, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Katharina Obeid
- Molecular Diagnostics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory "Genica" and Genome Center Bulgaria, Sofia, Bulgaria
| | - Milena Jankovic
- Neurology Clinic UCCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marie-Pierre Buisine
- Molecular Oncogenetics, Department of Biochemistry and Molecular Biology, Lille University Hospital, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, CANTHER, Lille, France
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marie Lorans
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Hanno Roomere
- Department of laboratory genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - François M Petit
- Department of Oncopharmacology, Centre Antoine Lacassagne, Nice, France
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland
| | - Claire Beneteau
- CHU Bordeaux, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Belén Pérez
- Genetics Department of CEDEM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Matthias Rath
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bibiana I Ferreira
- GENELAB by ABC, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Coralea Stephanou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, Ljubljana, Slovenia
| | - Cécile Rouzier
- Department of Medical Genetics, National Centre for Mitocondrial Diseases, CHU de NICE, Université Côte d'Azur, Nice, France
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Adela Chirita-Emandi
- Department of Microscopic Morphology Genetics Discipline, Center of Genomic Medicine, "Victor Babes" University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - João Gonçalves
- Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Wei Cheng David Kuek
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Kent Ridge, Singapore
| | - Martin Broly
- Laboratory of Rare and Autoinflammatory Genetic Diseases, Department of Genetics-LBM, Montpellier University Hospital, Montpellier, France
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Meow-Keong Thong
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok-Kun Tae
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ) München, Munich, Germany
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4
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Finsterer J, Scorza FA. Panel testing may not be sufficient to reveal the etiology of suspected genetic epilepsy. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2024; 70:e20231570. [PMID: 38808894 PMCID: PMC11135657 DOI: 10.1590/1806-9282.20231570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 05/30/2024]
Affiliation(s)
| | - Fulvio Alexandre Scorza
- Unibersidade Federal de São Paulo/Escola Paulista de Medicinal, Neuroscience Discipline – São Paulo (SP), Brazil
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5
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Basel-Salmon L. Phenotypic compatibility and specificity in genomic variant classification. Eur J Hum Genet 2024; 32:471-473. [PMID: 38351291 PMCID: PMC11061282 DOI: 10.1038/s41431-024-01554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, 4941492, Israel.
- Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.
- Felsenstein Medical Research Center, Petach Tikva, 4920235, Israel.
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6
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Mori T, Fujimaru T, Liu C, Patterson K, Yamamoto K, Suzuki T, Chiga M, Sekine A, Ubara Y, Miller DE, Zalusky MPG, Mandai S, Ando F, Mori Y, Kikuchi H, Susa K, Chong JX, Bamshad MJ, Tan YQ, Zhang F, Uchida S, Sohara E. CFAP47 is a novel causative gene implicated in X-linked polycystic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24304760. [PMID: 38633811 PMCID: PMC11023651 DOI: 10.1101/2024.04.05.24304760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a well-described condition in which ~80% of cases have a genetic explanation, while the genetic basis of sporadic cystic kidney disease in adults remains unclear in ~30% of cases. This study aimed to identify novel genes associated with polycystic kidney disease (PKD) in patients with sporadic cystic kidney disease in which a clear genetic change was not identified in established genes. A next-generation sequencing panel analyzed known genes related to renal cysts in 118 sporadic cases, followed by whole-genome sequencing on 47 unrelated individuals without identified candidate variants. Three male patients were found to have rare missense variants in the X-linked gene Cilia And Flagella Associated Protein 47 (CFAP47). CFAP47 was expressed in primary cilia of human renal tubules, and knockout mice exhibited vacuolation of tubular cells and tubular dilation, providing evidence that CFAP47 is a causative gene involved in cyst formation. This discovery of CFAP47 as a newly identified gene associated with PKD, displaying X-linked inheritance, emphasizes the need for further cases to understand the role of CFAP47 in PKD.
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Affiliation(s)
- Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chunyu Liu
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kohei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takefumi Suzuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinari Sekine
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Miranda PG Zalusky
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Feng Zhang
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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7
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Kim HH, Kim DW, Woo J, Lee K. Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders. Hum Genomics 2024; 18:28. [PMID: 38509596 PMCID: PMC10956189 DOI: 10.1186/s40246-024-00595-8] [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: 06/15/2023] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND In the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential. Previous variant prioritization tools mainly depend on the in-silico prediction of the pathogenicity of variants, which results in low sensitivity and difficulty in interpreting the prioritization result. In this study, we propose an explainable algorithm for variant prioritization, named 3ASC, with higher sensitivity and ability to annotate evidence used for prioritization. 3ASC annotates each variant with the 28 criteria defined by the ACMG/AMP genome interpretation guidelines and features related to the clinical interpretation of the variants. The system can explain the result based on annotated evidence and feature contributions. RESULTS We trained various machine learning algorithms using in-house patient data. The performance of variant ranking was assessed using the recall rate of identifying causative variants in the top-ranked variants. The best practice model was a random forest classifier that showed top 1 recall of 85.6% and top 3 recall of 94.4%. The 3ASC annotates the ACMG/AMP criteria for each genetic variant of a patient so that clinical geneticists can interpret the result as in the CAGI6 SickKids challenge. In the challenge, 3ASC identified causal genes for 10 out of 14 patient cases, with evidence of decreased gene expression for 6 cases. Among them, two genes (HDAC8 and CASK) had decreased gene expression profiles confirmed by transcriptome data. CONCLUSIONS 3ASC can prioritize genetic variants with higher sensitivity compared to previous methods by integrating various features related to clinical interpretation, including features related to false positive risk such as quality control and disease inheritance pattern. The system allows interpretation of each variant based on the ACMG/AMP criteria and feature contribution assessed using explainable AI techniques.
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Affiliation(s)
- Ho Heon Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Dong-Wook Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Junwoo Woo
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Kyoungyeul Lee
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea.
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8
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Schmidt RJ, Steeves M, Bayrak-Toydemir P, Benson KA, Coe BP, Conlin LK, Ganapathi M, Garcia J, Gollob MH, Jobanputra V, Luo M, Ma D, Maston G, McGoldrick K, Palculict TB, Pesaran T, Pollin TI, Qian E, Rehm HL, Riggs ER, Schilit SLP, Sergouniotis PI, Tvrdik T, Watkins N, Zec L, Zhang W, Lebo MS. Recommendations for risk allele evidence curation, classification, and reporting from the ClinGen Low Penetrance/Risk Allele Working Group. Genet Med 2024; 26:101036. [PMID: 38054408 PMCID: PMC10939896 DOI: 10.1016/j.gim.2023.101036] [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: 06/22/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE Genetic variants at the low end of the penetrance spectrum have historically been challenging to interpret because their high population frequencies exceed the disease prevalence of the associated condition, leading to a lack of clear segregation between the variant and disease. There is currently substantial variation in the classification of these variants, and no formal classification framework has been widely adopted. The Clinical Genome Resource Low Penetrance/Risk Allele Working Group was formed to address these challenges and promote harmonization within the clinical community. METHODS The work presented here is the product of internal and community Likert-scaled surveys in combination with expert consensus within the Working Group. RESULTS We formally recognize risk alleles and low-penetrance variants as distinct variant classes from those causing highly penetrant disease that require special considerations regarding their clinical classification and reporting. First, we provide a preferred terminology for these variants. Second, we focus on risk alleles and detail considerations for reviewing relevant studies and present a framework for the classification these variants. Finally, we discuss considerations for clinical reporting of risk alleles. CONCLUSION These recommendations support harmonized interpretation, classification, and reporting of variants at the low end of the penetrance spectrum.
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Affiliation(s)
- Ryan J Schmidt
- Children's Hospital Los Angeles, Keck School of Medicine of USC, Los Angeles, CA.
| | | | - Pinar Bayrak-Toydemir
- Department of Pathology, University of Utah Molecular Genetics and Genomics, ARUP Laboratories, Salt Lake City, UT
| | - Katherine A Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Ireland
| | - Bradley P Coe
- Department of Pathology & Lab Medicine, BC Children's & BC Women's Hospitals, Vancouver, Canada
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | | | - Michael H Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, Toronto General Hospital and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Vaidehi Jobanputra
- New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Deqiong Ma
- DNA diagnostic lab, Department of Genetics, School of Medicine, Yale University, New Haven, CT
| | | | | | | | | | - Toni I Pollin
- University of Maryland School of Medicine, Baltimore, MD
| | - Emily Qian
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Heidi L Rehm
- Center for Genomics Medicine, Massachusetts General Hospital, Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erin R Riggs
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA
| | - Samantha L P Schilit
- Mass General Brigham, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA
| | | | - Tatiana Tvrdik
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Nicholas Watkins
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Matthew S Lebo
- Mass General Brigham, Brigham and Woman's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, MA.
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9
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Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [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: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
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Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
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10
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Aklilu AM, Gulati A, Kolber KJ, Yang H, Harris PC, Dahl NK. The VUS Challenge in Cystic Kidney Disease: A Case-Based Review. KIDNEY360 2024; 5:152-159. [PMID: 37962562 PMCID: PMC10833605 DOI: 10.34067/kid.0000000000000298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Genetic testing in nephrology is becoming increasingly important to diagnose patients and to provide appropriate care. This is especially true for autosomal dominant polycystic kidney disease (ADPKD) because this is a common cause of kidney failure and genetically complex. In addition to the major genes, PKD1 and PKD2 , there are at least six minor loci, and phenotypic, and in some cases, genetic overlap with other cystic disorders. Targeted next-generation sequencing, a low-cost, high-throughput technique, has made routine genetic testing viable in nephrology clinics. Appropriate pre- and post-testing genetic counseling is essential to the testing process. Carefully assessing variants is also critical, with the genetic report classifying variants in accordance with American College of Medical Genetics and Genomics guidelines. However, variant of uncertain significance (VUSs) may pose a significant challenge for the ordering clinician. In ADPKD, and particularly within PKD1 , there is high allelic heterogeneity; no single variant is present in more than 2% of families. The Mayo/Polycystic Kidney Disease Foundation variant database, a research tool, is the best current database of PKD1 and PKD2 variants containing over 2300 variants identified in individuals with polycystic kidney disease, but novel variants are often identified. In patients with a high pretest probability of ADPKD on the basis of clinical criteria, but no finding of a pathogenic (P) or likely pathogenic (LP) variant in a cystic kidney gene, additional evaluation of cystic gene VUS can be helpful. In this case-based review, we propose an algorithm for the assessment of such variants in a clinical setting and show how some can be reassigned to a diagnostic grouping. When assessing the relevance of a VUS, we consider both patient/family-specific and allele-related factors using population and variant databases and available prediction tools, as well as genetic expertise. This analysis plus further family studies can aid in making a genetic diagnosis.
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Affiliation(s)
- Abinet M. Aklilu
- Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | | | - Kayla J. Kolber
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hana Yang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Neera K. Dahl
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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11
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Liu S, Zhong M, Huang Y, Zhang Q, Chen T, Xu X, Peng W, Wang X, Feng X, Kang L, Lu Y, Cheng J, Bu F, Yuan H. Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss. Genome Med 2023; 15:116. [PMID: 38111038 PMCID: PMC10726519 DOI: 10.1186/s13073-023-01271-7] [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: 07/21/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the PS4 criterion. However, quantitative support for PS4 thresholds from real-world Mendelian case-control cohorts is lacking. METHODS To address this gap, we evaluated and established PS4 thresholds using data from the Chinese Deafness Genetics Consortium. A total of 9,050 variants from 13,845 patients with hearing loss (HL) and 6,570 ancestry-matched controls were analyzed. Positive likelihood ratio and local positive likelihood ratio values were calculated to determine the thresholds corresponding to each strength of evidence across three variant subsets. RESULTS In subset 1, consisting of variants present in both cases and controls with an allele frequency (AF) in cases ≥ 0.0005, an odds ratio (OR) ≥ 6 achieved strong evidence, while OR ≥ 3 represented moderate evidence. For subset 2, which encompassed variants present in both cases and controls with a case AF < 0.0005, and subset 3, comprising variants found only in cases and absent from controls, we defined the PS4_Supporting threshold (OR > 2.27 or allele count ≥ 3) and the PS4_Moderate threshold (allele count ≥ 6), respectively. Reanalysis applying the adjusted PS4 criteria changed the classification of 15 variants and enabled diagnosis of an additional four patients. CONCLUSIONS Our study quantified evidence strength thresholds for variant enrichment in genetic HL cases, highlighting the importance of defining disease/gene-specific thresholds to improve the precision and accuracy of clinical genetic testing.
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Affiliation(s)
- Sihan Liu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Mingjun Zhong
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Huang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Qian Zhang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Ting Chen
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Wan Peng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaolu Wang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Lu Kang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Lu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Jing Cheng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Fengxiao Bu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
| | - Huijun Yuan
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
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12
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Gunning AC, Wright CF. Evaluating the use of paralogous protein domains to increase data availability for missense variant classification. Genome Med 2023; 15:110. [PMID: 38087376 PMCID: PMC10714540 DOI: 10.1186/s13073-023-01264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Classification of rare missense variants remains an ongoing challenge in genomic medicine. Evidence of pathogenicity is often sparse, and decisions about how to weigh different evidence classes may be subjective. We used a Bayesian variant classification framework to investigate the performance of variant co-localisation, missense constraint, and aggregating data across paralogous protein domains ("meta-domains"). METHODS We constructed a database of all possible coding single nucleotide variants in the human genome and used PFam predictions to annotate structurally-equivalent positions across protein domains. We counted the number of pathogenic and benign missense variants at these equivalent positions in the ClinVar database, calculated a regional constraint score for each meta-domain, and assessed this approach versus existing missense constraint metrics for classifying variant pathogenicity and benignity. RESULTS Alternative pathogenic missense variants at the same amino acid position in the same protein provide strong evidence of pathogenicity (positive likelihood ratio, LR+ = 85). Additionally, clinically annotated pathogenic or benign missense variants at equivalent positions in different proteins can provide moderate evidence of pathogenicity (LR+ = 7) or benignity (LR+ = 5), respectively. Applying these approaches sequentially (through PM5) increases sensitivity for classifying pathogenic missense variants from 27 to 41%. Missense constraint can also provide strong evidence of pathogenicity for some variants, but its absence provides no evidence of benignity. CONCLUSIONS We propose using structurally equivalent positions across related protein domains from different genes to augment evidence for variant co-localisation when classifying novel missense variants. Additionally, we advocate adopting a numerical evidence-based approach to integrating diverse data in variant interpretation.
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Affiliation(s)
- Adam Colin Gunning
- Department of Clinical and Biomedical Sciences (Medical School, Faculty of Health and Life Sciences, University of Exeter, RILD, Barrack Road, Exeter, EX2 5DW, UK.
- Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon University Healthcare NHS Foundation Trust, RILD, Barrack Road, Exeter, EX2 5DW, UK.
| | - Caroline Fiona Wright
- Department of Clinical and Biomedical Sciences (Medical School, Faculty of Health and Life Sciences, University of Exeter, RILD, Barrack Road, Exeter, EX2 5DW, UK.
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13
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Ohlsson S, Lainka E, Hünseler C, Bergmann C, Cirak S, Baba HA, Hoyer PF. CD55 Deficiency With Budd-Chiari Syndrome Treated by Liver Transplantation and Eculizumab. Pediatrics 2023; 152:e2022059335. [PMID: 38018238 DOI: 10.1542/peds.2022-059335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 11/30/2023] Open
Abstract
We report the case of a male patient who had a history of early-onset protein-losing enteropathy, chronic diarrhea, and repeated thrombotic events since early childhood. He developed Budd-Chiari syndrome with consequent acute liver failure that required liver transplantation when he was 12 years old. The initial graft failed to function and he required retransplantation. Steroid-resistant rejection complicated the clinical course after the second transplant. Treatment with antithymocyte globulin stabilized graft function but abdominal symptoms and enteral protein loss persisted. The patient remained dependent on intravenous albumin and immunoglobulin. Extended work-up for thrombophilia was unremarkable. Flow cytometry analysis of the peripheral blood cells revealed an unexplained CD55 deficiency. By sequencing of CD55 and, later, exclusion of alternative rare diseases by whole-exome sequencing, we discovered a novel, likely pathogenic homozygous splice-site variant in CD55 c.578 + 5G>A, NM_000574.4, OMIM 125240. The staining of liver and colon biopsies revealed a lack of CD55 protein expression. After initiation of treatment with eculizumab, the patient achieved and has maintained a complete clinical remission throughout 56 months of follow-up. We recommend testing for CD55 deficiency in patients with protein-losing enteropathy. In addition, CD55 deficiency should be considered in the differential diagnosis of patients with Budd-Chiari syndrome in whom an underlying cause is uncertain.
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Affiliation(s)
- Sinja Ohlsson
- Department of Pediatrics II, Pediatric Gastroenterology, Hepatology and Liver Transplantation, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Elke Lainka
- Department of Pediatrics II, Pediatric Gastroenterology, Hepatology and Liver Transplantation, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christoph Hünseler
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - Sebahattin Cirak
- Section of Social Pediatric Center and Neuropediatrics, University Children's Hospital Ulm, University of Ulm, Ulm, Germany
| | - Hideo A Baba
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter F Hoyer
- Department of Pediatrics II, Pediatric Gastroenterology, Hepatology and Liver Transplantation, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
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14
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Sergouniotis PI, Michaud V, Lasseaux E, Campbell C, Plaisant C, Javerzat S, Birney E, Ramsden SC, Black GC, Arveiler B. A multilayered approach to the analysis of genetic data from individuals with suspected albinism. J Med Genet 2023; 60:1245-1249. [PMID: 37460203 DOI: 10.1136/jmg-2022-109088] [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: 12/01/2022] [Accepted: 05/12/2023] [Indexed: 11/29/2023]
Abstract
Albinism is a clinically and genetically heterogeneous group of conditions characterised by visual abnormalities and variable degrees of hypopigmentation. Multiple studies have demonstrated the clinical utility of genetic investigations in individuals with suspected albinism. Despite this, the variation in the provision of genetic testing for albinism remains significant. One key issue is the lack of a standardised approach to the analysis of genomic data from affected individuals. For example, there is variation in how different clinical genetic laboratories approach genotypes that involve incompletely penetrant alleles, including the common, 'hypomorphic' TYR c.1205G>A (p.Arg402Gln) [rs1126809] variant. Here, we discuss the value of genetic testing as a frontline diagnostic tool in individuals with features of albinism and propose a practice pattern for the analysis of genomic data from affected families.
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Affiliation(s)
- Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Vincent Michaud
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claudio Plaisant
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Sophie Javerzat
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Benoit Arveiler
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
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15
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Cocostîrc V, Paștiu AI, Pusta DL. An Overview of Canine Inherited Neurological Disorders with Known Causal Variants. Animals (Basel) 2023; 13:3568. [PMID: 38003185 PMCID: PMC10668755 DOI: 10.3390/ani13223568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.
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Affiliation(s)
- Vlad Cocostîrc
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (A.I.P.); (D.L.P.)
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16
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Shil A, Levin L, Golan H, Meiri G, Michaelovski A, Sadaka Y, Aran A, Dinstein I, Menashe I. Comparison of three bioinformatics tools in the detection of ASD candidate variants from whole exome sequencing data. Sci Rep 2023; 13:18853. [PMID: 37914828 PMCID: PMC10620213 DOI: 10.1038/s41598-023-46258-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023] Open
Abstract
Autism spectrum disorder (ASD) is a heterogenous multifactorial neurodevelopmental condition with a significant genetic susceptibility component. Thus, identifying genetic variations associated with ASD is a complex task. Whole-exome sequencing (WES) is an effective approach for detecting extremely rare protein-coding single-nucleotide variants (SNVs) and short insertions/deletions (INDELs). However, interpreting these variants' functional and clinical consequences requires integrating multifaceted genomic information. We compared the concordance and effectiveness of three bioinformatics tools in detecting ASD candidate variants (SNVs and short INDELs) from WES data of 220 ASD family trios registered in the National Autism Database of Israel. We studied only rare (< 1% population frequency) proband-specific variants. According to the American College of Medical Genetics (ACMG) guidelines, the pathogenicity of variants was evaluated by the InterVar and TAPES tools. In addition, likely gene-disrupting (LGD) variants were detected based on an in-house bioinformatics tool, Psi-Variant, that integrates results from seven in-silico prediction tools. Overall, 372 variants in 311 genes distributed in 168 probands were detected by these tools. The overlap between the tools was 64.1, 22.9, and 23.1% for InterVar-TAPES, InterVar-Psi-Variant, and TAPES-Psi-Variant, respectively. The intersection between InterVar and Psi-Variant (I ∩ P) was the most effective approach in detecting variants in known ASD genes (PPV = 0.274; OR = 7.09, 95% CI = 3.92-12.22), while the union of InterVar and Psi Variant (I U P) achieved the highest diagnostic yield (20.5%).Our results suggest that integrating different variant interpretation approaches in detecting ASD candidate variants from WES data is superior to each approach alone. The inclusion of additional criteria could further improve the detection of ASD candidate variants.
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Affiliation(s)
- Apurba Shil
- Department of Epidemiology, Biostatistics, and Health Community Sciences, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Liron Levin
- Bioinformatics Core Facility, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hava Golan
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Meiri
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Preschool Psychiatric Unit, Soroka University Medical Center, Beer-Sheva, Israel
| | - Analya Michaelovski
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Child Development Center, Soroka University Medical Center, Beer-Sheva, Israel
| | - Yair Sadaka
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Child Development Center, Ministry of Health, Beer-Sheva, Israel
| | - Adi Aran
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilan Dinstein
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Psychology Department, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idan Menashe
- Department of Epidemiology, Biostatistics, and Health Community Sciences, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Azrieli National Centre for Autism and Neurodevelopment Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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17
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Santostefano M, Cappuccilli M, Gibertoni D, Fabbrizio B, Malvi D, Demetri M, Capelli I, Tringali E, Papa V, Biagini E, Cenacchi G, Galdi A, Donadio V, Liguori R, Zoli G, La Manna G, Pasquinelli G. Fabry Disease Nephropathy: Histological Changes With Nonclassical Mutations and Genetic Variants of Unknown Significance. Am J Kidney Dis 2023; 82:581-596.e0. [PMID: 37301502 DOI: 10.1053/j.ajkd.2023.03.015] [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: 04/26/2022] [Accepted: 03/12/2023] [Indexed: 06/12/2023]
Abstract
RATIONALE & OBJECTIVE Fabry disease (FD) is an X-linked genetic disorder that causes lysosomal storage of glycosphingolipids, primarily globotriaosylceramide (Gb3) and its derivative globotriaosylsphingosine (lyso-Gb3), with multiorgan dysfunction including chronic kidney disease. Affected individuals may be carriers of gene variants that are of uncertain significance (GVUS). We describe kidney pathology at the early stages of FD-related kidney disease to gain insights into its association with GVUS and sex. STUDY DESIGN Single-center, case series. SETTING & PARTICIPANTS Thirty-five consecutively biopsied patients (aged 48.1±15.4 years, 22 females) from among 64 patients with genetically diagnosed FD. Biopsies were retrospectively screened using the International Study Group of Fabry Nephropathy Scoring System. OBSERVATIONS Genetic mutation type, p.N215S and D313Y, sex, age, estimated glomerular filtration rate (eGFR), plasma lyso-Gb3 (pLyso-Gb3) levels, and histological parameters, including Gb3 deposits were recorded. Genetic analyses showed mostly missense mutations, p.N215S variant in 15, and the "benign polymorphism" D313Y in 4 of the biopsied patients. Morphological lesions were similar for men and women except for interstitial fibrosis and arteriolar hyalinosis being more common in men. Early in their clinical course, patients with normal/mild albuminuria had podocyte, tubular, and peritubular capillary vacuoles/inclusions, and evidence of chronicity, i.e., glomerulosclerosis, interstitial fibrosis, tubular atrophy. These findings appeared to be associated with pLyso-Gb3, eGFR, and age. LIMITATIONS Retrospective design and inclusion of outpatients partially based on family pedigree. CONCLUSIONS In early stages of kidney disease in the setting of FD, numerous histological abnormalities are present. These observations suggest that kidney biopsies early in FD may reveal activity of kidney involvement that may inform clinical management.
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Affiliation(s)
- Marisa Santostefano
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Alma Mater Studiorum, University of Bologna, Bologna
| | - Maria Cappuccilli
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Alma Mater Studiorum, University of Bologna, Bologna
| | - Dino Gibertoni
- Research and Innovation Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | | | - Deborah Malvi
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - Marcello Demetri
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - Irene Capelli
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Alma Mater Studiorum, University of Bologna, Bologna
| | - Edoardo Tringali
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Alma Mater Studiorum, University of Bologna, Bologna
| | - Valentina Papa
- Department of Biomedical and Neuromotor Sciences, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna
| | | | - Giovanna Cenacchi
- Biotechnology and Methods in Laboratory Medicine, University of Bologna, Bologna
| | - Adriana Galdi
- Department of Internal Medicine, S.S. Annunziata Hospital, University of Ferrara, Cento, Italy
| | - Vincenzo Donadio
- Neuromuscular and Neuroimmunology Unit, Bellaria Hospital, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - Rocco Liguori
- Neuromuscular and Neuroimmunology Unit, Bellaria Hospital, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - Giorgio Zoli
- Department of Internal Medicine, S.S. Annunziata Hospital, University of Ferrara, Cento, Italy
| | - Gaetano La Manna
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Alma Mater Studiorum, University of Bologna, Bologna.
| | - Gianandrea Pasquinelli
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Biotechnology and Methods in Laboratory Medicine, University of Bologna, Bologna
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18
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Vorstman JAS, Scherer SW. Contemplating syndromic autism. Genet Med 2023; 25:100919. [PMID: 37330697 DOI: 10.1016/j.gim.2023.100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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19
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Urbanska EM, Grauslund M, Koffeldt PR, Truelsen SLB, Löfgren JO, Costa JC, Melchior LC, Sørensen JB, Santoni-Rugiu E. Real-World Data on Combined EGFR-TKI and Crizotinib Treatment for Acquired and De Novo MET Amplification in Patients with Metastatic EGFR-Mutated NSCLC. Int J Mol Sci 2023; 24:13077. [PMID: 37685884 PMCID: PMC10487649 DOI: 10.3390/ijms241713077] [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: 07/30/2023] [Revised: 08/15/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Amplification of the mesenchymal epithelial transition (MET) gene is a mechanism of acquired resistance to epidermal growth factor receptor (EGFR)-tyrosine-kinase-inhibitors (TKIs) in over 20% of patients with advanced EGFR-mutated (EGFRm+) non-small lung cancer (NSCLC). However, it may also occur de novo in 2-8% of EGFRm+ NSCLC cases as a potential mechanism of intrinsic resistance. These patients represent a group with unmet needs, since there is no standard therapy currently approved. Several new MET inhibitors are being investigated in clinical trials, but the results are awaited. Meanwhile, as an alternative strategy, combinations of EGFR-TKIs with the MET/ALK/ROS1-TKI Crizotinib may be used in this setting, despite this use is principally off-label. Thus, we studied five of these MET amplified cases receiving EGFR-TKI and Crizotinib doublet after progression on EGFR-TKI treatment to assess the benefits and challenges related to this combination and the possible occurrence of genomic and phenotypic co-alterations. Furthermore, we compared our cases with other real-world reports on Crizotinib/EGFR-TKI combinations, which appeared effective, especially in patients with high-level MET amplification. Yet, we observed that the co-occurrence of other genomic and phenotypical alterations may affect the response to combined EGFR-TKI and Crizotinib. Finally, given the heterogeneity of MET amplification, the diagnostic methods for assessing it may be discrepant. In this respect, we observed that for optimal detection, immunohistochemistry, fluorescence in situ hybridization, and next-generation sequencing should be used together, as these methods possess different sensitivities and complement each other in characterizing MET amplification. Additionally, we addressed the issue of managing EGFR-mutated NSCLC patients with de novo MET amplification causing primary EGFR-TKI resistance. We conclude that, while data from clinical trials with new MET inhibitors are still pending, adding Crizotinib to EGFR-TKI in NSCLC patients acquiring MET amplification at progression on EGFR-TKI monotherapy is a reasonable approach, with a progression-free survival of 3-19 months.
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Affiliation(s)
- Edyta M. Urbanska
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark;
| | - Morten Grauslund
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; (M.G.); (P.R.K.); (S.L.B.T.); (L.C.M.)
| | - Peter R. Koffeldt
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; (M.G.); (P.R.K.); (S.L.B.T.); (L.C.M.)
| | - Sarah L. B. Truelsen
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; (M.G.); (P.R.K.); (S.L.B.T.); (L.C.M.)
| | - Johan O. Löfgren
- Department of Clinical Physiology and Nuclear Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark;
| | - Junia C. Costa
- Department of Radiology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark;
| | - Linea C. Melchior
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; (M.G.); (P.R.K.); (S.L.B.T.); (L.C.M.)
| | - Jens B. Sørensen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark;
- Department of Clinical Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; (M.G.); (P.R.K.); (S.L.B.T.); (L.C.M.)
- Department of Clinical Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
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20
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Maász A, Bodó T, Till Á, Molnár G, Masszi G, Labossa G, Herbert Z, Bene J, Hadzsiev K. Three-Year Follow-Up after Intrauterine mTOR Inhibitor Administration for Fetus with TSC-Associated Rhabdomyoma. Int J Mol Sci 2023; 24:12886. [PMID: 37629066 PMCID: PMC10454323 DOI: 10.3390/ijms241612886] [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: 06/30/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a multisystem disorder characterized by seizures, neuropsychiatric disorders, and tumors of the heart, brain, skin, lungs, and kidneys. We present a three-year follow-up of a patient with TSC-associated rhabdomyoma detected in utero. Genetic examination of the fetus and the parents revealed a de novo variant in the TSC2 gene (c.3037delG, p.Asp1013IlefsTer3). Oral everolimus was initiated in the pregnant mother to regress the fetal tumor, which was successful. To the best of our knowledge, there is very little information regarding the use of everolimus therapy during pregnancy. West-syndrome was diagnosed when the proband was four months old. The symptoms were well-manageable, however temporarily. Therapy-resistant focal seizures were frequent. The patient had good vitals and was under regular cardiological control, showed a balanced circulation, and did not require any medication. Subependymal giant cell astrocytoma (SEGA) identified by regular neuroimaging examinations remained unchanged, which may be a consequence of early intrauterine treatment. Early detection of the pathogenic TSC2 variant, followed by in utero administration of everolimus and early vigabatrin therapy, allowed the detection of a milder developmental delay of the proband. Our study emphasizes how early genetic testing and management of epilepsy are pivotal for proper neurodevelopmental impacts and therapeutic strategies.
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Affiliation(s)
- Anita Maász
- Department of Medical Genetics, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Tímea Bodó
- Bethesda Children’s Hospital, H-1146 Budapest, Hungary
| | - Ágnes Till
- Department of Medical Genetics, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Gábor Molnár
- Department of Obstetrics and Gynaecology, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - György Masszi
- Department of Paediatrics, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Gusztáv Labossa
- Department of Obstetrics and Gynaecology, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Zsuzsanna Herbert
- Department of Medical Imaging, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School and Clinical Centre, University of Pécs, H-7624 Pécs, Hungary
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21
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Lledo B, Marco A, Morales R, Ortiz JA, García-Hernández E, Lozano FM, Cascales A, Guerrero J, Bernabeu A, Bernabeu R. Identification of novel candidate genes associated with meiotic aneuploidy in human embryos by whole-exome sequencing. J Assist Reprod Genet 2023; 40:1755-1763. [PMID: 37171739 PMCID: PMC10352178 DOI: 10.1007/s10815-023-02825-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
PURPOSE To identify novel genetic variants responsible for meiotic embryonic aneuploidy. METHODS A prospective observational cohort study that included 29 couples who underwent trophectoderm biopsies from 127 embryos and performed whole-exome sequencing (WES) between November 2019 and March 2022. Patients were divided into two groups according to the expected embryo aneuploidy rate based on maternal age. RESULTS After variant filtering in the WES analysis of 58 patients/donors, five heterozygous variants were identified in female partners from the study group that had an impact on embryo aneuploidy. Additionally, a slowdown in embryo development and a decrease in the number of blastocysts available for biopsy were observed in the study group embryos. CONCLUSION This study has identified new candidate genes and variants not previously associated with meiotic embryo aneuploidy, but which are involved in important biological processes related to cell division and chromosome segregation. WES may be an efficient tool to identify patients with a higher-than-expected risk of embryo aneuploidy based on maternal age and allow for individualized genetic counselling prior to treatment.
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Affiliation(s)
- B Lledo
- Instituto Bernabeu Biotech, 03016, Alicante, Spain.
| | - A Marco
- Instituto Bernabeu Biotech, 03016, Alicante, Spain
| | - R Morales
- Instituto Bernabeu Biotech, 03016, Alicante, Spain
| | - J A Ortiz
- Instituto Bernabeu Biotech, 03016, Alicante, Spain
| | | | - F M Lozano
- Instituto Bernabeu Biotech, 03016, Alicante, Spain
| | - A Cascales
- Instituto Bernabeu Biotech, 03016, Alicante, Spain
| | - J Guerrero
- Instituto Bernabeu of Fertility and Gynaecology, 03016, Alicante, Spain
| | - A Bernabeu
- Instituto Bernabeu of Fertility and Gynaecology, 03016, Alicante, Spain
- Cátedra de Medicina Comunitaria y Salud Reproductiva, Miguel Hernández University, Alicante, Spain
| | - R Bernabeu
- Instituto Bernabeu of Fertility and Gynaecology, 03016, Alicante, Spain
- Cátedra de Medicina Comunitaria y Salud Reproductiva, Miguel Hernández University, Alicante, Spain
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22
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Sládeček T, Gažiová M, Kucharík M, Zaťková A, Pös Z, Pös O, Krampl W, Tomková E, Hýblová M, Minárik G, Radvánszky J, Budiš J, Szemes T. Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations. Sci Rep 2023; 13:10531. [PMID: 37386017 PMCID: PMC10310736 DOI: 10.1038/s41598-023-37352-1] [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: 02/10/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Clinical interpretation of copy number variants (CNVs) is a complex process that requires skilled clinical professionals. General recommendations have been recently released to guide the CNV interpretation based on predefined criteria to uniform the decision process. Several semiautomatic computational methods have been proposed to recommend appropriate choices, relieving clinicians of tedious searching in vast genomic databases. We have developed and evaluated such a tool called MarCNV and tested it on CNV records collected from the ClinVar database. Alternatively, the emerging machine learning-based tools, such as the recently published ISV (Interpretation of Structural Variants), showed promising ways of even fully automated predictions using broader characterization of affected genomic elements. Such tools utilize features additional to ACMG criteria, thus providing supporting evidence and the potential to improve CNV classification. Since both approaches contribute to evaluation of CNVs clinical impact, we propose a combined solution in the form of a decision support tool based on automated ACMG guidelines (MarCNV) supplemented by a machine learning-based pathogenicity prediction (ISV) for the classification of CNVs. We provide evidence that such a combined approach is able to reduce the number of uncertain classifications and reveal potentially incorrect classifications using automated guidelines. CNV interpretation using MarCNV, ISV, and combined approach is available for non-commercial use at https://predict.genovisio.com/ .
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Affiliation(s)
- Tomáš Sládeček
- Geneton Ltd., Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | - Michaela Gažiová
- Geneton Ltd., Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Marcel Kucharík
- Geneton Ltd., Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | - Andrea Zaťková
- Geneton Ltd., Bratislava, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Pös
- Geneton Ltd., Bratislava, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ondrej Pös
- Geneton Ltd., Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | - Werner Krampl
- Geneton Ltd., Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | | | - Michaela Hýblová
- Medirex Group Academy NPO, Nitra, Slovakia
- Trisomy Ltd., Nitra, Slovakia
| | - Gabriel Minárik
- Medirex Group Academy NPO, Nitra, Slovakia
- Trisomy Ltd., Nitra, Slovakia
| | - Ján Radvánszky
- Geneton Ltd., Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jaroslav Budiš
- Geneton Ltd., Bratislava, Slovakia.
- Comenius University Science Park, Bratislava, Slovakia.
- Slovak Center of Scientific and Technical Information, Bratislava, Slovakia.
| | - Tomáš Szemes
- Geneton Ltd., Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
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23
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Farag CM, Johnston EK, Antar RM, Issa SG, Gadiwalla Q, Tariq Z, Kim SA, Whalen MJ. Unveiling the genomic landscape of possible metastatic malignant transformation of teratoma secondary to cisplatin-chemotherapy: a Tempus gene analysis-based case report literature review. Front Oncol 2023; 13:1192843. [PMID: 37427132 PMCID: PMC10324607 DOI: 10.3389/fonc.2023.1192843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
In this case report, we describe a patient who developed metastatic liver cancer of unknown primary origin one year following the surgical removal of a retroperitoneal adenocarcinoma. The retroperitoneal adenocarcinoma is considered a malignant transformation of teratoma (MTT), given the patient's distant history of testicular tumor excised 25 years prior and treated with chemotherapy. Despite no primary tumor being identified, the leading primary hypothesis is that the liver metastasis stemmed from the resected retroperitoneal adenocarcinoma from one year prior. We theorize that the patient's cisplatin-based chemotherapy 25 years ago may have triggered the MTT, as documented in the existing literature. Using TEMPUS gene testing on both the retroperitoneal adenocarcinoma and the recently discovered liver metastasis, we identified several genes with variants of unknown significance (VUS) that could potentially be linked to cisplatin chemotherapy resistance. While we cannot conclude that this patient definitively underwent MTT, it remains the most plausible explanation. Future research should investigate both the validity of the genes we have uncovered with respect to cisplatin resistance, as well as other genes associated with cisplatin resistance to further understand the pathogenesis of cisplatin resistance for better prediction of treatment response. As the world of medicine shifts towards individualized therapies and precision medicine, reporting and analyzing genetic mutations derived from tumors remains imperative. Our case report aims to contribute to the growing database of defined mutations and underscores the immense potential of genetic analysis in directing personalized treatment options.
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Affiliation(s)
- Christian M. Farag
- Department of Medicine, George Washington University School of Medicine, Washington, DC, United States
| | - Elena K. Johnston
- Department of Medicine, George Washington University School of Medicine, Washington, DC, United States
| | - Ryan M. Antar
- Department of Urology, George Washington University School of Medicine, Washington, DC, United States
| | - Shaher G. Issa
- Department of Medicine, George Washington University School of Medicine, Washington, DC, United States
| | - Qasim Gadiwalla
- Department of Surgery, George Washington University School of Medicine, Washington, DC, United States
| | - Zoon Tariq
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Sun A. Kim
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Michael J. Whalen
- Department of Urology, George Washington University School of Medicine, Washington, DC, United States
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24
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Lesmann H, Klinkhammer H, M. Krawitz PDMDPP. The future role of facial image analysis in ACMG classification guidelines. MED GENET-BERLIN 2023; 35:115-121. [PMID: 38840866 PMCID: PMC10842539 DOI: 10.1515/medgen-2023-2014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The use of next-generation sequencing (NGS) has dramatically improved the diagnosis of rare diseases. However, the analysis of genomic data has become complex with the increasing detection of variants by exome and genome sequencing. The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) developed a 5-tier classification scheme in 2015 for variant interpretation, that has since been widely adopted. Despite efforts to minimise discrepancies in the application of these criteria, inconsistencies still occur. Further specifications for individual genes were developed by Variant Curation Expert Panels (VCEPs) of the Clinical Genome Resource (ClinGen) consortium, that also take into consideration gene or disease specific features. For instance, in disorders with a highly characerstic facial gestalt a "phenotypic match" (PP4) has higher pathogenic evidence than e.g. in a non-syndromic form of intellectual disability. With computational approaches for quantifying the similarity of dysmorphic features results of such analysis can now be used in a refined Bayesian framework for the ACMG/AMP criteria.
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Affiliation(s)
- Hellen Lesmann
- University of Bonn, Medical Faculty & University Hospital BonnInstitute of Human GeneticsVenusberg-Campus 153127BonnGermany
| | - Hannah Klinkhammer
- University of BonnInstitute for Genomic Statistics and BioinformaticsBonnGermany
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25
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Ritch EJ, Herberts C, Warner EW, Ng SWS, Kwan EM, Bacon JVW, Bernales CQ, Schönlau E, Fonseca NM, Giri VN, Maurice-Dror C, Vandekerkhove G, Jones SJM, Chi KN, Wyatt AW. A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes. NPJ Precis Oncol 2023; 7:27. [PMID: 36914848 PMCID: PMC10011564 DOI: 10.1038/s41698-023-00366-z] [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: 11/12/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Specific classes of DNA damage repair (DDR) defect can drive sensitivity to emerging therapies for metastatic prostate cancer. However, biomarker approaches based on DDR gene sequencing do not accurately predict DDR deficiency or treatment benefit. Somatic alteration signatures may identify DDR deficiency but historically require whole-genome sequencing of tumour tissue. We assembled whole-exome sequencing data for 155 high ctDNA fraction plasma cell-free DNA and matched leukocyte DNA samples from patients with metastatic prostate or bladder cancer. Labels for DDR gene alterations were established using deep targeted sequencing. Per sample mutation and copy number features were used to train XGBoost ensemble models. Naive somatic features and trinucleotide signatures were associated with specific DDR gene alterations but insufficient to resolve each class. Conversely, XGBoost-derived models showed strong performance including an area under the curve of 0.99, 0.99 and 1.00 for identifying BRCA2, CDK12, and mismatch repair deficiency in metastatic prostate cancer. Our machine learning approach re-classified several samples exhibiting genomic features inconsistent with original labels, identified a metastatic bladder cancer sample with a homozygous BRCA2 copy loss, and outperformed an existing exome-based classifier for BRCA2 deficiency. We present DARC Sign (DnA Repair Classification SIGNatures); a public machine learning tool leveraging clinically-practical liquid biopsy specimens for simultaneously identifying multiple types of metastatic prostate cancer DDR deficiencies. We posit that it will be useful for understanding differential responses to DDR-directed therapies in ongoing clinical trials and may ultimately enable prospective identification of prostate cancers with phenotypic evidence of DDR deficiency.
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Affiliation(s)
- Elie J Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Evan W Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jack V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elena Schönlau
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Veda N Giri
- Yale School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada. .,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
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26
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Mendelian inheritance revisited: dominance and recessiveness in medical genetics. Nat Rev Genet 2023:10.1038/s41576-023-00574-0. [PMID: 36806206 DOI: 10.1038/s41576-023-00574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/22/2023]
Abstract
Understanding the consequences of genotype for phenotype (which ranges from molecule-level effects to whole-organism traits) is at the core of genetic diagnostics in medicine. Many measures of the deleteriousness of individual alleles exist, but these have limitations for predicting the clinical consequences. Various mechanisms can protect the organism from the adverse effects of functional variants, especially when the variant is paired with a wild type allele. Understanding why some alleles are harmful in the heterozygous state - representing dominant inheritance - but others only with the biallelic presence of pathogenic variants - representing recessive inheritance - is particularly important when faced with the deluge of rare genetic alterations identified by high throughput DNA sequencing. Both awareness of the specific quantitative and/or qualitative effects of individual variants and the elucidation of allelic and non-allelic interactions are essential to optimize genetic diagnosis and counselling.
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27
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Costain G, Andrade DM. Third-generation computational approaches for genetic variant interpretation. Brain 2023; 146:411-412. [PMID: 36691296 DOI: 10.1093/brain/awad011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 01/25/2023] Open
Abstract
This scientific commentary refers to ‘Delineation of functionally essential protein regions for 242 neurodevelopmental genes’ by Iqbal et al. (https://doi.org/10.1093/brain/awac381).
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Affiliation(s)
- Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, and Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada.,Departments of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Danielle M Andrade
- Adult Genetic Epilepsy (AGE) Program, Toronto Western Hospital, Krembil Brain Institute, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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28
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De Pasquale L, Meo P, Fulia F, Anania A, Meli V, Mondello A, Raimondo MT, Tulino V, Coletta MS, Cacace C. A fatal case of neonatal onset multiple acyl-CoA dehydrogenase deficiency caused by novel mutation of ETFDH gene: case report. Ital J Pediatr 2022; 48:164. [PMID: 36064718 PMCID: PMC9446717 DOI: 10.1186/s13052-022-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple acyl-CoA dehydrogenase deficiency (MADD) or glutaric aciduria type II is an extremely rare autosomal recessive inborn error of fatty acid beta oxidation and branched-chain amino acids, secondary to mutations in the genes encoding the electron transfer flavoproteins A and B (ETFs; ETFA or ETFB) or ETF dehydrogenase (ETFDH). The clinical manifestation of MADD are heterogeneous, from severe neonatal forms to mild late-onset forms. CASE PRESENTATION We report the case of a preterm newborn who died a few days after birth for a severe picture of untreatable metabolic acidosis. The diagnosis of neonatal onset MADD was suggested on the basis of clinical features displaying congenital abnormalities and confirmed by the results of expanded newborn screening, which arrived the day the newborn died. Molecular genetic test revealed a homozygous indel variant c.606 + 1 _606 + 2insT in the ETFDH gene, localized in a canonical splite site. This variant, segregated from the two heterozygous parents, is not present in the general population frequency database and has never been reported in the literature. DISCUSSION AND CONCLUSION Recently introduced Expanded Newborn Screening is very important for a timely diagnosis of Inherited Metabolic Disorders like MADD. In some cases which are the most severe, diagnosis may arrive after symptoms are already present or may be the neonate already died. This stress the importance of collecting all possible samples to give parents a proper diagnosis and a genetic counselling for future pregnacies.
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Affiliation(s)
- Loredana De Pasquale
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy.
| | - Petronilla Meo
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Francesco Fulia
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Antonio Anania
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Valerio Meli
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Antonina Mondello
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Maria Tindara Raimondo
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Viviana Tulino
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Maria Sole Coletta
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Caterina Cacace
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
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Bouzinier MA, Etin D, Trifonov SI, Evdokimova VN, Ulitin V, Shen J, Kokorev A, Ghazani AA, Chekaluk Y, Albertyn Z, Giersch A, Morton CC, Abraamyan F, Bendapudi PK, Sunyaev S, Undiagnosed Diseases Network, Brigham Genomic Medicine, SEQuencing A Baby For An Optimal Outcome, Quantori, Krier JB. AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease. J Biomed Inform 2022; 133:104174. [PMID: 35998814 DOI: 10.1016/j.jbi.2022.104174] [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: 10/27/2021] [Revised: 07/23/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases pose challenges for reproducible and traceable automated genetic diagnostics tools. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.
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Affiliation(s)
- M A Bouzinier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - D Etin
- Forome Association, Boston, MA, USA; Oracle Corporation, USA.
| | | | - V N Evdokimova
- Forome Association, Boston, MA, USA; SBCS Scientific Biomedical Consulting Services, London, UK
| | - V Ulitin
- Forome Association, Boston, MA, USA
| | - J Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Kokorev
- ITMO University, St. Petersburg, Russian Federation
| | - A A Ghazani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Brigham Genomic Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Y Chekaluk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Albertyn
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Giersch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - C C Morton
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Manchester Centre for Audiology and Deafness (ManCAD), School of Health Sciences, University of Manchester, UK
| | - F Abraamyan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - P K Bendapudi
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA, USA; Division of Hematology and Blood Transfusion Service, Massachusetts General Hospital, Boston, MA, USA
| | - S Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - J B Krier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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30
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Masson E, Zou WB, Génin E, Cooper DN, Le Gac G, Fichou Y, Pu N, Rebours V, Férec C, Liao Z, Chen JM. Expanding ACMG variant classification guidelines into a general framework. Hum Genomics 2022; 16:31. [PMID: 35974416 PMCID: PMC9380380 DOI: 10.1186/s40246-022-00407-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)-recommended five variant classification categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign) have been widely used in medical genetics. However, these guidelines are fundamentally constrained in practice owing to their focus upon Mendelian disease genes and their dichotomous classification of variants as being either causal or not. Herein, we attempt to expand the ACMG guidelines into a general variant classification framework that takes into account not only the continuum of clinical phenotypes, but also the continuum of the variants' genetic effects, and the different pathological roles of the implicated genes. MAIN BODY As a disease model, we employed chronic pancreatitis (CP), which manifests clinically as a spectrum from monogenic to multifactorial. Bearing in mind that any general conceptual proposal should be based upon sound data, we focused our analysis on the four most extensively studied CP genes, PRSS1, CFTR, SPINK1 and CTRC. Based upon several cross-gene and cross-variant comparisons, we first assigned the different genes to two distinct categories in terms of disease causation: CP-causing (PRSS1 and SPINK1) and CP-predisposing (CFTR and CTRC). We then employed two new classificatory categories, "predisposing" and "likely predisposing", to replace ACMG's "pathogenic" and "likely pathogenic" categories in the context of CP-predisposing genes, thereby classifying all pathologically relevant variants in these genes as "predisposing". In the case of CP-causing genes, the two new classificatory categories served to extend the five ACMG categories whilst two thresholds (allele frequency and functional) were introduced to discriminate "pathogenic" from "predisposing" variants. CONCLUSION Employing CP as a disease model, we expand ACMG guidelines into a five-category classification system (predisposing, likely predisposing, uncertain significance, likely benign, and benign) and a seven-category classification system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, and benign) in the context of disease-predisposing and disease-causing genes, respectively. Taken together, the two systems constitute a general variant classification framework that, in principle, should span the entire spectrum of variants in any disease-related gene. The maximal compliance of our five-category and seven-category classification systems with the ACMG guidelines ought to facilitate their practical application.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Na Pu
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Department of Critical Care Medicine, Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Vinciane Rebours
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, Assistance Publique-Hôpitaux de Paris, Clichy, Université de Paris, Paris, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.
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31
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Mroczek M, Inashkina I, Stavusis J, Zayakin P, Khrunin A, Micule I, Kenina V, Zdanovica A, Zídková J, Fajkusová L, Limborska S, van der Kooi AJ, Brusse E, Leonardis L, Maver A, Pajusalu S, Õunap K, Puusepp S, Dobosz P, Sypniewski M, Burnyte B, Lace B. CAPN3 c.1746-20C>G variant is hypomorphic for LGMD R1 calpain 3-related. Hum Mutat 2022; 43:1347-1353. [PMID: 35731190 DOI: 10.1002/humu.24421] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]
Abstract
The investigated intronic CAPN3 variant NM_000070.3:c.1746-20C>G occurs in the Central and Eastern Europe with a frequency of >1% and there are conflicting interpretations on its pathogenicity. We collected data on 14 patients carrying the CAPN3 c.1746-20C>G variant in trans position with another CAPN3 pathogenic/likely pathogenic variant. The patients compound heterozygous for the CAPN3 c.1746-20C>G variant presented a phenotype consistent with calpainopathy of mild/medium severity. This variant is most frequent in the North/West regions of Russia and may originate from that area. Molecular studies revealed that different splicing isoforms are produced in the muscle. We hypothesize that c.1746-20C>G is a hypomorphic variant with a reduction of RNA and protein expression and only individuals having a higher ratio of abnormal isoforms are affected. Reclassification of the CAPN3 variant c.1746-20C>G from variant with a conflicting interpretation of pathogenicity to hypomorphic variant explains many unidentified cases of limb girdle muscular dystrophy R1 calpain 3-related in Eastern and Central Europe.
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Affiliation(s)
- Magdalena Mroczek
- Department of Neurology and Neurophysiology, Balgrist University Hospital, University of Zurich, Zürich, Switzerland
| | | | | | | | - Andrey Khrunin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ieva Micule
- Biomedical Research and Study Center, Riga, Latvia
| | - Victorija Kenina
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia.,Rare Disease Center, Riga East Clinical University Hospital, Riga, Latvia
| | | | - Jana Zídková
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology And Genetics, University Hospital, Brno, Czech Republic
| | - Svetlana Limborska
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Anneke J van der Kooi
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lea Leonardis
- Department of Neurology, University Medical Centre Ljubljana, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sanna Puusepp
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Paula Dobosz
- MNM Diagnostics Sp. z o.o., Poznań, Poland.,Department of Hematology, Transplantation and Internal Medicine, University Clinical Center of the Medical University of Warsaw, Warsaw, Poland.,Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | | | - Birute Burnyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Baiba Lace
- Biomedical Research and Study Center, Riga, Latvia.,Medical Genetics Clinic, Children's Clinical University Hospital, Riga, Latvia
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32
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Lyon E, Temple-Smolkin RL, Hegde M, Gastier-Foster JM, Palomaki GE, Richards CS. An Educational Assessment of Evidence Used for Variant Classification: A Report of the Association for Molecular Pathology. J Mol Diagn 2022; 24:555-565. [PMID: 35429647 DOI: 10.1016/j.jmoldx.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
The Association for Molecular Pathology Variant Interpretation Testing Among Laboratories (VITAL) Working Group convened to evaluate the Standards and Guidelines for the Interpretation of Sequence Variants implementation into clinical practice, identify problematic classification rules, and define implementation challenges. Variants and associated clinical information were provided to volunteer respondents. Participant variant classifications were compared with intended consensus-derived classifications of the Working Group. The 24 variant challenges received 1379 responses; 1119 agreed with the intended response (81%; 95% CI, 79% to 83%). Agreement ranged from 44% to 100%, with 16 challenges (67%; 47% to 82%) reaching consensus (≥80% agreement). Participant classifications were also compared to a calculated interpretation of the ACMG Guidelines using the participant-reported criteria as input. The 24 variant challenges had 1368 responses with specific evidence provided and 1121 (82%; 80% to 84%) agreed with the calculated interpretation. Agreement for challenges ranged from 63% to 98%; 15 (63%; 43% to 79%) reaching consensus. Among 81 individual participants, 32 (40%; 30% to 50%) reached agreement with at least 80% of the intended classifications and 42 (52%; 41% to 62%) with the calculated classifications. This study demonstrated that although variant classification remains challenging, published guidelines are being utilized and adapted to improve variant calling consensus. This study identified situations where clarifications are warranted and provides a model for competency assessment.
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Affiliation(s)
- Elaine Lyon
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Madhuri Hegde
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Global Genetics Laboratory, PerkinElmer Genomics, Pittsburgh, Pennsylvania
| | - Julie M Gastier-Foster
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Departments of Pediatrics and Pathology/Immunology, Baylor College of Medicine, Houston, Texas; Pathology Department, Texas Children's Hospital, Houston, Texas; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Glenn E Palomaki
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, Rhode Island
| | - C Sue Richards
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Molecular and Medical Genetics and Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon.
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33
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Kaczmarek AT, Bender D, Gehling T, Kohl JB, Daimagüler HS, Santamaria-Araujo JA, Liebau MC, Koy A, Cirak S, Schwarz G. A defect in molybdenum cofactor binding causes an attenuated form of sulfite oxidase deficiency. J Inherit Metab Dis 2022; 45:169-182. [PMID: 34741542 DOI: 10.1002/jimd.12454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Isolated sulfite oxidase deficiency (ISOD) is a rare recessive and infantile lethal metabolic disorder, which is caused by functional loss of sulfite oxidase (SO) due to mutations of the SUOX gene. SO is a mitochondrially localized molybdenum cofactor (Moco)- and heme-dependent enzyme, which catalyzes the vital oxidation of toxic sulfite to sulfate. Accumulation of sulfite and sulfite-related metabolites such as S-sulfocysteine (SSC) are drivers of severe neurodegeneration leading to early childhood death in the majority of ISOD patients. Full functionality of SO is dependent on correct insertion of the heme cofactor and Moco, which is controlled by a highly orchestrated maturation process. This maturation involves the translation in the cytosol, import into the intermembrane space (IMS) of mitochondria, cleavage of the mitochondrial targeting sequence, and insertion of both cofactors. Moco insertion has proven as the crucial step in this maturation process, which enables the correct folding of the homodimer and traps SO in the IMS. Here, we report on a novel ISOD patient presented at 17 months of age carrying the homozygous mutation NM_001032386.2 (SUOX):c.1097G > A, which results in the expression of SO variant R366H. Our studies show that histidine substitution of Arg366, which is involved in coordination of the Moco-phosphate, causes a severe reduction in Moco insertion efficacy in vitro and in vivo. Expression of R366H in HEK SUOX-/- cells mimics the phenotype of patient's fibroblasts, representing a loss of SO expression and specific activity. Our studies disclose a general paradigm for a kinetic defect in Moco insertion into SO caused by residues involved in Moco coordination resulting in the case of R366H in an attenuated form of ISOD.
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Affiliation(s)
- Alexander Tobias Kaczmarek
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Daniel Bender
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Department of Pediatric Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Titus Gehling
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Joshua Benedict Kohl
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Hülya-Sevcan Daimagüler
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | | | - Max Christoph Liebau
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Anne Koy
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Sebahattin Cirak
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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34
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An all-encompassing variant classification system proposed. Eur J Hum Genet 2022; 30:139. [PMID: 34716404 PMCID: PMC8821586 DOI: 10.1038/s41431-021-00992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/17/2021] [Indexed: 02/03/2023] Open
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35
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A new system for variant classification? Eur J Hum Genet 2022; 30:137-138. [PMID: 35132196 PMCID: PMC8821601 DOI: 10.1038/s41431-021-01032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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36
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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37
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Cristofoli F, Sorrentino E, Guerri G, Miotto R, Romanelli R, Zulian A, Cecchin S, Paolacci S, Miertus J, Bertelli M, Maltese PE, Chiurazzi P, Stuppia L, Castori M, Marceddu G. Variant Selection and Interpretation: An Example of Modified VarSome Classifier of ACMG Guidelines in the Diagnostic Setting. Genes (Basel) 2021; 12:1885. [PMID: 34946832 PMCID: PMC8700904 DOI: 10.3390/genes12121885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
Variant interpretation is challenging as it involves combining different levels of evidence in order to evaluate the role of a specific variant in the context of a patient's disease. Many in-depth refinements followed the original 2015 American College of Medical Genetics (ACMG) guidelines to overcome subjective interpretation of criteria and classification inconsistencies. Here, we developed an ACMG-based classifier that retrieves information for variant interpretation from the VarSome Stable-API environment and allows molecular geneticists involved in clinical reporting to introduce the necessary changes to criterion strength and to add or exclude criteria assigned automatically, ultimately leading to the final variant classification. We also developed a modified ACMG checklist to assist molecular geneticists in adjusting criterion strength and in adding literature-retrieved or patient-specific information, when available. The proposed classifier is an example of integration of automation and human expertise in variant curation, while maintaining the laboratory analytical workflow and the established bioinformatics pipeline.
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Affiliation(s)
- Francesca Cristofoli
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
| | - Elisa Sorrentino
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
| | - Giulia Guerri
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Roberta Miotto
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
| | - Roberta Romanelli
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Alessandra Zulian
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Stefano Cecchin
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Stefano Paolacci
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Jan Miertus
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Matteo Bertelli
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Paolo Enrico Maltese
- Diagnostics Unit, MAGI’S LAB, 38068 Rovereto, Italy; (G.G.); (R.R.); (A.Z.); (S.C.); (P.E.M.)
| | - Pietro Chiurazzi
- Section of Genomic Medicine, Department of Life Science and Public Health, “Sacro Cuore” Catholic University, 00168 Rome, Italy;
- Policlinic University Foundation “A. Gemelli” IRCCS, UOC Medical Genetics, 00168 Rome, Italy
| | - Liborio Stuppia
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, “G. D’Annunzio” University, Chieti-Pescara, 66100 Chieti, Italy;
| | - Marco Castori
- Division of Medical Genetics, IRCCS Foundation “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy;
| | - Giuseppe Marceddu
- Diagnostics Unit, MAGI EUREGIO, 39100 Bolzano, Italy; (F.C.); (E.S.); (R.M.); (J.M.); (M.B.); (G.M.)
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