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Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
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Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
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Kim Y, Kim JM, Cho HW, Park HY, Park MH. Frequency of actionable secondary findings in 7472 Korean genomes derived from the National Project of Bio Big Data pilot study. Hum Genet 2023; 142:1561-1569. [PMID: 37728764 PMCID: PMC10602966 DOI: 10.1007/s00439-023-02592-8] [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: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023]
Abstract
Exome and genome sequencing (ES/GS) in genetic medicine and research leads to discovering genomic secondary findings (SFs) unrelated to the purpose of the primary test. There is a lack of agreement to return the SF results for individuals undergoing the test. The aim of this study is to investigate the frequency of actionable secondary findings using GS data obtained from the rare disease study and the Korean Genome and Epidemiology Study (KoGES) in the National Project of Bio Big Data pilot study. Pathogenic (P) or likely pathogenic (LP) variants of 78 SF genes recommended by the American College of Medical Genetics and Genomics (ACMG) were screened in the rare disease study and KoGES. The pathogenicity of SF gene variants was determined according to the ACMG interpretation. The overall SF rate was 3.75% for 280 individuals with 298 P/LP variants of 41 ACMG SF genes which were identified among 7472 study participants. The frequencies of genes associated with cardiovascular, cancer, and miscellaneous phenotypes were 2.17%, 1.22%, and 0.58%, respectively. The most frequent SF gene was TTN followed by BRCA2. The frequency of actionable SFs among participants with rare disease and general population participants in the Korean population presented here will assist in reporting results of medically actionable SFs in genomic medicine.
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Affiliation(s)
- Youngjun Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Jeong-Min Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Hye-Won Cho
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Hyun-Young Park
- Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea.
| | - Mi-Hyun Park
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea.
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Oladayo A, Gowans LJJ, Awotoye W, Alade A, Busch T, Naicker T, Eshete MA, Adeyemo WL, Hetmanski JB, Zeng E, Adamson O, Adeleke C, Li M, Sule V, Kayali S, Olotu J, Mossey PA, Obiri‐Yeboah S, Buxo CJ, Beaty T, Taub M, Donkor P, Marazita ML, Odukoya O, Adeyemo AA, Murray JC, Prince A, Butali A. Clinically actionable secondary findings in 130 triads from sub-Saharan African families with non-syndromic orofacial clefts. Mol Genet Genomic Med 2023; 11:e2237. [PMID: 37496383 PMCID: PMC10568375 DOI: 10.1002/mgg3.2237] [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: 01/30/2023] [Revised: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023] Open
Abstract
INTRODUCTION The frequency and implications of secondary findings (SFs) from genomic testing data have been extensively researched. However, little is known about the frequency or reporting of SFs in Africans, who are underrepresented in large-scale population genomic studies. The availability of data from the first whole-genome sequencing for orofacial clefts in an African population motivated this investigation. METHODS In total, 130 case-parent trios were analyzed for SFs within the ACMG SFv.3.0 list genes. Additionally, we filtered for four more genes (HBB, HSD32B, G6PD and ACADM). RESULTS We identified 246 unique variants in 55 genes; five variants in four genes were classified as pathogenic or likely pathogenic (P/LP). The P/LP variants were seen in 2.3% (9/390) of the subjects, a frequency higher than ~1% reported for diverse ethnicities. On the ACMG list, pathogenic variants were observed in PRKAG (p. Glu183Lys). Variants in the PALB2 (p. Glu159Ter), RYR1 (p. Arg2163Leu) and LDLR (p. Asn564Ser) genes were predicted to be LP. CONCLUSION This study provides information on the frequency and pathogenicity of SFs in an African cohort. Early risk detection will help reduce disease burden and contribute to efforts to increase knowledge of the distribution and impact of actionable genomic variants in diverse populations.
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Affiliation(s)
- Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
| | - Lord Jephthah Joojo Gowans
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
- Department of Biochemistry and BiotechnologyKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Department of Epidemiology, College of Public HealthUniversity of IowaIowa CityIowaUSA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Thirona Naicker
- Department of PediatricsUniversity of KwaZulu‐NatalPinetownSouth Africa
| | - Mekonen A. Eshete
- School Medicine, Surgical DepartmentAddis Ababa UniversityAddis AbabaEthiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Jacqueline B. Hetmanski
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Olawale Adamson
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Veronica Sule
- Department of Operative Dentistry, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Joy Olotu
- Department of AnatomyUniversity of Port HarcourtPort HarcourtNigeria
| | | | - Solomon Obiri‐Yeboah
- Department of Surgery, School of Medicine and DentistryKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Carmen J. Buxo
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto RicoUSA
| | - Terri Beaty
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Margaret Taub
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Peter Donkor
- Department of Surgery, School of Medicine and DentistryKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Oluwakemi Odukoya
- Department of Community Health and Primary Care, College of MedicineUniversity of LagosLagosNigeria
| | | | | | - Anya Prince
- College of LawUniversity of IowaIowa CityIowaUSA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
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Mazel B, Bertolone G, Baurand A, Cosset E, Sawka C, Robert M, Gautier E, Lançon A, Réda M, Favier L, Dérangère V, Richard C, Binquet C, Boidot R, Goussot V, Albuisson J, Ghiringhelli F, Faivre L, Nambot S. Advancing precision oncology through systematic germline and tumor genetic analysis: The oncogenetic point of view on findings from a prospective multicenter clinical trial of 666 patients. Cancer Med 2023; 12:18786-18796. [PMID: 37694493 PMCID: PMC10557826 DOI: 10.1002/cam4.6498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/07/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
INTRODUCTION With the emergence of targeted therapies, there is a need to accurately identify more tumor biomarkers. The EXOMA trial was designed to offer tumor and germline exome sequencing (ES) to patients with solid malignant tumors and facing therapeutic failure. As hereditary cancer predispositions could be identified, with genetic counseling and health management implications, a genetic consultation was systematically established. This design needs to be discussed as genetic human resources are limited and indication of theranostic tests will increase. METHODS Genetic counseling was conducted within 15 days following inclusion in the study for patients recruited between December 2015 and July 2019. In silico analyses from theranostic ES were limited to 317 genes involved in oncogenesis, from both tumor and blood DNA. RESULTS Six hundred and sixty six patients had a genetic consultation before ES. In 65/666 patients, 66 germline pathogenic or likely pathogenic (P/LP) variants were identified in 16 actionable genes and seven non-actionable genes according to French guidelines. 24/65 patients had previously received genetic analysis for diagnostic purposes, and for 17 of them, a P/LP variant had already been identified. Among the 48/65 remaining cases for which the EXOMA protocol revealed a previously unknown P/LP variant, only 19 met the criteria for genetic testing for inherited cancer risk after familial survey. These criteria had not been identified by the oncologist in 10 cases. In 21/65 cases, the variant was considered incidental. DISCUSSION In 7.4% of patients, an undiagnosed hereditary genetic predisposition was identified, whether or not related to the clinical presentation, and germline analysis impacted oncological management for only 6.3% of the cohort. This low percentage should be weighed against the burden of systematic genetic consultation and urgent circuits. Information or training tools to form oncologists to the prescription of germline genetic analyses should be explored, as well as information supports and patient preferences.
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Affiliation(s)
- Benoit Mazel
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- INSERM UMR 1231 GAD, Génétique des Anomalies du Développement, Université Bourgogne Franche‐ComtéDijonFrance
| | - Geoffrey Bertolone
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Amandine Baurand
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Elodie Cosset
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Caroline Sawka
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Marion Robert
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Elodie Gautier
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
| | - Allan Lançon
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Manon Réda
- Département d'Oncologie MédicaleCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- Plateforme de Transfert en Biologie CancérologiqueCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Laure Favier
- Département d'Oncologie MédicaleCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- Plateforme de Transfert en Biologie CancérologiqueCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Valentin Dérangère
- Plateforme de Transfert en Biologie CancérologiqueCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Corentin Richard
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
| | - Christine Binquet
- INSERM, CIC1432, Module Epidémiologie Clinique, Dijon, France; Centre Hospitalier Universitaire Dijon‐Bourgogne, Centre d'Investigation Clinique, module Epidémiologie clinique/essais cliniquesDijonFrance
| | - Romain Boidot
- Unité de Biologie MoléculaireCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302DijonFrance
| | - Vincent Goussot
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
- Unité de Biologie MoléculaireCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - Juliette Albuisson
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
- Unité de Biologie MoléculaireCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
| | - François Ghiringhelli
- Département d'Oncologie MédicaleCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- Plateforme de Transfert en Biologie CancérologiqueCentre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
| | - Laurence Faivre
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- INSERM UMR 1231 GAD, Génétique des Anomalies du Développement, Université Bourgogne Franche‐ComtéDijonFrance
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
| | - Sophie Nambot
- Centre de Génétique, FHU‐TRANSLAD, Centre Hospitalier Universitaire Dijon‐BourgogneDijonFrance
- INSERM UMR 1231 GAD, Génétique des Anomalies du Développement, Université Bourgogne Franche‐ComtéDijonFrance
- Unité d'Oncogénétique, Centre de Lutte Contre le Cancer Georges François Leclerc—UNICANCERDijonFrance
- INSERM UMR 1231 GIMI, Genomic and Immunotherapy Medical Institute, Université Bourgogne Franche‐ComtéDijonFrance
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Tudini E, Haas MA, Mattiske T, Spurdle AB. Reporting clinically relevant genetic variants unrelated to genomic test requests: a survey of Australian clinical laboratory policies and practices. J Med Genet 2023; 60:609-614. [PMID: 36604177 DOI: 10.1136/jmg-2022-108808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/02/2022] [Indexed: 01/07/2023]
Abstract
Approaches to reporting clinically important genetic findings unrelated to the initial test request vary internationally. We sought to investigate practices regarding the management and return of these findings in Australia. Australian clinically accredited genetic testing laboratories were surveyed in 2017 and 2020 regarding their opinions on issues relating to the return of clinically important genetic findings unrelated to the initial test request. Responses were collated and analysed for 15 laboratories in 2017, and 17 laboratories in 2020. Content analysis was also performed on seven laboratory policies in 2020. Analysis showed that overall there was a lack of consensus about the terminology used to describe such findings and reporting practices across different testing contexts. A clear exception was that no laboratories were actively searching for a list of medically actionable genes (eg, American College of Medical Genetics and Genomics secondary findings gene list). Laboratory policies showed little consistency in the documentation of issues related to the handling of these findings. These findings indicate a need for Australian-specific policy guidance that covers all aspects of clinically important genetic findings unrelated to the initial test request. We present recommendations for consideration when developing laboratory policies.
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Affiliation(s)
- Emma Tudini
- Australian Genomics Health Alliance, Parkville, Victoria, Australia.,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matilda A Haas
- Australian Genomics Health Alliance, Parkville, Victoria, Australia .,Genetics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tessa Mattiske
- Australian Genomics Health Alliance, Parkville, Victoria, Australia.,Genetics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Härtl J, Hartberger J, Wunderlich S, Cordts I, Bafligil C, Sturm M, Westphal D, Haack T, Hemmer B, Ikenberg BD, Deschauer M. Exome-based gene panel analysis in a cohort of acute juvenile ischemic stroke patients:relevance of NOTCH3 and GLA variants. J Neurol 2023; 270:1501-1511. [PMID: 36411388 PMCID: PMC9971083 DOI: 10.1007/s00415-022-11401-7] [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: 06/20/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Genetic variants are considered to have a crucial impact on the occurrence of ischemic stroke. In clinical routine, the diagnostic value of next-generation sequencing (NGS) in the medical clarification of acute juvenile stroke has not been investigated so far. MATERIAL AND METHODS We analyzed an exome-based gene panel of 349 genes in 172 clinically well-characterized patients with magnetic resonance imaging (MRI)-proven, juvenile (age ≤ 55 years), ischemic stroke admitted to a single comprehensive stroke center. RESULTS Monogenetic diseases causing ischemic stroke were observed in five patients (2.9%): In three patients with lacunar stroke (1.7%), we identified pathogenic variants in NOTCH3 causing cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Hence, CADASIL was identified at a frequency of 12.5% in the lacunar stroke subgroup. Further, in two male patients (1.2%) suffering from lacunar and cardioembolic stroke, pathogenic variants in GLA causing Fabry's disease were present. Additionally, genetic variants in monogenetic diseases lacking impact on stroke occurrence, variants of unclear significance (VUS) in monogenetic diseases, and (cardiovascular-) risk genes in ischemic stroke were observed in a total of 15 patients (15.7%). CONCLUSION Genetic screening for Fabry's disease in cardioembolic and lacunar stroke as well as CADASIL in lacunar stroke might be beneficial in routine medical work-up of acute juvenile ischemic stroke.
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Affiliation(s)
- Johanna Härtl
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Julia Hartberger
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Silke Wunderlich
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Isabell Cordts
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Cemsel Bafligil
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Marc Sturm
- School of Medicine, Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, Universitaetsklinikum Tuebingen, Tuebingen, Germany
| | | | - Dominik Westphal
- School of Medicine, Klinikum rechts der Isar, Department of Cardiology, Technical University of Munich, Munich, Germany ,School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Institute of Human Genetics, Munich, Germany
| | - Tobias Haack
- School of Medicine, Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, Universitaetsklinikum Tuebingen, Tuebingen, Germany ,School of Medicine, Centre for Rare Diseases, Eberhard Karls University, Universitaetsklinikum Tuebingen, Tuebingen, Germany
| | - Bernhard Hemmer
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany ,Munich Cluster for Systems Neurology, (SyNergy), Munich, Germany
| | - Benno David Ikenberg
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Marcus Deschauer
- School of Medicine, Klinikum rechts der Isar, Department of Neurology, Technical University of Munich, Ismaningerstr. 22, 81675, Munich, Germany.
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7
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Zhou Y, Lauschke VM. Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy. Handb Exp Pharmacol 2023; 280:237-260. [PMID: 35792943 DOI: 10.1007/164_2022_596] [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] [Indexed: 06/15/2023]
Abstract
Over the last decade, next-generation sequencing (NGS) methods have become increasingly used in various areas of human genomics. In routine clinical care, their use is already implemented in oncology to profile the mutational landscape of a tumor, as well as in rare disease diagnostics. However, its utilization in pharmacogenomics is largely lacking behind. Recent population-scale genome data has revealed that human pharmacogenes carry a plethora of rare genetic variations that are not interrogated by conventional array-based profiling methods and it is estimated that these variants could explain around 30% of the genetically encoded functional pharmacogenetic variability.To interpret the impact of such variants on drug response a multitude of computational tools have been developed, but, while there have been major advancements, it remains to be shown whether their accuracy is sufficient to improve personalized pharmacogenetic recommendations in robust trials. In addition, conventional short-read sequencing methods face difficulties in the interrogation of complex pharmacogenes and high NGS test costs require stringent evaluations of cost-effectiveness to decide about reimbursement by national healthcare programs. Here, we illustrate current challenges and discuss future directions toward the clinical implementation of NGS to inform genotype-guided decision-making.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tuebingen, Tuebingen, Germany.
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8
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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
| | - Caroline F. Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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The 90 plus: longevity and COVID-19 survival. Mol Psychiatry 2022; 27:1936-1944. [PMID: 35136227 DOI: 10.1038/s41380-022-01461-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/08/2022]
Abstract
The world population is getting older and studies aiming to enhance our comprehension of the underlying mechanisms responsible for health span are of utmost interest for longevity and as a measure for health care. In this review, we summarized previous genetic association studies (GWAS) and next-generation sequencing (NGS) of elderly cohorts. We also present the updated hypothesis for the aging process, together with the factors associated with healthy aging. We discuss the relevance of studying older individuals and build databanks to characterize the presence and resistance against late-onset disorders. The identification of about 2 million novel variants in our cohort of more than 1000 elderly Brazilians illustrates the importance of studying highly admixed populations of non-European ancestry. Finally, the ascertainment of nonagenarians and particularly of centenarians who were recovered from COVID-19 or remained asymptomatic opens new avenues of research aiming to enhance our comprehension of biological mechanisms associated with resistance against pathogens.
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Elfatih A, Da’as SI, Abdelrahman D, Mbarek H, Mohammed I, Hasan W, Fakhro KA, Estivill X, Mifsud B. Analysis of incidental findings in Qatar genome participants reveals novel functional variants in LMNA and DSP. Hum Mol Genet 2022; 31:2796-2809. [PMID: 35348702 PMCID: PMC9402234 DOI: 10.1093/hmg/ddac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/21/2022] Open
Abstract
In order to report clinically actionable incidental findings in genetic testing, the American College of Medical Genetics and Genomics (ACMG) recommended the evaluation of variants in 59 genes associated with highly penetrant mutations. However, there is a lack of epidemiological data on medically actionable rare variants in these genes in Arab populations. We used whole genome sequencing data from 6045 participants from the Qatar Genome Programme and integrated it with phenotypic data collected by the Qatar Biobank. We identified novel putative pathogenic variants in the 59 ACMG genes by filtering previously unrecorded variants based on computational prediction of pathogenicity, variant rarity and segregation evidence. We assessed the phenotypic associations of candidate variants in genes linked to cardiovascular diseases. Finally, we used a zebrafish knockdown and synthetic human mRNA co-injection assay to functionally characterize two of these novel variants. We assessed the zebrafish cardiac function in terms of heart rate, rhythm and hemodynamics, as well as the heart structure. We identified 52 492 novel variants, which have not been reported in global and disease-specific databases. A total of 74 novel variants were selected with potentially pathogenic effect. We prioritized two novel cardiovascular variants, DSP c.1841A > G (p.Asp614Gly) and LMNA c.326 T > G (p.Val109Gly) for functional characterization. Our results showed that both variants resulted in abnormal zebrafish heart rate, rhythm and structure. This study highlights medically actionable variants that are specific to the Middle Eastern Qatari population.
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Affiliation(s)
- Amal Elfatih
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Sahar I Da’as
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Programme, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Idris Mohammed
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Waseem Hasan
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qGenomics), 08950 Barcelona, Spain
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- William Harvey Research Institute, Queen Mary University London, EC1M 6BQ London, United Kingdom
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Scholz T, Dufke A, Haack T, Elbracht M, Eggermann T, Roggia C, Riess O, Kurth I, Hempel M. Exomsequenzierung bei Kindern und Jugendlichen mit seltenen Erkrankungen. Monatsschr Kinderheilkd 2021. [DOI: 10.1007/s00112-021-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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