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Vuocolo B, German RJ, Lalani SR, Murali CN, Bacino CA, Baskin S, Littlejohn R, Odom JD, McLean S, Schmid C, Nutter M, Stuebben M, Magness E, Juarez O, El Achi D, Mitchell B, Glinton KE, Robak L, Nagamani SCS, Saba L, Ritenour A, Zhang L, Streff H, Chan K, Kemere KJ, Carter K, Owen N, Vossaert L, Liu P, Bellen H, Wangler MF. Improving access to exome sequencing in a medically underserved population through the Texome Project. Genet Med 2024; 26:101102. [PMID: 38431799 PMCID: PMC11161315 DOI: 10.1016/j.gim.2024.101102] [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: 09/26/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Genomic medicine can end diagnostic odysseys for patients with complex phenotypes; however, limitations in insurance coverage and other systemic barriers preclude individuals from accessing comprehensive genetics evaluation and testing. METHODS The Texome Project is a 4-year study that reduces barriers to genomic testing for individuals from underserved and underrepresented populations. Participants with undiagnosed, rare diseases who have financial barriers to obtaining exome sequencing (ES) clinically are enrolled in the Texome Project. RESULTS We highlight the Texome Project process and describe the outcomes of the first 60 ES results for study participants. Participants received a genetic evaluation, ES, and return of results at no cost. We summarize the psychosocial or medical implications of these genetic diagnoses. Thus far, ES provided molecular diagnoses for 18 out of 60 (30%) of Texome participants. Plus, in 11 out of 60 (18%) participants, a partial or probable diagnosis was identified. Overall, 5 participants had a change in medical management. CONCLUSION To date, the Texome Project has recruited a racially, ethnically, and socioeconomically diverse cohort. The diagnostic rate and medical impact in this cohort support the need for expanded access to genetic testing and services. The Texome Project will continue reducing barriers to genomic care throughout the future study years.
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Affiliation(s)
- Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Stephanie Baskin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | | | - John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Scott McLean
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Carrie Schmid
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Morgan Nutter
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Melissa Stuebben
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Emily Magness
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Olivia Juarez
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Dina El Achi
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Bailey Mitchell
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Lisa Saba
- Texas Children's Hospital Department of Pathology, Houston, TX
| | - Adasia Ritenour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lilei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Katie Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - K Jordan Kemere
- Department of Internal Medicine, Section Transition Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Kent Carter
- Department of Pediatrics, University of Texas Rio Grande Valley, Harlingen, TX
| | | | | | | | - Hugo Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.
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Xu Z, Sadleir L, Goel H, Jiao X, Niu Y, Zhou Z, de Valles-Ibáñez G, Poke G, Hildebrand M, Lieffering N, Qin J, Yang Z. Genotype and phenotype correlation of PHACTR1-related neurological disorders. J Med Genet 2024; 61:536-542. [PMID: 38272663 DOI: 10.1136/jmg-2023-109638] [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: 09/14/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND PHACTR1 (phosphatase and actin regulators) plays a key role in cortical migration and synaptic activity by binding and regulating G-actin and PPP1CA. This study aimed to expand the genotype and phenotype of patients with de novo variants in PHACTR1 and analyse the impact of variants on protein-protein interaction. METHODS We identified seven patients with PHACTR1 variants by trio-based whole-exome sequencing. Additional two subjects were ascertained from two centres through GeneMatcher. The genotype-phenotype correlation was determined, and AlphaFold-Multimer was used to predict protein-protein interactions and interfaces. RESULTS Eight individuals carried missense variants and one had CNV in the PHACTR1. Infantile epileptic spasms syndrome (IESS) was the unifying phenotype in eight patients with missense variants of PHACTR1. They could present with other types of seizures and often exhibit drug-resistant epilepsy with a poor prognosis. One patient with CNV displayed a developmental encephalopathy phenotype. Using AlphaFold-Multimer, our findings indicate that PHACTR1 and G-actin-binding sequences overlap with PPP1CA at the RPEL3 domain, which suggests possible competition between PPP1CA and G-actin for binding to PHACTR1 through a similar polymerisation interface. In addition, patients carrying missense variants located at the PHACTR1-PPP1CA or PHACTR1-G-actin interfaces consistently exhibit the IESS phenotype. These missense variants are mostly concentrated in the overlapping sequence (RPEL3 domain). CONCLUSIONS Patients with variants in PHACTR1 can have a phenotype of developmental encephalopathy in addition to IESS. Moreover, our study confirmed that the variants affect the binding of PHACTR1 to G-actin or PPP1CA, resulting in neurological disorders in patients.
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Affiliation(s)
- Zhao Xu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, Australia
| | - Xianru Jiao
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zongpu Zhou
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Guillem de Valles-Ibáñez
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Gemma Poke
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Michael Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Victoria, Australia
- Neuroscience Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, South Brisbane, Queensland, Australia
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
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3
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Hramyka D, Sczakiel HL, Zhao MX, Stolpe O, Nieminen M, Adam R, Danyel M, Einicke L, Hägerling R, Knaus A, Mundlos S, Schwartzmann S, Seelow D, Ehmke N, Mensah MA, Boschann F, Beule D, Holtgrewe M. REEV: review, evaluate and explain variants. Nucleic Acids Res 2024:gkae366. [PMID: 38769069 DOI: 10.1093/nar/gkae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/07/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platform for clinicians and researchers in the field of rare disease genetics. Supporting data was aggregated from public data sources. We compared REEV with seven other tools for clinical variant evaluation. REEV (semi-)automatically fills individual ACMG criteria facilitating variant interpretation. REEV can store disease and phenotype data related to a case to use these for phenotype similarity measures. Users can create public permanent links for individual variants that can be saved as browser bookmarks and shared. REEV may help in the fast diagnostic assessment of genetic variants in a clinical as well as in a research context. REEV (https://reev.bihealth.org/) is free and open to all users and there is no login requirement.
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Affiliation(s)
- Dzmitry Hramyka
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Xiaohang Zhao
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Stolpe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Mikko Nieminen
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health , BIH Center for Regenerative Therapies, Berlin, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Martin Atta Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
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4
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Brock DC, Wang M, Hussain HMJ, Rauch DE, Marra M, Pennesi ME, Yang P, Everett L, Ajlan RS, Colbert J, Porto FBO, Matynia A, Gorin MB, Koenekoop RK, Lopez I, Sui R, Zou G, Li Y, Chen R. Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. Hum Mol Genet 2024; 33:945-957. [PMID: 38453143 PMCID: PMC11102593 DOI: 10.1093/hmg/ddae028] [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: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.
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Affiliation(s)
- Daniel C Brock
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Hafiz Muhammad Jafar Hussain
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - David E Rauch
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Lesley Everett
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 515 SW Campus Drive, Portland, OR 97239, United States
| | - Radwan S Ajlan
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Jason Colbert
- Department of Ophthalmology, University of Kansas School of Medicine, 3901 Rainbow Blvd, Kansas City, KS 66160, United States
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Rua dos Otoni, 735/507 - Santa Efigênia, Belo Horizonte, MG 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Av. Francisco Sales, 1111 - Santa Efigênia, Belo Horizonte, MG 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, R. Santa Catarina, 941 - Lourdes, Belo Horizonte, MG 30180070, Brazil
| | - Anna Matynia
- College of Optometry, University of Houston, 4401 Martin Luther King Boulevard, Houston, TX 77004, United States
| | - Michael B Gorin
- Jules Stein Eye Institute, University of California Los Angeles, 100 Stein Plaza, Los Angeles, CA 90095, United States
- Department of Ophthalmology, University of California Los Angeles David Geffen School of Medicine, 10833 Le Conte Ave, Los Angeles, CA 90095, United States
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, 5252 Boul de Maisonneuve ouest, Montreal, QC H4A 3S5, Canada
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, WC67+HW Dongcheng, Beijing 100005, China
| | - Gang Zou
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, F4RJ+43 Xixia District, Yinchuan, Ningxia, China
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
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Makhamreh MM, Shivashankar K, Araji S, Critchlow E, O'Brien BM, Wodoslawsky S, Berger SI, Al-Kouatly HB. RASopathies are the most common set of monogenic syndromes identified by exome sequencing for nonimmune hydrops fetalis: A systematic review and meta-analysis. Am J Med Genet A 2024; 194:e63494. [PMID: 38156365 DOI: 10.1002/ajmg.a.63494] [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: 02/19/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
RASopathies are a group of malformation syndromes known to lead to nonimmune hydrops fetalis (NIHF) in severe presentations. Pathogenic variants can be de novo or parentally inherited. Despite being a known frequent presentation, the fraction of monogenic NIHF cases due to RASopathies is limited in the literature. Also, the specific parental contribution of RASopathies to NIHF is not well described. Our objective was to review pooled exome sequencing (ES) diagnostic yield of RASopathies for NIHF and to determine the parental contribution of RASopathy to NIHF. We performed a systematic review of prenatal ES studies from January 1, 2000 to August 1, 2022. Thirty-six studies met inclusion criteria. Cases with RASopathy gene variants were reviewed. NIHF cases were further classified as isolated or non-isolated. Thirty-six ES studies including 46 pregnancies with NIHF and a diagnosed RASopathy were reviewed. Forty-four diagnostic variants and 2 variants of uncertain significance in 12 RASopathy genes were identified. Expanding on what was previously published, a total of 506 NIHF cases were extracted with 191 cases yielding a positive diagnosis by ES. The overall rate of RASopathy diagnosis in clinically diagnosed NIHF cases was 9% (44/506). The rate of RASopathy diagnosis among NIHF cases with positive genetic diagnosis by ES was 23% (44/191). Of the 46 cases identified, 13 (28%) variants were parentally inherited; specifically, 5/13 (38%) maternal, 3/13 (23%) paternal, 2/13 (15%) biparental, and 3/13 (23%) unspecified. Majority of NIHF cases 29/46 (63%) were isolated. Among NIHF cases with positive ES diagnoses, RASopathy diagnostic yield by ES was 23%. NIHF secondary to RASopathies was parentally inherited in 28% of cases. Most cases of NIHF due to RASopathy were isolated, with no prenatal detection of associated anomalies.
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Affiliation(s)
- Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Sarah Araji
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Mississippi, Jackson, Mississippi, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Barbara M O'Brien
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research and Rare Disease Institute, Children's National Medical Center, Washington, DC, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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6
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Morren MA, Fodstad H, Brems H, Bedoni N, Guenova E, Jacot-Guillarmod M, Busiah K, Giuliano F, Gilliet M, Atallah I. Mosaic RASopathies concept: different skin lesions, same systemic manifestations? J Med Genet 2024; 61:411-419. [PMID: 38290824 DOI: 10.1136/jmg-2023-109306] [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: 04/01/2023] [Accepted: 12/30/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND Cutaneous epidermal nevi are genotypically diverse mosaic disorders. Pathogenic hotspot variants in HRAS, KRAS, and less frequently, NRAS and BRAF may cause isolated keratinocytic epidermal nevi and sebaceous nevi or several different syndromes when associated with extracutaneous anomalies. Therefore, some authors suggest the concept of mosaic RASopathies to group these different disorders. METHODS In this paper, we describe three new cases of syndromic epidermal nevi caused by mosaic HRAS variants: one associating an extensive keratinocytic epidermal nevus with hypomastia, another with extensive mucosal involvement and a third combining a small sebaceous nevus with seizures and intellectual deficiency. Moreover, we performed extensive literature of all cases of syndromic epidermal nevi and related disorders with confirmed pathogenic postzygotic variants in HRAS, KRAS, NRAS or BRAF. RESULTS Most patients presented with bone, ophthalmological or neurological anomalies. Rhabdomyosarcoma, urothelial cell carcinoma and pubertas praecox are also repeatedly reported. KRAS pathogenic variants are involved in 50% of the cases, especially in sebaceous nevi, oculoectodermal syndrome and encephalocraniocutaneous lipomatosis. They are frequently associated with eye and brain anomalies. Pathogenic variants in HRAS are rather present in syndromic keratinocytic epidermal nevi and phacomatosis pigmentokeratotica. CONCLUSION This review delineates genotype/phenotype correlations of syndromic epidermal nevi with somatic RAS and BRAF pathogenic variants and may help improve their follow-up.
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Affiliation(s)
- Marie-Anne Morren
- Pediatric Dermatology Unit, Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Heidi Fodstad
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Hilde Brems
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Emmanuella Guenova
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Martine Jacot-Guillarmod
- Pediatric Gynecology Unit, Department of Mother-Woman-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kanetee Busiah
- Pediatric Endocrinology, Diabetology, and Obesity Unit, Department of Mother-Woman-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Michel Gilliet
- Dermatology and Venereology Department, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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7
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Caillot C, Saurin JC, Hervieu V, Faoucher M, Reversat J, Decullier E, Poncet G, Bailly S, Giraud S, Dupuis-Girod S. Phenotypic characterisation of SMAD4 variant carriers. J Med Genet 2024:jmg-2023-109632. [PMID: 38575304 DOI: 10.1136/jmg-2023-109632] [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: 09/13/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Both hereditary haemorrhagic telangiectasia (HHT) and juvenile polyposis syndrome (JPS) are known to be caused by SMAD4 pathogenic variants, with overlapping symptoms for both disorders in some patients. Additional connective tissue disorders have also been reported. Here, we describe carriers of SMAD4 variants followed in an HHT reference centre to further delineate the phenotype. METHODS Observational study based on data collected from the Clinical Investigation for the Rendu-Osler Cohort database. RESULTS Thirty-three participants from 15 families, out of 1114 patients with HHT, had an SMAD4 variant (3%).Regarding HHT, 26 out of 33 participants (88%) had a definite clinical diagnosis based on Curaçao criteria. Complication frequencies were as follows: epistaxis (n=27/33, 82%), cutaneous telangiectases (n=19/33, 58%), pulmonary arteriovenous malformations (n=17/32, 53%), hepatic arteriovenous malformations (AVMs) (n=7/18, 39%), digestive angiodysplasia (n=13/22, 59%). No cerebral AVMs were diagnosed.Regarding juvenile polyposis, 25 out of 31 participants (81%) met the criteria defined by Jass et al for juvenile polyposis syndrome. Seven patients (21%) had a prophylactic gastrectomy due to an extensive gastric polyposis incompatible with endoscopic follow-up, and four patients (13%) developed a digestive cancer.Regarding connective tissue disorders, 20 (61%) had at least one symptom, and 4 (15%) participants who underwent echocardiography had an aortic dilation. CONCLUSION We describe a large cohort of SMAD4 variant carriers in the context of HHT. Digestive complications are frequent, early and diffuse, justifying endoscopy every 2 years. The HHT phenotype, associating pulmonary and hepatic AVMs, warrants systematic screening. Connective tissue disorders broaden the phenotype associated with SMAD4 gene variants and justify systematic cardiac ultrasound and skeletal complications screening.
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Affiliation(s)
- Claire Caillot
- Service de Génétique et Centre de référence pour la maladie de Rendu-Osler, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, Bron, France
| | - Jean-Christophe Saurin
- Service de Gastroenterologie, Hôpital E. Herriot, Hospices Civils de Lyon, Lyon, France
- Pôle Santé Publique, Hospices Civils de Lyon, Lyon, France
| | - Valérie Hervieu
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Marie Faoucher
- Service de génétique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Julie Reversat
- Service de génétique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Evelyne Decullier
- Pôle Santé Publique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Gilles Poncet
- Université Claude Bernard Lyon 1, Villeurbanne, France
- Service de Chirurgie Digestive, Hôpital E. Herriot Lyon, Hospices Civils de Lyon, Lyon, France
| | - Sabine Bailly
- Biosanté Lab, Unit U1292, Health Department of IRIG, CEA de Grenoble, Grenoble, France
| | - Sophie Giraud
- Service de génétique, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Sophie Dupuis-Girod
- Service de Génétique et Centre de référence pour la maladie de Rendu-Osler, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, Bron, France
- Biosanté Lab, Unit U1292, Health Department of IRIG, CEA de Grenoble, Grenoble, France
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8
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Cook S, Dunn E, Kornish J, Calderwood L, Campion M, Cusmano-Ozog KP, Tise CG. Molecular testing in newborn screening: VUS burden among true positives and secondary reproductive limitations via expanded carrier screening panels. Genet Med 2024; 26:101055. [PMID: 38146699 DOI: 10.1016/j.gim.2023.101055] [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: 06/23/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023] Open
Abstract
PURPOSE Expanded carrier screening (ECS) gene panels have several limitations, including variable content, current knowledge of disease-causing variants, and differing reporting policies. This study evaluated if the disease-associated variants identified in affected neonates who screened positive by California newborn screening (NBS) for an inherited metabolic disorder (IMD) by tandem mass spectrometry (MS/MS) would likely be reported by ECS gene panels. METHODS Retrospective review of neonates referred by the California Department of Public Health for a positive NBS by multianalyte MS/MS from January 1, 2020 through June 30, 2021. RESULTS One hundred thirty-six neonates screened positive for ≥1 NBS MS/MS indication. Nineteen neonates (14%) were ultimately diagnosed with an IMD, all of whom had abnormal biochemical testing. Eighteen of the 19 underwent molecular testing; 10 (56%) neonates had ≥1 variants of uncertain significance, 9 of whom were of non-White ancestry. ECS panels would have been negative for 56% (20/36) of parents with an affected neonate, 85% (17/20) of whom were of non-White ancestry. CONCLUSION The number of variants of uncertain significance identified in this cohort highlights the need for more diversified variant databases. Due in part to the lack of diversity in currently sequenced populations, genomic sequencing cannot replace biochemical testing for the diagnosis of an IMD.
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Affiliation(s)
- Sabina Cook
- Masters Program in Human Genetics and Genetic Counseling, Stanford University, Stanford, CA
| | - Emily Dunn
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA.
| | | | - Laurel Calderwood
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA; Lucile Packard Children's Hospital, Stanford, CA
| | - MaryAnn Campion
- Masters Program in Human Genetics and Genetic Counseling, Stanford University, Stanford, CA
| | | | - Christina G Tise
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA
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9
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Laulhé M, Kuhn E, Bouligand J, Amazit L, Perrot J, Lebigot E, Kamenickỷ P, Lombès M, Fagart J, Viengchareun S, Martinerie L. A novel mutation in the NR3C1 gene associated with reversible glucocorticoid resistance. Eur J Endocrinol 2024; 190:284-295. [PMID: 38584335 DOI: 10.1093/ejendo/lvae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVE Glucocorticoid resistance is a rare endocrine disease caused by variants of the NR3C1 gene encoding the glucocorticoid receptor (GR). We identified a novel heterozygous variant (GRR569Q) in a patient with uncommon reversible glucocorticoid resistance syndrome. METHODS We performed ex vivo functional characterization of the variant in patient fibroblasts and in vitro through transient transfection in undifferentiated HEK 293T cells to assess transcriptional activity, affinity, and nuclear translocation. We studied the impact of the variant on the tertiary structure of the ligand-binding domain through 3D modeling. RESULTS The patient presented initially with an adrenal adenoma with mild autonomous cortisol secretion and undetectable adrenocorticotropin hormone (ACTH) levels. Six months after surgery, biological investigations showed elevated cortisol and ACTH (urinary free cortisol 114 µg/24 h, ACTH 10.9 pmol/L) without clinical symptoms, evoking glucocorticoid resistance syndrome. Functional characterization of the GRR569Q showed decreased expression of target genes (in response to 100 nM cortisol: SGK1 control +97% vs patient +20%, P < .0001) and impaired nuclear translocation in patient fibroblasts compared to control. Similar observations were made in transiently transfected cells, but higher cortisol concentrations overcame glucocorticoid resistance. GRR569Q showed lower ligand affinity (Kd GRWT: 1.73 nM vs GRR569Q: 4.61 nM). Tertiary structure modeling suggested a loss of hydrogen bonds between H3 and the H1-H3 loop. CONCLUSION This is the first description of a reversible glucocorticoid resistance syndrome with effective negative feedback on corticotroph cells regarding increased plasma cortisol concentrations due to the development of mild autonomous cortisol secretion.
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Affiliation(s)
- Margaux Laulhé
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
| | - Emmanuelle Kuhn
- Unité Hypophyse, Hôpital Pitié-Salpêtrière, AP-HP, Paris 75013, France
| | - Jérôme Bouligand
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpital Bicêtre APHP Paris Saclay, Le Kremlin Bicêtre 94270, France
| | - Larbi Amazit
- UMS 44/Institut Biomédical du Val de Bièvre, Université Paris-Saclay, Le Kremlin Bicêtre 94276, France
| | - Julie Perrot
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
| | - Elise Lebigot
- Service de Biochimie, Hôpital Bicêtre APHP Paris Saclay, Le Kremlin Bicêtre 94270, France
| | - Peter Kamenickỷ
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
- Service d'Endocrinologie et des Maladies de la Reproduction, Hôpital Bicêtre APHP Paris Saclay, Le Kremlin-Bicêtre 94270, France
| | - Marc Lombès
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
| | - Jérôme Fagart
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Say Viengchareun
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
| | - Laetitia Martinerie
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, 94276 Le Kremlin-Bicêtre, France
- Endocrinologie Pédiatrique, Centre de Référence Maladies Endocriniennes Rares de la Croissance et du Développement, Hôpital Universitaire Robert-Debré APHP Nord, Paris 75019, France
- Faculté de Santé, Université Paris Cité, UFR de Médecine, Paris 75006, France
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10
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Jurgens JA, Barry BJ, Chan WM, MacKinnon S, Whitman MC, Matos Ruiz PM, Pratt BM, England EM, Pais L, Lemire G, Groopman E, Glaze C, Russell KA, Singer-Berk M, Di Gioia SA, Lee AS, Andrews C, Shaaban S, Wirth MM, Bekele S, Toffoloni M, Bradford VR, Foster EE, Berube L, Rivera-Quiles C, Mensching FM, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Wilson MW, Weisburd B, Lek M, Brand H, Talkowski ME, MacArthur DG, O’Donnell-Luria A, Robson CD, Hunter DG, Engle EC. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304594. [PMID: 38585811 PMCID: PMC10996726 DOI: 10.1101/2024.03.22.24304594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Purpose To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs). Methods We coupled phenotyping with exome or genome sequencing of 467 pedigrees with genetically unsolved oCCDDs, integrating analyses of pedigrees, human and animal model phenotypes, and de novo variants to identify rare candidate single nucleotide variants, insertion/deletions, and structural variants disrupting protein-coding regions. Prioritized variants were classified for pathogenicity and evaluated for genotype/phenotype correlations. Results Analyses elucidated phenotypic subgroups, identified pathogenic/likely pathogenic variant(s) in 43/467 probands (9.2%), and prioritized variants of uncertain significance in 70/467 additional probands (15.0%). These included known and novel variants in established oCCDD genes, genes associated with syndromes that sometimes include oCCDDs (e.g., MYH10, KIF21B, TGFBR2, TUBB6), genes that fit the syndromic component of the phenotype but had no prior oCCDD association (e.g., CDK13, TGFB2), genes with no reported association with oCCDDs or the syndromic phenotypes (e.g., TUBA4A, KIF5C, CTNNA1, KLB, FGF21), and genes associated with oCCDD phenocopies that had resulted in misdiagnoses. Conclusion This study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies.
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Affiliation(s)
- Julie A. Jurgens
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brenda J. Barry
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Mary C. Whitman
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | | | - Brandon M. Pratt
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Eleina M. England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carmen Glaze
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn A. Russell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA
| | - Arthur S. Lee
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline Andrews
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Megan M. Wirth
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Sarah Bekele
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Melissa Toffoloni
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | - Emma E. Foster
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Lindsay Berube
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack M. Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E. Talkowski
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline D. Robson
- Division of Neuroradiology, Department of Radiology, Boston Children’s Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - David G. Hunter
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth C. Engle
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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11
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Hall HN, Parry D, Halachev M, Williamson KA, Donnelly K, Campos Parada J, Bhatia S, Joseph J, Holden S, Prescott TE, Bitoun P, Kirk EP, Newbury-Ecob R, Lachlan K, Bernar J, van Heyningen V, FitzPatrick DR, Meynert A. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia. J Med Genet 2024; 61:250-261. [PMID: 38050128 DOI: 10.1136/jmg-2023-109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. METHODS Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. RESULTS Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. CONCLUSION Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
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Affiliation(s)
- Hildegard Nikki Hall
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - David Parry
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Illumina United Kingdom, Edinburgh, UK
| | - Mihail Halachev
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kathleen A Williamson
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kevin Donnelly
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jose Campos Parada
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Shipra Bhatia
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jeffrey Joseph
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
| | - Simon Holden
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Trine E Prescott
- Department of Medical Genetics, Telemark Hospital, Skien, Norway
| | - Pierre Bitoun
- Consultations de Génétique médicale, Service de Pédiatrie, CHU Paris-Nord, Hôpital Jean Verdier, Bondy, France
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Katherine Lachlan
- University Hospital Southampton, NHS Foundation Trust Wessex Clinical Genetics Service, Southampton, UK
| | - Juan Bernar
- Department of Genetics, Hospital Ruber Internacional, Madrid, Spain
| | - Veronica van Heyningen
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
- Institute of Ophthalmology, University College London, London, UK
| | - David R FitzPatrick
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Alison Meynert
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
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12
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Singh S, Pezeshkpoor B, Jamil MA, Dodt J, Sharma A, Ramar V, Ivaskevicius V, Hethershaw E, Philippou H, Pavlova A, Oldenburg J, Biswas A. Heterozygosity in factor XIII genes and the manifestation of mild inherited factor XIII deficiency. J Thromb Haemost 2024; 22:379-393. [PMID: 37832789 DOI: 10.1016/j.jtha.2023.09.032] [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: 06/02/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND The characterization of inherited mild factor XIII deficiency is more imprecise than its rare, inherited severe forms. It is known that heterozygosity at FXIII genetic loci results in mild FXIII deficiency, characterized by circulating FXIII activity levels ranging from 20% to 60%. There exists a gap in information on 1) how genetic heterozygosity renders clinical bleeding manifestations among these individuals and 2) the reversal of unexplained bleeding upon FXIII administration in mild FXIII-deficient individuals. OBJECTIVES To assess the prevalence and burden of mild FXIII deficiency among the apparently healthy German-Caucasian population and correlate it with genetic heterozygosity at FXIII and fibrinogen gene loci. METHODS Peripheral blood was collected from 752 donors selected from the general population with essentially no bleeding complications to ensure asymptomatic predisposition. These were assessed for FXIII and fibrinogen activity, and FXIII and fibrinogen genes were resequenced using next-generation sequencing. For comparison, a retrospective analysis was performed on a cohort of mild inherited FXIII deficiency patients referred to us. RESULTS The prevalence of mild FXIII deficiency was high (∼0.8%) among the screened German-Caucasian population compared with its rare-severe forms. Although no new heterozygous missense variants were found, certain combinations were relatively dominant/prevalent among the mild FXIII-deficient individuals. CONCLUSION This extensive, population-based quasi-experimental approach revealed that the burden of heterozygosity in FXIII and fibrinogen gene loci causes the clinical manifestation of inherited mild FXIII deficiency, resulting in ''unexplained bleeding'' upon provocation.
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Affiliation(s)
- Sneha Singh
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Behnaz Pezeshkpoor
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Muhammad Ahmer Jamil
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | | | - Amit Sharma
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Vasanth Ramar
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Vytautas Ivaskevicius
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Emma Hethershaw
- Division of Cardiovascular and Diabetes Research, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Helen Philippou
- Division of Cardiovascular and Diabetes Research, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Anna Pavlova
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Johannes Oldenburg
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany
| | - Arijit Biswas
- Institute for Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, North-Rheine Westfalen, Germany.
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Singer A, Aartsma-Rus A, Grinshpun-Cohen J, Sagi-Dain L. Lessons learned from the first national population-based genetic carrier-screening program for Duchenne muscular dystrophy. Genet Med 2023; 25:100981. [PMID: 37712502 DOI: 10.1016/j.gim.2023.100981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
PURPOSE To summarize the results of first year implementation of pan-ethnic screening testing for Duchenne muscular dystrophy (DMD) and present the ensuing challenges. METHODS Data acquisition for this study was performed by retrospective search of Ministry of Health registry for reports of all laboratories performing genetic screening tests. DMD testing was performed by multiplex ligation-dependent probe amplification technology. In case of single-exon deletion, sequencing of the specific exon was performed to rule out underlying single-nucleotide variant. RESULTS Of overall 85,737 DMD tests, 82 clinically significant findings were noted (0.095%, or 1:1,046 women). In addition, 80 findings with uncertain clinical significance were detected (0.093%, or 1:1072), as well as 373 cases (0.4%, or 1:230) of single-exon deletions subsequently identified as false positives because of underlying single-nucleotide variant, mostly variants in exon 8 in North African Jewish population, and in exon 48 in Arab Muslim population. CONCLUSION Interpretation of population-based DMD carrier screening is complex, occasionally requiring additional genetic testing methods and ethical considerations. Multicenter data registry, including ethnic origin and familial segregation in selected cases, is crucial for optimal definition of the results during genetic counseling and informed decisions regarding prenatal testing.
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Affiliation(s)
- Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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14
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Militello AM, Orsi G, Cavaliere A, Niger M, Avallone A, Salvatore L, Tortora G, Rapposelli IG, Giordano G, Noventa S, Giommoni E, Bozzarelli S, Macchini M, Peretti U, Procaccio L, Puccini A, Cascinu S, Montagna C, Milella M, Reni M. Clinical outcomes and response to chemotherapy in a cohort of pancreatic cancer patients with germline variants of unknown significance (VUS) in BRCA1 and BRCA2 genes. Cancer Chemother Pharmacol 2023; 92:501-510. [PMID: 37725113 DOI: 10.1007/s00280-023-04585-w] [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: 02/05/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE The clinical outcome and the efficacy of chemotherapy in pancreatic cancer patients with BRCA1/2 Variants of Unknown Significance (VUS) is unknown. We explored the effects of chemotherapy with or without Platinum in non metastatic and metastatic pancreatic cancer patients with BRCA1/2 VUS. METHODS A retrospective analysis of non-metastatic or metastatic pancreatic cancer patients with gBRCA1/2 VUS treated in 13 Italian centers between November 2015 and December 2020 was performed. All patients were assessed for toxicity and RECIST 1.1 response. Metastatic patients were evaluated for survival outcome. RESULTS 30 pancreatic cancer patients with gBRCA1/2 VUS were considered: 20 were M+ and 10 were non-M+. Pl-CT was recommended to 16 patients: 10 M+ (6 FOLFIRINOX and 4 PAXG) and 6 non-M+ (3 FOLFIRINOX and 3 PAXG); 11 patients received Nabpaclitaxel-Gemcitabine (AG; 8 M+) and 3 patients (2 M+) were treated with Gemcitabine (G). The RECIST 1.1 response rate was 27% for AG and 44% for Pl-CT (22% for (m) FOLFIRINOX and 71% PAXG). 1 year Progression-Free Survival was 37.5% for patients treated with AG and 33% in the Pl-CT subgroup. Median Overall Survival (OS) was 23.5 months for patients treated with AG and 14 months for the Pl-CT subgroup. 1 Year and 2 Year OS were numerically better for AG (1 Year OS: 75% vs 60% and 2 Year OS: 50% and 20% in AG and Pl-CT subgroups, respectively) as well. CONCLUSIONS Pl-CT does not seem to be associated with a better outcome compared to AG chemotherapy in PDAC patients with BRCA 1/2 VUS.
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Affiliation(s)
- Anna Maria Militello
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Orsi
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Cavaliere
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO - IRCCS Candiolo, Candiolo, Italy
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Dei Tumori Di Milano, Milan, Italy
| | - Antonio Avallone
- Biologia Cellulare e Bioterapie, Istituto Nazionale per lo Studio e la Cura dei Tumori ''Fondazione Giovanni Pascale'' - IRCCS, Naples, Italy
| | - Lisa Salvatore
- Unit of Medical Oncology, Comprehensive Cancer Center, Fondazione Policlinico Universitario, Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giampaolo Tortora
- Unit of Medical Oncology, Comprehensive Cancer Center, Fondazione Policlinico Universitario, Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ilario Giovanni Rapposelli
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) ''Dino Amadori'', Meldola, Italy
| | - Guido Giordano
- Unit of Medical Oncology and Biomolecular Therapy, Policlinico Riuniti, Foggia, Italy
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Silvia Noventa
- Department of Medical Oncology, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Elisa Giommoni
- Medical Oncology Division, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Silvia Bozzarelli
- Department of Medical Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Marina Macchini
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Umberto Peretti
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Letizia Procaccio
- Medical Oncology 1 Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Alberto Puccini
- University of Genoa, Ospedale Policlinico San Martino IRCCS, Genoa, Italy
| | - Stefano Cascinu
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Montagna
- Department of Radiation Oncology and Genomic Instability and Cancer Genetics, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Michele Milella
- Section of Oncology, Department of Medicine, University of Verona School of Medicine and Verona University Hospital Trust, Verona, Italy
| | - Michele Reni
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Vita-Salute University, Via Olgettina 60, 20123, Milan, Italy.
- Pancreas Translational & Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy.
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15
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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2023:10.1007/s12020-023-03581-7. [PMID: 37940764 DOI: 10.1007/s12020-023-03581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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16
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van Vliet K, Dijkstra AM, Bouva MJ, van der Krogt J, Bijsterveld K, van der Sluijs F, de Sain-van der Velden MG, Koop K, Rossi A, Thomas JA, Patera CA, Kiewiet MBG, Waters PJ, Cyr D, Boelen A, van Spronsen FJ, Heiner-Fokkema MR. Maleic acid is a biomarker for maleylacetoacetate isomerase deficiency; implications for newborn screening of tyrosinemia type 1. J Inherit Metab Dis 2023; 46:1104-1113. [PMID: 37545091 DOI: 10.1002/jimd.12669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Dried blood spot succinylacetone (SA) is often used as a biomarker for newborn screening (NBS) for tyrosinemia type 1 (TT1). However, false-positive SA results are often observed. Elevated SA may also be due to maleylacetoacetate isomerase deficiency (MAAI-D), which appears to be clinically insignificant. This study investigated whether urine organic acid (uOA) and quantitative urine maleic acid (Q-uMA) analyses can distinguish between TT1 and MAAI-D. We reevaluated/measured uOA (GC-MS) and/or Q-uMA (LC-MS/MS) in available urine samples of nine referred newborns (2 TT1, 7 false-positive), eight genetically confirmed MAAI-D children, and 66 controls. Maleic acid was elevated in uOA of 5/7 false-positive newborns and in the three available samples of confirmed MAAI-D children, but not in TT1 patients. Q-uMA ranged from not detectable to 1.16 mmol/mol creatinine in controls (n = 66) and from 0.95 to 192.06 mmol/mol creatinine in false-positive newborns and MAAI-D children (n = 10). MAAI-D was genetically confirmed in 4/7 false-positive newborns, all with elevated Q-uMA, and rejected in the two newborns with normal Q-uMA. No sample was available for genetic analysis of the last false-positive infant with elevated Q-uMA. Our study shows that MAAI-D is a recognizable cause of false-positive TT1 NBS results. Elevated urine maleic acid excretion seems highly effective in discriminating MAAI-D from TT1.
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Affiliation(s)
- K van Vliet
- Section of Metabolic Diseases, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - A M Dijkstra
- Section of Metabolic Diseases, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M J Bouva
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J van der Krogt
- Laboratory of Metabolic diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - K Bijsterveld
- Laboratory of Metabolic diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - F van der Sluijs
- Laboratory of Metabolic diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M G de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - K Koop
- Department of Pediatrics, section Metabolic Diseases, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - A Rossi
- Department of Translational Medicine, Section of Pediatrics, University of Naples "Federico II", Italy
| | - J A Thomas
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - C A Patera
- Department of Genetics and Metabolism, Shodair Children's Hospital, Helena, Montana, USA
| | - M B G Kiewiet
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - P J Waters
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - D Cyr
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - A Boelen
- Endocrine Laboratory, Department of Laboratory Medicine, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - F J van Spronsen
- Section of Metabolic Diseases, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M R Heiner-Fokkema
- Laboratory of Metabolic diseases, Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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17
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Wang N, Khan S, Elo LL. VarSCAT: A computational tool for sequence context annotations of genomic variants. PLoS Comput Biol 2023; 19:e1010727. [PMID: 37566612 PMCID: PMC10446208 DOI: 10.1371/journal.pcbi.1010727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/23/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
The sequence contexts of genomic variants play important roles in understanding biological significances of variants and potential sequencing related variant calling issues. However, methods for assessing the diverse sequence contexts of genomic variants such as tandem repeats and unambiguous annotations have been limited. Herein, we describe the Variant Sequence Context Annotation Tool (VarSCAT) for annotating the sequence contexts of genomic variants, including breakpoint ambiguities, flanking bases of variants, wildtype/mutated DNA sequences, variant nomenclatures, distances between adjacent variants, tandem repeat regions, and custom annotation with user customizable options. Our analyses demonstrate that VarSCAT is more versatile and customizable than the currently available methods or strategies for annotating variants in short tandem repeat (STR) regions or insertions and deletions (indels) with breakpoint ambiguity. Variant sequence context annotations of high-confidence human variant sets with VarSCAT revealed that more than 75% of all human individual germline and clinically relevant indels have breakpoint ambiguities. Moreover, we illustrate that more than 80% of human individual germline small variants in STR regions are indels and that the sizes of these indels correlated with STR motif sizes. VarSCAT is available from https://github.com/elolab/VarSCAT.
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Affiliation(s)
- Ning Wang
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Sofia Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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18
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Rashid S, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Genet Med 2023; 25:100884. [PMID: 37161864 PMCID: PMC10524927 DOI: 10.1016/j.gim.2023.100884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains below 50%, suggesting that clinically relevant variants may be missed by standard analyses. Here, we analyze "poison exons" (PEs), which are evolutionarily conserved alternative exons often absent from standard gene annotations. Variants that alter PE inclusion can lead to loss of function and may be highly penetrant contributors to disease. METHODS We curated published RNA sequencing data from developing mouse cortex to define 1937 conserved PE regions potentially relevant to NDDs, and we analyzed variants found by genome sequencing in multiple NDD cohorts. RESULTS Across 2999 probands, we found 6 novel clinically relevant variants in PE regions. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family (SCN1A, SCN2A, and SCN8A), which is associated with epilepsies. One variant is in SNRPB, associated with cerebrocostomandibular syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and in genes with gene-phenotype associations consistent with each probands reported features. CONCLUSION With a very minimal increase in variant analysis burden (average of 0.77 variants per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | | | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | | | | | | | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | | | | | | | | | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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19
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Tafazoli A, Mikros J, Khaghani F, Alimardani M, Rafigh M, Hemmati M, Siamoglou S, Golińska AK, Kamiński KA, Niemira M, Miltyk W, Patrinos GP. Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics. Hum Genomics 2023; 17:62. [PMID: 37452347 PMCID: PMC10347842 DOI: 10.1186/s40246-023-00508-1] [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: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have tested novel deep computational analysis in addition to artificial intelligence as possible approaches for functional analysis of unknown markers within less studied drug-related genes. METHODS Pharmacovariants from 1800 drug-related genes from 100 WES data files underwent (a) deep computational analysis by eight bioinformatic algorithms (overall containing 23 tools) and (b) random forest (RF) classifier as the machine learning (ML) approach separately. ML model efficiency was calculated by internal and external cross-validation during recursive feature elimination. Protein modelling was also performed for predicted highly damaging variants with lower frequencies. Genotype-phenotype correlations were implemented for top selected variants in terms of highest possibility of being damaging. RESULTS Five deleterious pharmacovariants in the RYR1, POLG, ANXA11, CCNH, and CDH23 genes identified in step (a) and subsequent analysis displayed high impact on drug-related phenotypes. Also, the utilization of recursive feature elimination achieved a subset of 175 malfunction pharmacovariants in 135 drug-related genes that were used by the RF model with fivefold internal cross-validation, resulting in an area under the curve of 0.9736842 with an average accuracy of 0.9818 (95% CI: 0.89, 0.99) on predicting whether a carrying individuals will develop adverse drug reactions or not. However, the external cross-validation of the same model indicated a possible false positive result when dealing with a low number of observations, as only 60 important variants in 49 genes were displayed, giving an AUC of 0.5384848 with an average accuracy of 0.9512 (95% CI: 0.83, 0.99). CONCLUSION While there are some technologies for functionally assess not-interpreted pharmacovariants, there is still an essential need for the development of tools, methods, and algorithms which are able to provide a functional prediction for every single pharmacovariant in both large-scale datasets and small cohorts. Our approaches may bring new insights for choosing the right computational assessment algorithms out of high throughput DNA sequencing data from small cohorts to be used for personalized drug therapy implementation.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - John Mikros
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Faeze Khaghani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Rafigh
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Hemmati
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | - Karol A Kamiński
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Białystok, Poland
- Department of Cardiology, Medical University of Bialystok, Białystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland.
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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20
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Zukin E, Culver JO, Liu Y, Yang Y, Ricker CN, Hodan R, Sturgeon D, Kingham K, Chun NM, Rowe-Teeter C, Singh K, Zell JA, Ladabaum U, McDonnell KJ, Ford JM, Parmigiani G, Braun D, Kurian AW, Gruber SB, Idos GE. Clinical implications of conflicting variant interpretations in the cancer genetics clinic. Genet Med 2023; 25:100837. [PMID: 37057674 PMCID: PMC10416421 DOI: 10.1016/j.gim.2023.100837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE The aim of this study was to describe the clinical impact of commercial laboratories issuing conflicting classifications of genetic variants. METHODS Results from 2000 patients undergoing a multigene hereditary cancer panel by a single laboratory were analyzed. Clinically significant discrepancies between the laboratory-provided test reports and other major commercial laboratories were identified, including differences between pathogenic/likely pathogenic and variant of uncertain significance (VUS) classifications, via review of ClinVar archives. For patients carrying a VUS, clinical documentation was assessed for evidence of provider awareness of the conflict. RESULTS Fifty of 975 (5.1%) patients with non-negative results carried a variant with a clinically significant conflict, 19 with a pathogenic/likely pathogenic variant reported in APC or MUTYH, and 31 with a VUS reported in CDKN2A, CHEK2, MLH1, MSH2, MUTYH, RAD51C, or TP53. Only 10 of 28 (36%) patients with a VUS with a clinically significant conflict had a documented discussion by a provider about the conflict. Discrepant counseling strategies were used for different patients with the same variant. Among patients with a CDKN2A variant or a monoallelic MUTYH variant, providers were significantly more likely to make recommendations based on the laboratory-reported classification. CONCLUSION Our findings highlight the frequency of variant interpretation discrepancies and importance of clinician awareness. Guidance is needed on managing patients with discrepant variants to support accurate risk assessment.
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Affiliation(s)
- Elyssa Zukin
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA; University of California, Irvine, Irvine, CA
| | - Julie O Culver
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Yuxi Liu
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yunqi Yang
- Dana-Farber Cancer Institute, Boston, MA
| | - Charité N Ricker
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Rachel Hodan
- Stanford University School of Medicine, Stanford, CA
| | - Duveen Sturgeon
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Kerry Kingham
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Uri Ladabaum
- Stanford University School of Medicine, Stanford, CA
| | - Kevin J McDonnell
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - James M Ford
- Stanford University School of Medicine, Stanford, CA
| | - Giovanni Parmigiani
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Danielle Braun
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Stephen B Gruber
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Gregory E Idos
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA.
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21
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Angwin C, Zschocke J, Kammin T, Björck E, Bowen J, Brady AF, Burns H, Cummings C, Gardner R, Ghali N, Gröbner R, Harris J, Higgins M, Johnson D, Lepperdinger U, Milnes D, Pope FM, Sehra R, Kapferer-Seebacher I, Sobey G, Van Dijk FS. Non-oral manifestations in adults with a clinical and molecularly confirmed diagnosis of periodontal Ehlers-Danlos syndrome. Front Genet 2023; 14:1136339. [PMID: 37323685 PMCID: PMC10264792 DOI: 10.3389/fgene.2023.1136339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/03/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Periodontal Ehlers-Danlos Syndrome (pEDS) is a rare autosomal dominant type of EDS characterised by severe early-onset periodontitis, lack of attached gingiva, pretibial plaques, joint hypermobility and skin hyperextensibility as per the 2017 International EDS Classification. In 2016, deleterious pathogenic heterozygous variants were identified in C1R and C1S, which encode components of the complement system. Materials and Methods: Individuals with a clinical suspicion of pEDS were clinically and molecularly assessed through the National EDS Service in London and Sheffield and in genetic services in Austria, Sweden and Australia. Transmission electron microscopy and fibroblast studies were performed in a small subset of patients. Results: A total of 21 adults from 12 families were clinically and molecularly diagnosed with pEDS, with C1R variants in all families. The age at molecular diagnosis ranged from 21-73 years (mean 45 years), male: female ratio 5:16. Features of easy bruising (90%), pretibial plaques (81%), skin fragility (71%), joint hypermobility (24%) and vocal changes (38%) were identified as well as leukodystrophy in 89% of those imaged. Discussion: This cohort highlights the clinical features of pEDS in adults and contributes several important additional clinical features as well as novel deleterious variants to current knowledge. Hypothetical pathogenic mechanisms which may help to progress understanding and management of pEDS are also discussed.
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Affiliation(s)
- C. Angwin
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, United Kingdom
| | - J. Zschocke
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - T. Kammin
- National EDS Diagnostic Service, Sheffield Children’s NHS Foundation Trust, Sheffield, United Kingdom
| | - E. Björck
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - J. Bowen
- National EDS Diagnostic Service, Sheffield Children’s NHS Foundation Trust, Sheffield, United Kingdom
| | - A. F. Brady
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, United Kingdom
| | - H. Burns
- Department Otolaryngology Head and Neck Surgery, Children’s Health QLD, Brisbane, QLD, Australia
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - C. Cummings
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
| | - R. Gardner
- Clinical Genetics, Genetic Health Queensland, Brisbane, QLD, Australia
| | - N. Ghali
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, United Kingdom
| | - R. Gröbner
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - J. Harris
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
| | - M. Higgins
- Clinical Genetics, Genetic Health Queensland, Brisbane, QLD, Australia
| | - D. Johnson
- National EDS Diagnostic Service, Sheffield Children’s NHS Foundation Trust, Sheffield, United Kingdom
| | - U. Lepperdinger
- Department of Operative and Restorative Dentistry, Medical University of Innsbruck, Innsbruck, Austria
| | - D. Milnes
- Clinical Genetics, Genetic Health Queensland, Brisbane, QLD, Australia
| | - F. M. Pope
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
- Department of Dermatology, Chelsea and Westminster Hospital NHS Foundation Trust, London, United Kingdom
| | - R. Sehra
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
| | - I. Kapferer-Seebacher
- Department of Operative and Restorative Dentistry, Medical University of Innsbruck, Innsbruck, Austria
| | - G. Sobey
- National EDS Diagnostic Service, Sheffield Children’s NHS Foundation Trust, Sheffield, United Kingdom
| | - F. S. Van Dijk
- National EDS Service, London North West University Healthcare NHS Trust, London, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, United Kingdom
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22
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Mazzarotto F, Argirò A, Zampieri M, Magri C, Giotti I, Boschi B, Frusconi S, Gennarelli M, Buxbaum J, Polimanti R, Olivotto I, Perfetto F, Cappelli F. Investigation on the high recurrence of the ATTRv-causing transthyretin variant Val142Ile in central Italy. Eur J Hum Genet 2023; 31:541-547. [PMID: 36380086 PMCID: PMC10172197 DOI: 10.1038/s41431-022-01235-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
The p.Val142Ile variant in transthyretin (encoded by the TTR gene) is the most common genetic cause of transthyretin-related amyloidosis. This allele is particularly prevalent in communities ofAfrican descent compared with populations of different ancestries, where its frequency is two orders of magnitude lower. For this reason, p.Val142Ile has always been considered an "African" variant, with limited studies performed on individuals of European descent. However, recent reports of higher-than-expected prevalence in European-ancestry populations question the African specificity of this allele. Here we show that the high recurrence of p.Val142Ile in central Italy is due to a founder effect and not to recent admixture from African populations, highlighting how this may be the case in other communities. This suggests a probable underestimate of the global prevalence of p.Val142Ile, and further emphasizes the importance of routine inclusion of TTR in gene panels used for clinical genetic testing in hypertrophic cardiomyopathy (independently of the patient's geographical origin), that transthyretin-related amyloidosis can mimic.
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Affiliation(s)
- Francesco Mazzarotto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Alessia Argirò
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Mattia Zampieri
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Irene Giotti
- Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | | | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Joel Buxbaum
- The Scripps Research Institute, La Jolla, CA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Iacopo Olivotto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Federico Perfetto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Tuscan Regional Amyloidosis Centre, Careggi University Hospital, Florence, Italy
| | - Francesco Cappelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Tuscan Regional Amyloidosis Centre, Careggi University Hospital, Florence, Italy
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23
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Owusu-Ansah M, Guptan N, Alindogan D, Morizono M, Caldovic L. NAGS, CPS1, and SLC25A13 (Citrin) at the Crossroads of Arginine and Pyrimidines Metabolism in Tumor Cells. Int J Mol Sci 2023; 24:ijms24076754. [PMID: 37047726 PMCID: PMC10094985 DOI: 10.3390/ijms24076754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 (CPS1) and SLC25A13 (citrin) genes has been associated with faster proliferation of tumor cells due to metabolic reprogramming that increases the activity of the CAD complex and pyrimidine biosynthesis. N-acetylglutamate (NAG), produced by NAG synthase (NAGS), is an essential activator of CPS1. Although NAGS is expressed in lung cancer derived cell lines, expression of the NAGS gene and its product was not evaluated in tumors with aberrant expression of CPS1 and citrin. We used data mining approaches to identify tumor types that exhibit aberrant overexpression of NAGS, CPS1, and citrin genes, and evaluated factors that may contribute to increased expression of the three genes and their products in tumors. Median expression of NAGS, CPS1, and citrin mRNA was higher in glioblastoma multiforme (GBM), glioma, and stomach adenocarcinoma (STAD) samples compared to the matched normal tissue. Median expression of CPS1 and citrin mRNA was higher in the lung adenocarcinoma (LUAD) sample while expression of NAGS mRNA did not differ. High NAGS expression was associated with an unfavorable outcome in patients with glioblastoma and GBM. Low NAGS expression was associated with an unfavorable outcome in patients with LUAD. Patterns of DNase hypersensitive sites and histone modifications in the upstream regulatory regions of NAGS, CPS1, and citrin genes were similar in liver tissue, lung tissue, and A549 lung adenocarcinoma cells despite different expression levels of the three genes in the liver and lung. Citrin gene copy numbers correlated with its mRNA expression in glioblastoma, GBM, LUAD, and STAD samples. There was little overlap between NAGS, CPS1, and citrin sequence variants found in patients with respective deficiencies, tumor samples, and individuals without known rare genetic diseases. The correlation between NAGS, CPS1, and citrin mRNA expression in the individual glioblastoma, GBM, LUAD, and STAD samples was very weak. These results suggest that the increased cytoplasmic supply of either carbamylphosphate, produced by CPS1, or aspartate may be sufficient to promote tumorigenesis, as well as the need for an alternative explanation of CPS1 activity in the absence of NAGS expression and NAG.
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Affiliation(s)
- Melissa Owusu-Ansah
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20052, USA
| | - Nikita Guptan
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
| | - Dylon Alindogan
- Columbian College of Arts and Sciences, George Washington University, Washington, DC 20052, USA
| | - Michio Morizono
- School of Mathematics, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ljubica Caldovic
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20052, USA
- Center for Genetic Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010, USA
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24
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Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C. The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis. PNAS NEXUS 2023; 2:pgad043. [PMID: 36909829 PMCID: PMC10003751 DOI: 10.1093/pnasnexus/pgad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of ocular conditions characterized by an elevated genetic and clinical heterogeneity. They are transmitted almost invariantly as monogenic traits. However, with more than 280 disease genes identified so far, association of clinical phenotypes with genotypes can be very challenging, and molecular diagnosis is essential for genetic counseling and correct management of the disease. In addition, the prevalence and the assortment of IRD mutations are often population-specific. In this work, we examined 230 families from Portugal, with individuals suffering from a variety of IRD diagnostic classes (270 subjects in total). Overall, we identified 157 unique mutations (34 previously unreported) in 57 distinct genes, with a diagnostic rate of 76%. The IRD mutational landscape was, to some extent, different from those reported in other European populations, including Spanish cohorts. For instance, the EYS gene appeared to be the most frequently mutated, with a prevalence of 10% among all IRD cases. This was, in part, due to the presence of a recurrent and seemingly founder mutation involving the deletion of exons 13 and 14 of this gene. Moreover, our analysis highlighted that as many as 51% of our cases had mutations in a homozygous state. To our knowledge, this is the first study assessing a cross-sectional genotype-phenotype landscape of IRDs in Portugal. Our data reveal a rather unique distribution of mutations, possibly shaped by a small number of rare ancestral events that have now become prevalent alleles in patients.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, Bern 3010, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Cristina Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal.,iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Liliana P Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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25
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Al-Kouatly HB, Shivashankar K, Mossayebi MH, Makhamreh M, Critchlow E, Gao Z, Fasehun LK, Alkuraya FS, Ryan EE, Hegde M, Wodoslawsky S, Hughes J, Berger SI. Diagnostic yield from prenatal exome sequencing for non-immune hydrops fetalis: A systematic review and meta-analysis. Clin Genet 2023; 103:503-512. [PMID: 36757664 DOI: 10.1111/cge.14309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Non-immune hydrops fetalis (NIHF) has multiple genetic etiologies diagnosable by exome sequencing (ES). We evaluated the yield of prenatal ES for NIHF, and the contribution of additional clinical findings and history. Systematic review was performed with PROSPERO tag 232951 using CINAHL, PubMed, and Ovid MEDLINE from January 1, 2000 through December 1, 2021. Selected studies performed ES to augment standard prenatal diagnostic approaches. Cases meeting a strict NIHF phenotype were tabulated with structured data imputed from papers or requested from authors. Genetic variants and diagnostic outcomes were harmonized across studies using current ACMG and ClinGen variant classification guidelines. Thirty-one studies reporting 445 NIHF cases had a 37% (95% CI: 32%-41%) diagnostic rate. There was no significant difference between isolated NIHF and NIHF with fetal malformations or between recurrent and simplex cases. Diagnostic rate was higher for consanguineous than non-consanguineous cases. Disease categories included RASopathies (24%), neuromuscular (21%), metabolic (17%), lymphatic (13%), other syndromes (9%), cardiovascular (5%), hematologic (2%), skeletal (2%), and other categories (7%). Inheritance patterns included recessive (55%), dominant (41%), and X-linked (4%). ES should be considered in the diagnostic workup of NIHF with and without associated ultrasound findings regardless of history of recurrence or consanguinity.
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Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Matthew H Mossayebi
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Luther-King Fasehun
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Erin E Ryan
- Genomic Data / Genetic Counseling, GeneDx, Gaithersburg, Maryland, USA
| | - Madhuri Hegde
- Global Lab Services, PerkinElmer Genomics, Atlanta, Georgia, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joel Hughes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
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26
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Ulhaq ZS, Nurputra DK, Soraya GV, Kurniawati S, Istifiani LA, Pamungkas SA, Tse WKF. A systematic review on Treacher Collins syndrome: Correlation between molecular genetic findings and clinical severity. Clin Genet 2023; 103:146-155. [PMID: 36203321 DOI: 10.1111/cge.14243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/20/2023]
Abstract
Treacher Collins syndrome (TCS, OMIM: 154500) is a rare congenital craniofacial disorder that is caused by variants in the genes TCOF1, POLR1D, POLR1C, and POLR1B. Studies on the association between phenotypic variability and their relative variants are very limited. This systematic review summarized the 53 literatures from PubMed and Scopus to explore the potential TCS genotype-phenotype correlations with statistical analysis. Studies reporting both complete molecular genetics and clinical data were included. We identified that the molecular anomaly within TCOF1 (88.71%) accounted for most TCS cases. The only true hot spot for TCOF1 was detected in exon 24, with recurrent c.4369_4373delAAGAA variant is identified. While the hot spot for POLR1D, POLR1C, and POLR1B were identified in exons 3, 8, and 15, respectively. Our result suggested that the higher severity level was likely to be observed in Asian patients harboring TCOF1 variants rather than POLR1. Moreover, common 5-bp deletions tended to have a higher severity degree in comparison to any variants within exon 24 of TCOF1. In summary, this report suggested the relationship between genetic and clinical data in TCS. Our findings could be used as a reference for clinical diagnosis and further biological studies.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Pre-clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University, Batu, Indonesia
| | | | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
- Department of Neurology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Siti Kurniawati
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University, Malang, Indonesia
| | - Lola Ayu Istifiani
- Department of Nutrition, Faculty of Medicine, Brawijaya University, Malang, Indonesia
| | | | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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27
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Vihinen M. Systematic errors in annotations of truncations, loss-of-function and synonymous variants. Front Genet 2023; 14:1015017. [PMID: 36713076 PMCID: PMC9880313 DOI: 10.3389/fgene.2023.1015017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.
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28
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523654. [PMID: 36711854 PMCID: PMC9882217 DOI: 10.1101/2023.01.12.523654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Purpose Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains around 50%, suggesting some clinically relevant rare variants may be missed by standard analyses. Here we analyze "poison exons" (PEs) which, while often absent from standard gene annotations, are alternative exons whose inclusion results in a premature termination codon. Variants that alter PE inclusion can lead to loss-of-function and may be highly penetrant contributors to disease. Methods We curated published RNA-seq data from developing mouse cortex to define 1,937 PE regions conserved between humans and mice and potentially relevant to NDDs. We then analyzed variants found by genome sequencing in multiple NDD cohorts. Results Across 2,999 probands, we found six clinically relevant variants in PE regions that were previously overlooked. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family ( SCN1A, SCN2A , and SCN8A ), associated with epilepsies. One variant is in SNRPB , associated with Cerebrocostomandibular Syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and were observed in probands with features consistent with those reported for the associated gene. Conclusion With only a minimal increase in variant analysis burden (most probands had zero or one candidate PE variants in a known NDD gene, with an average of 0.77 per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | - James MJ Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Kevin M Bowling
- Washington University School of Medicine, Saint Louis, MO, USA 63110
| | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA 10467
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Anna CE Hurst
- University of Alabama in Birmingham, Birmingham, AL, USA 35294
| | | | | | - Laura G Hendon
- University of Mississippi Medical Center, Jackson, MS, 39216
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA 35294
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
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29
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Fan S, Zhao T, Sun L. The global prevalence and ethnic heterogeneity of iron-refractory iron deficiency anaemia. Orphanet J Rare Dis 2023; 18:2. [PMID: 36604716 PMCID: PMC9814447 DOI: 10.1186/s13023-022-02612-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Iron-refractory iron deficiency anaemia (IRIDA) is an autosomal recessive iron deficiency anaemia caused by mutations in the TMPRSS6 gene. Iron deficiency anaemia is common, whereas IRIDA is rare. The prevalence of IRIDA is unclear. This study aimed to estimate the carrier frequency and genetic prevalence of IRIDA using Genome Aggregation Database (gnomAD) data. METHODS The pathogenicity of TMPRSS6 variants was interpreted according to the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) standards and guidelines. The minor allele frequency (MAF) of TMPRSS6 gene disease-causing variants in 141,456 unique individuals was examined to estimate the global prevalence of IRIDA in seven ethnicities: African/African American (afr), American Admixed/Latino (amr), Ashkenazi Jewish (asj), East Asian (eas), Finnish (fin), Non-Finnish European (nfe) and South Asian (sas). The global and population-specific carrier frequencies and genetic prevalence of IRIDA were calculated using the Hardy-Weinberg equation. RESULTS In total, 86 pathogenic/likely pathogenic variants (PV/LPV) were identified according to ACMG/AMP guideline. The global carrier frequency and genetic prevalence of IRIDA were 2.02 per thousand and 1.02 per million, respectively. CONCLUSIONS The prevalence of IRIDA is greater than previous estimates.
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Affiliation(s)
- Shanghua Fan
- grid.412632.00000 0004 1758 2270Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060 China
| | - Ting Zhao
- grid.414011.10000 0004 1808 090XDepartment of Neurology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 China
| | - Liu Sun
- Department of Information Technology, School of Mathematics and Information Technology, Yuxi Normal University, Yuxi, 653100, China.
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Kim YG, Ha C, Shin S, Park JH, Jang JH, Kim JW. Enrichment of titin-truncating variants in exon 327 in dilated cardiomyopathy and its relevance to reduced nonsense-mediated mRNA decay efficiency. Front Genet 2023; 13:1087359. [PMID: 36685919 PMCID: PMC9845391 DOI: 10.3389/fgene.2022.1087359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023] Open
Abstract
Titin truncating variants (TTNtvs) are the most common genetic cause of dilated cardiomyopathy (DCM). Among four regions of titin, A-band enrichment of DCM-causing TTNtvs is widely accepted but the underlying mechanism is still unknown. Meanwhile, few reports have identified exon 327 as a highly mutated A-band exon but the degree of exon 327 enrichment has not been quantitatively investigated. To find the real hotspot of DCM-causing TTNtvs, we aimed to reassess the degree of TTNtv enrichment in known titin regions and in exon 327, separately. In addition, we tried to explain exon 327 clustering in terms of nonsense-mediated mRNA decay (NMD) efficiency and a dominant negative mechanism recently proposed. Research papers focusing on TTNtvs found in patients with DCM were collected. A total of 612 patients with TTNtv-realated DCM were obtained from 10 studies. In the four regions of TTN and exon 327, the degree of TTNtvs enrichment was calculated in a way that the effect of distribution of highly expressed exons was normalized. As a result, exon 327 was the only region that showed significant enrichment for DCM-related TTNtv (p < .001). On the other hand, other A-band exons had almost the same number of TTNtv of random distribution. A review of RNAseq data revealed that the median allelic imbalance deviation of exon 327 TTNtvs was .04, indicating almost zero NMD. From these findings, we propose that the widely accepted A-band enrichment of DCM-related TTNtv is mostly attributable to exon 327 enrichment. In addition, based on the recently demonstrated dominant negative mechanism, the extremely low NMD efficiency seems to contribute to exon 327 enrichment.
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Affiliation(s)
- Young-gon Kim
- Samsung Medical Center, Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Changhee Ha
- Samsung Medical Center, Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sunghwan Shin
- Samsung Medical Center, Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong-ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul, South Korea
| | - Ja-Hyun Jang
- Samsung Medical Center, Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong-Won Kim
- Samsung Medical Center, Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, South Korea,Clinical Genomics Center, Samsung Medical Center, Seoul, South Korea,*Correspondence: Jong-Won Kim,
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Vis JK, Santcroos MA, Kosters WA, Laros JFJ. A Boolean algebra for genetic variants. Bioinformatics 2023; 39:6967432. [PMID: 36594541 PMCID: PMC9879725 DOI: 10.1093/bioinformatics/btad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/06/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
MOTIVATION Beyond identifying genetic variants, we introduce a set of Boolean relations, which allows for a comprehensive classification of the relations of every pair of variants by taking all minimal alignments into account. We present an efficient algorithm to compute these relations, including a novel way of efficiently computing all minimal alignments within the best theoretical complexity bounds. RESULTS We show that these relations are common, and many non-trivial, for variants of the CFTR gene in dbSNP. Ultimately, we present an approach for the storing and indexing of variants in the context of a database that enables efficient querying for all these relations. AVAILABILITY AND IMPLEMENTATION A Python implementation is available at https://github.com/mutalyzer/algebra/tree/v0.2.0 as well as an interface at https://mutalyzer.nl/algebra.
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Affiliation(s)
| | - Mark A Santcroos
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands,Department of Clinical Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Walter A Kosters
- Leiden Institute of Advanced Computer Science, Leiden University, 2333 CA Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands,National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
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32
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Kechin A, Boyarskikh U, Barinov A, Tanas A, Kazakova S, Zhevlova A, Khrapov E, Subbotin S, Mishukova O, Kekeeva T, Demidova I, Filipenko M. A spectrum of BRCA1 and BRCA2 germline deleterious variants in ovarian cancer in Russia. Breast Cancer Res Treat 2023; 197:387-395. [PMID: 36367610 DOI: 10.1007/s10549-022-06782-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022]
Abstract
PURPOSE Pathogenic variants (PVs) in BRCA1 and BRCA2 genes are essential biomarkers of an increased breast and ovarian cancer risk and tumor sensitivity to poly ADP ribose polymerase inhibitors. In Russia, eight PVs were thought to be the most common, among which BRCA1 c.5266dup is the most frequently identified one. METHODS We show the distribution of BRCA1/2 PVs identified with quantitative PCR and targeted next-generation sequencing in 1399 ovarian cancer patients recruited into the study from 72 Russian regions in 2015-2021. RESULTS The most abundant PVs were c.5266dup (41.0%), c.4035del (7.0%), c.1961del (6.3%), c.181 T > G (5.2%), c.3756_3759del (1.8%), c.3700_3704del (1.5%), and c.68_69del (1.5%), all found in BRCA1 and known to be recurrent in Russia. Several other frequent PVs were identified: c.5152 + 1G > T (1.2%), c.1687C > T (1.0%), c.4689C > G (0.9%), c.1510del (0.6%), c.2285_2286del (0.6%) in the BRCA1 gene; and c.5286 T > G (1.2%), c.2808_2811del (0.8%), c.3847_3848del (0.8%), c.658_659del (0.7%), c.7879A > T (0.6%), in the BRCA2 gene. For the most common PV in the BRCA2 gene c.5286 T > G, we suggested that it arose about 700 years ago and is a new founder mutation. CONCLUSION This study extends our knowledge about the BRCA1 and BRCA2 pathogenic variants variability.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey Barinov
- Moscow City Oncology Hospital No 62 of the Moscow Health Department, Istra, 143423, Russia
| | - Alexander Tanas
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | | | | | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergey Subbotin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga Mishukova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Tatiana Kekeeva
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | - Irina Demidova
- Moscow City Oncology Hospital No 62 of the Moscow Health Department, Istra, 143423, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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Postma AV, Rapp CK, Knoflach K, Volk AE, Lemke JR, Ackermann M, Regamey N, Latzin P, Celant L, Jansen SM, Bogaard HJ, Ilgun A, Alders M, van Spaendonck-Zwarts KY, Jonigk D, Klein C, Gräf S, Kubisch C, Houweling AC, Griese M. Biallelic variants in the calpain regulatory subunit CAPNS1 cause pulmonary arterial hypertension. GENETICS IN MEDICINE OPEN 2023; 1:100811. [PMID: 38230350 PMCID: PMC10790724 DOI: 10.1016/j.gimo.2023.100811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 01/18/2024]
Abstract
Purpose The aim of this study was to identify the monogenic cause of pulmonary arterial hypertension (PAH), a multifactorial and often fatal disease, in 2 unrelated consanguine families. Methods We performed exome sequencing and validated variant pathogenicity by whole-blood RNA and protein expression analysis in both families. Further RNA sequencing of preserved lung tissue was performed to investigate the consequences on selected genes that are involved in angiogenesis, proliferation, and apoptosis. Results We identified 2 rare biallelic variants in CAPNS1, encoding the regulatory subunit of calpain. The variants cosegregated with PAH in the families. Both variants lead to loss of function (LoF), which is demonstrated by aberrant splicing resulting in the complete absence of the CAPNS1 protein in affected patients. No other LoF CAPNS1 variant was identified in the genome data of more than 1000 patients with unresolved PAH. Conclusion The calpain holoenzyme was previously linked to pulmonary vascular development and progression of PAH in patients. We demonstrated that biallelic LoF variants in CAPNS1 can cause idiopathic PAH by the complete absence of CAPNS1 protein. Screening of this gene in patients who are affected by PAH, especially with suspected autosomal recessive inheritance, should be considered.
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Affiliation(s)
- Alex V. Postma
- Department of Medical Biology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Christina K. Rapp
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum, Ludwig Maximilians University of Munich, German Center for Lung Research (DZL), Munich, Germany
| | - Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum, Ludwig Maximilians University of Munich, German Center for Lung Research (DZL), Munich, Germany
| | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes R. Lemke
- Institute of Human Genetics, Leipzig University Medical Center, Leipzig, Germany
- Center for Rare Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Maximilian Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Centre, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nicolas Regamey
- Division of Paediatric Pulmonology, Children’s Hospital, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | - Philipp Latzin
- Division of Paediatric Respiratory Medicine and Allergology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
| | - Lucas Celant
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Samara M.A. Jansen
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Harm J. Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Aho Ilgun
- Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | | | - Danny Jonigk
- Institute of Pathology, Medizinische Hochschule Hannover, Hanover, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum, Ludwig Maximilians University of Munich, German Center for Lung Research (DZL), Munich, Germany
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute, Cambridge, United Kingdom
- NIHR BioResource for Translational Research–Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arjan C. Houweling
- Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum, Ludwig Maximilians University of Munich, German Center for Lung Research (DZL), Munich, Germany
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Chiorean A, Farncombe KM, Delong S, Andric V, Ansar S, Chan C, Clark K, Danos AM, Gao Y, Giles RH, Goldenberg A, Jani P, Krysiak K, Kujan L, Macpherson S, Maher ER, McCoy LG, Salama Y, Saliba J, Sheta L, Griffith M, Griffith OL, Erdman L, Ramani A, Kim RH. Large scale genotype- and phenotype-driven machine learning in Von Hippel-Lindau disease. Hum Mutat 2022; 43:1268-1285. [PMID: 35475554 PMCID: PMC9356987 DOI: 10.1002/humu.24392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 12/30/2022]
Abstract
Von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome where individuals are predisposed to tumor development in the brain, adrenal gland, kidney, and other organs. It is caused by pathogenic variants in the VHL tumor suppressor gene. Standardized disease information has been difficult to collect due to the rarity and diversity of VHL patients. Over 4100 unique articles published until October 2019 were screened for germline genotype-phenotype data. Patient data were translated into standardized descriptions using Human Genome Variation Society gene variant nomenclature and Human Phenotype Ontology terms and has been manually curated into an open-access knowledgebase called Clinical Interpretation of Variants in Cancer. In total, 634 unique VHL variants, 2882 patients, and 1991 families from 427 papers were captured. We identified relationship trends between phenotype and genotype data using classic statistical methods and spectral clustering unsupervised learning. Our analyses reveal earlier onset of pheochromocytoma/paraganglioma and retinal angiomas, phenotype co-occurrences and genotype-phenotype correlations including hotspots. It confirms existing VHL associations and can be used to identify new patterns and associations in VHL disease. Our database serves as an aggregate knowledge translation tool to facilitate sharing information about the pathogenicity of VHL variants.
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Affiliation(s)
- Andreea Chiorean
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Kirsten M. Farncombe
- Toronto General Hospital Research InstituteUniversity Health NetworkTorontoOntarioCanada
| | - Sean Delong
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Veronica Andric
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Safa Ansar
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Clarissa Chan
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Kaitlin Clark
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Arpad M. Danos
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Yizhuo Gao
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Rachel H. Giles
- International Kidney Cancer Coalition, Duivendrecht‐AmsterdamDuivendrechtThe Netherlands
| | - Anna Goldenberg
- Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Payal Jani
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Lynzey Kujan
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Samantha Macpherson
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Eamonn R. Maher
- Department of Medical GeneticsUniversity of CambridgeCambridgeUK,NIHR Cambridge Biomedical Research CentreCambridge Biomedical CampusCambridgeUK
| | - Liam G. McCoy
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Yasser Salama
- Department of Medicine, Division of Medical OncologyUniversity Health NetworkTorontoOntarioCanada
| | - Jason Saliba
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Lana Sheta
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of MedicineWashington UniversitySt. LouisMissouriUSA,McDonnell Genome InstituteWashington University School of MedicineMissouriSt. LouisUSA
| | - Lauren Erdman
- Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Arun Ramani
- Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Raymond H. Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer CentreUniversity Health Network and Sinai Health SystemTorontoOntarioCanada,Division of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenTorontoOntarioCanada,Ontario Institute for Cancer ResearchTorontoOntarioCanada,Department of MedicineUniversity of TorontoTorontoOntarioCanada
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When a Synonymous Variant Is Nonsynonymous. Genes (Basel) 2022; 13:genes13081485. [PMID: 36011397 PMCID: PMC9408308 DOI: 10.3390/genes13081485] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022] Open
Abstract
Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences.
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Lin SJ, Vona B, Porter HM, Izadi M, Huang K, Lacassie Y, Rosenfeld JA, Khan S, Petree C, Ali TA, Muhammad N, Khan SA, Muhammad N, Liu P, Haymon ML, Rüschendorf F, Kong IK, Schnapp L, Shur N, Chorich L, Layman L, Haaf T, Pourkarimi E, Kim HG, Varshney GK. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Hum Mutat 2022; 43:1472-1489. [PMID: 35815345 DOI: 10.1002/humu.24435] [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: 05/03/2022] [Revised: 06/12/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a C. elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hillary M Porter
- Children's National Hospital, Rare Disease Institute, 111 Michigan Ave. NW, Washington, DC, 20010, USA
| | - Mahmoud Izadi
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Yves Lacassie
- Department of Pediatrics, Louisiana State University Health Sciences Center, Head Division of Clinical Genetics and Dept. of Genetics Children's Hospital 1986-2016, 200 Henry Clay Avenue, New Orleans, LA, 70118, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Tayyiba Akbar Ali
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Marie-Louise Haymon
- Children Hospital New Orleans Louisiana, Pediatric Radiology, Tulane Associate Professor of Radiology, New Orleans, LA, 70118, USA
| | - Franz Rüschendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Il-Keun Kong
- Department of Animal Sciences, Division of Applied Life Science (BK21 Four), Gyeongsang National University, 52828, Jinju, South Korea
| | - Linda Schnapp
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Natasha Shur
- Children's National Hospital, Rare Disease Institute, 111 Michigan Ave. NW, Washington, DC, 20010, USA
| | - Lynn Chorich
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics and Gynecology, Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 30912, Augusta, USA
| | - Lawrence Layman
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics and Gynecology, Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 30912, Augusta, USA
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Ehsan Pourkarimi
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, 34110, Doha, Qatar
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
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Díaz-Zabala H, Guo X, Ping J, Wen W, Shu XO, Long J, Lipworth L, Li B, Fadden MK, Pal T, Blot WJ, Cai Q, Haiman CA, Palmer JR, Sanderson M, Zheng W. Evaluating breast cancer predisposition genes in women of African ancestry. Genet Med 2022; 24:1468-1475. [PMID: 35396981 PMCID: PMC9597482 DOI: 10.1016/j.gim.2022.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Studies conducted primarily among European ancestry women reported 12 breast cancer predisposition genes. However, etiologic roles of these genes in breast cancer among African ancestry women have been less well-investigated. METHODS We conducted a case-control study in African American women, which included 1117 breast cancer cases and 2169 cancer-free controls, and a pooled analysis, which included 7096 cases and 8040 controls of African descent. Odds ratios of associations with breast cancer risk were estimated. RESULTS Using sequence data, we identified 61 pathogenic variants in 12 breast cancer predisposition genes, including 11 pathogenic variants not yet reported in previous studies. Pooled analysis showed statistically significant associations of breast cancer risk with pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, TP53, NF1, RAD51C, and RAD51D (all P < .05). The associations with BRCA1, PALB2, and RAD51D were stronger for estrogen receptor (ER)-negative than for ER-positive breast cancer (P heterogeneity < .05), whereas the association with CHEK2 was stronger for ER-positive than for ER-negative breast cancer. CONCLUSION Our study confirmed previously identified associations of breast cancer risk with BRCA1, BRCA2, PALB2, ATM, TP53, NF1, and CHEK2 and provided new evidence to extend the associations of breast cancer risk with RAD51C and RAD51D, which was identified previously in European ancestry populations, to African ancestry women.
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Affiliation(s)
- Héctor Díaz-Zabala
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Xingyi Guo
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jie Ping
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Wanqing Wen
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jirong Long
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Loren Lipworth
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Mary Kay Fadden
- Department of Family & Community Medicine, Meharry Medical College, Nashville, TN
| | - Tuya Pal
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Cancer Health Disparities, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - William J Blot
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Julie R Palmer
- Department of Medicine, Boston University School of Medicine, Slone Epidemiology Center, Boston University, Boston, MA
| | - Maureen Sanderson
- Department of Family & Community Medicine, Meharry Medical College, Nashville, TN
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN.
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Dalgleish R. Re: Long-term evaluation of anabolic and anti-resorptive agents in adults with familial osteoporosis due to pro205ala variant of the col1a1 gene. Osteoporos Int 2022; 33:1403-1404. [PMID: 35234990 DOI: 10.1007/s00198-022-06334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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39
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Schroeder M, Peter VG, Gränse L, Andréasson S, Rivolta C, Kjellström U. A novel phenotype associated with the R162W variant in the KCNJ13 gene. Ophthalmic Genet 2022; 43:500-507. [PMID: 35477418 DOI: 10.1080/13816810.2022.2068041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Pathogenic variants in KCNJ13 have been associated with both autosomal dominant Snowflake vitreoretinal degeneration (SVD) and autosomal recessive Leber congenital amaurosis. SVD is characterized by aberrant vitreoretinal interface leading to increased risk of retinal detachment, crystalline retinal snowflake deposits, optic disc abnormalities, early-onset cataract, and cornea guttae. Reduced dark adaptation and reduced scotopic rod b-waves have also been described. We report a novel phenotype associated with the R162W variant in KCNJ13. METHODS Four affected members of a Swedish family were included. Three of them were examined with best corrected visual acuity, Goldmann perimetry, full-field-and multifocal electroretinography, optical coherence tomography, fundus color photographs, fundus autofluorescence images, slit lamp inspection, and genetic testing. The fourth subject only managed genetic testing. RESULTS All subjects carry the pathogenic missense variant; c.484C>T (NM_002242.4), R162W, in KCNJ13. ERG measurements revealed reduced macular-as well as general retinal function. Two of the subjects had a history of retinal detachment and the two younger subjects demonstrated early onset cataract. They all had structural macular changes and slightly gliotic optic discs. CONCLUSION In this family, the R162W variant in KCNJ13, previously described in association with SVD, causes a somewhat novel phenotype including macular dystrophy and moderate reduction of general retinal function as the main features combined with disc abnormalities, retinal detachment, and presenile cataract that has been described before. In times of up-coming gene-based therapies, it is important to report new genotype-phenotype associations to improve the possibilities to identify future treatment candidates.
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Affiliation(s)
- Marion Schroeder
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lotta Gränse
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
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40
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Palles C, Martin L, Domingo E, Chegwidden L, McGuire J, Cuthill V, Heitzer E, Kerr R, Kerr D, Kearsey S, Clark SK, Tomlinson I, Latchford A. The clinical features of polymerase proof-reading associated polyposis (PPAP) and recommendations for patient management. Fam Cancer 2022; 21:197-209. [PMID: 33948826 PMCID: PMC8964588 DOI: 10.1007/s10689-021-00256-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/07/2021] [Indexed: 10/28/2022]
Abstract
Pathogenic germline exonuclease domain (ED) variants of POLE and POLD1 cause the Mendelian dominant condition polymerase proof-reading associated polyposis (PPAP). We aimed to describe the clinical features of all PPAP patients with probably pathogenic variants. We identified patients with a variants mapping to the EDs of POLE or POLD1 from cancer genetics clinics, a colorectal cancer (CRC) clinical trial, and systematic review of the literature. We used multiple evidence sources to separate ED variants into those with strong evidence of pathogenicity and those of uncertain importance. We performed quantitative analysis of the risk of CRC, colorectal adenomas, endometrial cancer or any cancer in the former group. 132 individuals carried a probably pathogenic ED variant (105 POLE, 27 POLD1). The earliest malignancy was colorectal cancer at 14. The most common tumour types were colorectal, followed by endometrial in POLD1 heterozygotes and duodenal in POLE heterozygotes. POLD1-mutant cases were at a significantly higher risk of endometrial cancer than POLE heterozygotes. Five individuals with a POLE pathogenic variant, but none with a POLD1 pathogenic variant, developed ovarian cancer. Nine patients with POLE pathogenic variants and one with a POLD1 pathogenic variant developed brain tumours. Our data provide important evidence for PPAP management. Colonoscopic surveillance is recommended from age 14 and upper-gastrointestinal surveillance from age 25. The management of other tumour risks remains uncertain, but surveillance should be considered. In the absence of strong genotype-phenotype associations, these recommendations should apply to all PPAP patients.
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Affiliation(s)
- Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Lynn Martin
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Enric Domingo
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Josh McGuire
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Vicky Cuthill
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
| | - Ellen Heitzer
- Diagnostic and Research Institute of Human Genetics, University of Gratz, Graz, Austria
| | - Rachel Kerr
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Stephen Kearsey
- ZRAB, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Susan K Clark
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Andrew Latchford
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
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Tamana S, Xenophontos M, Minaidou A, Stephanou C, Harteveld CL, Bento C, Traeger-Synodinos J, Fylaktou I, Yasin NM, Abdul Hamid FS, Esa E, Halim-Fikri H, Zilfalil BA, Kakouri AC, Kleanthous M, Kountouris P. Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies. eLife 2022; 11:79713. [PMID: 36453528 PMCID: PMC9731569 DOI: 10.7554/elife.79713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
Haemoglobinopathies are the commonest monogenic diseases worldwide and are caused by variants in the globin gene clusters. With over 2400 variants detected to date, their interpretation using the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines is challenging and computational evidence can provide valuable input about their functional annotation. While many in silico predictors have already been developed, their performance varies for different genes and diseases. In this study, we evaluate 31 in silico predictors using a dataset of 1627 variants in HBA1, HBA2, and HBB. By varying the decision threshold for each tool, we analyse their performance (a) as binary classifiers of pathogenicity and (b) by using different non-overlapping pathogenic and benign thresholds for their optimal use in the ACMG/AMP framework. Our results show that CADD, Eigen-PC, and REVEL are the overall top performers, with the former reaching moderate strength level for pathogenic prediction. Eigen-PC and REVEL achieve the highest accuracies for missense variants, while CADD is also a reliable predictor of non-missense variants. Moreover, SpliceAI is the top performing splicing predictor, reaching strong level of evidence, while GERP++ and phyloP are the most accurate conservation tools. This study provides evidence about the optimal use of computational tools in globin gene clusters under the ACMG/AMP framework.
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Affiliation(s)
- Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Cornelis L Harteveld
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Leiden University Medical CenterLeidenNetherlands
| | - Celeste Bento
- Centro Hospitalar e Universitário de CoimbraCoimbraPortugal
| | | | - Irene Fylaktou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of AthensAthensGreece
| | - Norafiza Mohd Yasin
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Faidatul Syazlin Abdul Hamid
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Ezalia Esa
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Andrea C Kakouri
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | | | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
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42
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Genome sequencing as a first-line diagnostic test for hospitalized infants. Genet Med 2021; 24:851-861. [PMID: 34930662 DOI: 10.1016/j.gim.2021.11.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/21/2022] Open
Abstract
PURPOSE SouthSeq is a translational research study that undertook genome sequencing (GS) for infants with symptoms suggestive of a genetic disorder. Recruitment targeted racial/ethnic minorities and rural, medically underserved areas in the Southeastern United States, which are historically underrepresented in genomic medicine research. METHODS GS and analysis were performed for 367 infants to detect disease-causal variation concurrent with standard of care evaluation and testing. RESULTS Definitive diagnostic (DD) or likely diagnostic (LD) genetic findings were identified in 30% of infants, and 14% of infants harbored an uncertain result. Only 43% of DD/LD findings were identified via concurrent clinical genetic testing, suggesting that GS testing is better for obtaining early genetic diagnosis. We also identified phenotypes that correlate with the likelihood of receiving a DD/LD finding, such as craniofacial, ophthalmologic, auditory, skin, and hair abnormalities. We did not observe any differences in diagnostic rates between racial/ethnic groups. CONCLUSION We describe one of the largest-to-date GS cohorts of ill infants, enriched for African American and rural patients. Our results show the utility of GS because it provides early-in-life detection of clinically relevant genetic variations not detected by current clinical genetic testing, particularly for infants exhibiting certain phenotypic features.
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43
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Bosch E, Hebebrand M, Popp B, Penger T, Behring B, Cox H, Towner S, Kraus C, Wilson WG, Khan S, Krumbiegel M, Ekici AB, Uebe S, Trollmann R, Woelfle J, Reis A, Vasileiou G. BDV Syndrome: An Emerging Syndrome With Profound Obesity and Neurodevelopmental Delay Resembling Prader-Willi Syndrome. J Clin Endocrinol Metab 2021; 106:3413-3427. [PMID: 34383079 DOI: 10.1210/clinem/dgab592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Indexed: 12/17/2022]
Abstract
CONTEXT CPE encodes carboxypeptidase E, an enzyme that converts proneuropeptides and propeptide hormones to bioactive forms. It is widely expressed in the endocrine and central nervous system. To date, 4 individuals from 2 families with core clinical features including morbid obesity, neurodevelopmental delay, and hypogonadotropic hypogonadism, harboring biallelic loss-of-function (LoF) CPE variants, have been reported. OBJECTIVE We describe 4 affected individuals from 3 unrelated consanguineous families, 2 siblings of Syrian, 1 of Egyptian, and 1 of Pakistani descent, all harboring novel homozygous CPE LoF variants. METHODS After excluding Prader-Willi syndrome (PWS), exome sequencing was performed in both Syrian siblings. The variants identified in the other 2 individuals were reported as research variants in a large-scale exome study and in the ClinVar database. Computational modeling of all possible missense alterations allowed assessing CPE tolerance to missense variants. RESULTS All affected individuals were severely obese with neurodevelopmental delay and other endocrine anomalies. Three individuals from 2 families shared the same CPE homozygous truncating variant c.361C > T, p.(Arg121*), while the fourth carried the c.994del, p.(Ser333Alafs*22) variant. Comparison of clinical features with previously described cases and standardization according to the Human Phenotype Ontology terms indicated a recognizable clinical phenotype, which we termed Blakemore-Durmaz-Vasileiou (BDV) syndrome. Computational analysis indicated high conservation of CPE domains and intolerance to missense changes. CONCLUSION Biallelic truncating CPE variants are associated with BDV syndrome, a clinically recognizable monogenic recessive syndrome with childhood-onset obesity, neurodevelopmental delay, hypogonadotropic hypogonadism, and hypothyroidism. BDV syndrome resembles PWS. Our findings suggest missense variants may also be clinically relevant.
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Affiliation(s)
- Elisabeth Bosch
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Moritz Hebebrand
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, 04103 Leipzig, Germany
| | - Theresa Penger
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Bettina Behring
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Helen Cox
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Shelley Towner
- Department of Pediatrics, Division of Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - William G Wilson
- Department of Pediatrics, Division of Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Shagufta Khan
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Mandy Krumbiegel
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Regina Trollmann
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Joachim Woelfle
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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44
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Rowlands C, Thomas HB, Lord J, Wai HA, Arno G, Beaman G, Sergouniotis P, Gomes-Silva B, Campbell C, Gossan N, Hardcastle C, Webb K, O'Callaghan C, Hirst RA, Ramsden S, Jones E, Clayton-Smith J, Webster AR, Douglas AGL, O'Keefe RT, Newman WG, Baralle D, Black GCM, Ellingford JM. Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders. Sci Rep 2021; 11:20607. [PMID: 34663891 PMCID: PMC8523691 DOI: 10.1038/s41598-021-99747-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as 'pathogenic' or 'likely pathogenic'; one in five of these cases could lead to new or refined diagnoses.
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Affiliation(s)
- Charlie Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Huw B Thomas
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Htoo A Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Glenda Beaman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Panagiotis Sergouniotis
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Beatriz Gomes-Silva
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Christopher Campbell
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Nicole Gossan
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Claire Hardcastle
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Kevin Webb
- Manchester Adult Cystic Fibrosis Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Christopher O'Callaghan
- Respiratory, Critical Care and Anaesthesia, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Children's Hospital & NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Simon Ramsden
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Elizabeth Jones
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Jill Clayton-Smith
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Andrew R Webster
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - William G Newman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Graeme C M Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK.
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK.
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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45
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Park KJ, Park JH. Variations in Nomenclature of Clinical Variants between Annotation Tools. Lab Med 2021; 53:242-245. [PMID: 34612497 DOI: 10.1093/labmed/lmab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Accurate nomenclature of variants is an essential element for genetic diagnosis and patient care. OBJECTIVE To investigate annotation differences of clinical variants between annotation tools. METHODS We analyzed 218,156 clinical variants from the Human Gene Mutation Database. Multiple nomenclatures based on RefSeq transcripts were provided using ANNOVAR and snpEff. RESULTS The concordance rate between ANNOVAR and snpEff was approximately 85%. Based on the Human Genome Variation Society (HGVS) nomenclature, snpEff was more accurate than ANNOVAR (coding variants, 99.3% vs 84.9%; protein variants, 94.3% vs 79.8%). When annotating each variant with ANNOVAR and snpEff, the accuracy of nomenclature was 99.5%. CONCLUSIONS There were substantial differences between ANNOVAR and snpEff annotations. The findings of this study suggest that simultaneous use of multiple annotation tools could decrease nomenclature errors and contribute to providing standardized clinical reporting.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine & Genetics, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, South Korea
| | - Jong-Ho Park
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Seoul, South Korea
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46
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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47
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Cisarova K, Garavelli L, Caraffi SG, Peluso F, Valeri L, Gargano G, Gavioli S, Trimarchi G, Neri A, Campos-Xavier B, Superti-Furga A. A monoallelic SEC23A variant E599K associated with cranio-lenticulo-sutural dysplasia. Am J Med Genet A 2021; 188:319-325. [PMID: 34580982 PMCID: PMC9291540 DOI: 10.1002/ajmg.a.62506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/06/2022]
Abstract
Cranio-lenticulo-sutural dysplasia (CLSD; MIM 607812) is a rare or underdiagnosed condition, as only two families have been reported. The original family (Boyadjiev et al., Human Genetics, 2003, 113, 1-9 and Boyadjiev et al., Nature Genetics, 2006, 38, 1192-1197) showed recessive inheritance of the condition with a biallelic SEC23A missense variant in affected individuals. In contrast, another child with sporadic CLSD had a monoallelic SEC23A variant inherited from the reportedly unaffected father (Boyadjiev et al., Clinical Genetics, 2011, 80, 169-176), raising questions on possible digenism. Here, we report a 2-month-old boy seen because of large fontanels with wide cranial sutures, a large forehead, hypertelorism, a thin nose, a high arched palate, and micrognathia. His mother was clinically unremarkable, while his father had a history of large fontanels in infancy who had closed only around age 10 years; he also had a large forehead, hypertelorism, a thin, beaked nose and was operated for bilateral glaucoma with exfoliation of the lens capsule. Trio genome sequencing and familial segregation revealed a monoallelic c.1795G > A transition in SEC23A that was de novo in the father and transmitted to the proband. The variant predicts a nonconservative substitution (p.E599K) in an ultra-conserved residue that is seen in 3D models of yeast SEC23 to be involved in direct binding between SEC23 and SAR1 subunits of the coat protein complex II coat. This observation confirms the link between SEC23A variants and CLSD but suggests that in addition to the recessive inheritance described in the original family, SEC23A variants may result in dominant inheritance of CLSD, possibly by a dominant-negative disruptive effect on the SEC23 multimer.
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Affiliation(s)
- Katarina Cisarova
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Livia Garavelli
- Clinical Genetics Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | | | - Francesca Peluso
- Clinical Genetics Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Lara Valeri
- Clinical Genetics Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Sara Gavioli
- Neonatal Intensive Care Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Clinical Genetics Unit, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Alberto Neri
- Ophthalmology Unit, Department of Surgery, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Belinda Campos-Xavier
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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48
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The LOVD3 platform: efficient genome-wide sharing of genetic variants. Eur J Hum Genet 2021; 29:1796-1803. [PMID: 34521998 PMCID: PMC8632977 DOI: 10.1038/s41431-021-00959-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/05/2021] [Accepted: 08/26/2021] [Indexed: 01/23/2023] Open
Abstract
Gene variant databases are the backbone of DNA-based diagnostics. These databases, also called Locus-Specific DataBases (LSDBs), store information on variants in the human genome and the observed phenotypic consequences. The largest collection of public databases uses the free, open-source LOVD software platform. To cope with the current demand for online databases, we have entirely redesigned the LOVD software. LOVD3 is genome-centered and can be used to store summary variant data, as well as full case-level data with information on individuals, phenotypes, screenings, and variants. While built on a standard core, the software is highly flexible and allows personalization to cope with the largely different demands of gene/disease database curators. LOVD3 follows current standards and includes tools to check variant descriptions, generate HTML files of reference sequences, predict the consequences of exon deletions/duplications on the reading frame, and link to genomic views in the different genomes browsers. It includes APIs to collect and submit data. The software is used by about 100 databases, of which 56 public LOVD instances are registered on our website and together contain 1,000,000,000 variant observations in 1,500,000 individuals. 42 LOVD instances share data with the federated LOVD data network containing 3,000,000 unique variants in 23,000 genes. This network can be queried directly, quickly identifying LOVD instances containing relevant information on a searched variant.
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49
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Bedoni N, Quinodoz M, Pinelli M, Cappuccio G, Torella A, Nigro V, Testa F, Simonelli F, Corton M, Lualdi S, Lanza F, Morana G, Ayuso C, Di Rocco M, Filocamo M, Banfi S, Brunetti-Pierri N, Superti-Furga A, Rivolta C. An Alu-mediated duplication in NMNAT1, involved in NAD biosynthesis, causes a novel syndrome, SHILCA, affecting multiple tissues and organs. Hum Mol Genet 2021; 29:2250-2260. [PMID: 32533184 DOI: 10.1093/hmg/ddaa112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients' fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.
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Affiliation(s)
- Nicola Bedoni
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | | | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Susanna Lualdi
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Federica Lanza
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Giovanni Morana
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Maja Di Rocco
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
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50
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Ten simple rules for teaching applied programming in an authentic and immersive online environment. PLoS Comput Biol 2021; 17:e1009184. [PMID: 34351897 PMCID: PMC8341656 DOI: 10.1371/journal.pcbi.1009184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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