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Tung N, Ricker C, Messersmith H, Balmaña J, Domchek S, Stoffel EM, Almhanna K, Arun B, Chavarri-Guerra Y, Cohen SA, Cragun D, Crew KD, Hall MJ, Idos G, Lopez G, Pal T, Pirzadeh-Miller S, Pritchard C, Rana HQ, Swami U, Vidal GA. Selection of Germline Genetic Testing Panels in Patients With Cancer: ASCO Guideline. J Clin Oncol 2024; 42:2599-2615. [PMID: 38759122 DOI: 10.1200/jco.24.00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 05/19/2024] Open
Abstract
PURPOSE To guide use of multigene panels for germline genetic testing for patients with cancer. METHODS An ASCO Expert Panel convened to develop recommendations on the basis of a systematic review of guidelines, consensus statements, and studies of germline and somatic genetic testing. RESULTS Fifty-two guidelines and consensus statements met eligibility criteria for the primary search; 14 studies were identified for Clinical Question 4. RECOMMENDATIONS Patients should have a family history taken and recorded that includes details of cancers in first- and second-degree relatives and the patient's ethnicity. When more than one gene is relevant based on personal and/or family history, multigene panel testing should be offered. When considering what genes to include in the panel, the minimal panel should include the more strongly recommended genes from Table 1 and may include those less strongly recommended. A broader panel may be ordered when the potential benefits are clearly identified, and the potential harms from uncertain results should be mitigated. Patients who meet criteria for germline genetic testing should be offered germline testing regardless of results from tumor testing. Patients who would not normally be offered germline genetic testing based on personal and/or family history criteria but who have a pathogenic or likely pathogenic variant identified by tumor testing in a gene listed in Table 2 under the outlined circumstances should be offered germline testing.Additional information is available at www.asco.org/molecular-testing-and-biomarkers-guidelines.
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Affiliation(s)
- Nadine Tung
- Beth Israel Deaconess Medical Center, Sharon, MA
| | | | | | | | | | | | | | - Banu Arun
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yanin Chavarri-Guerra
- Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán, Mexico City, Mexico
| | | | | | | | | | - Gregory Idos
- City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Ghecemy Lopez
- USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Tuya Pal
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Sara Pirzadeh-Miller
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
| | | | | | - Umang Swami
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT
| | - Gregory A Vidal
- The West Cancer Center and Research Institute and The University of Tennessee Health Sciences Center, Germantown, TN
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2
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Wyatt Castillo RB, Nielsen SM, Chen E, Heald B, Ellsworth RE, Esplin ED, Tomlinson GE. Disparate Rates of Germline Variants in Cancer Predisposition Genes in African American/Black Compared With Non-Hispanic White Individuals Between 2015 and 2022. JCO Precis Oncol 2024; 8:e2300715. [PMID: 38991178 DOI: 10.1200/po.23.00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
PURPOSE African American/Black (AA/B) individuals are under-represented in genomic databases and thus less likely to receive definitive information from germline genetic testing (GGT) than non-Hispanic White (NHW) individuals. With nearly 500,000 AA/B and NHW individuals having undergone multigene panel testing (MGPT) for hereditary cancer risk at a single commercial laboratory, to our knowledge, we present the largest study to date investigating cancer GGT results in AA/B and NHW individuals. METHODS MGPT results from a retrospective cohort of AA/B (n = 48,684) and NHW (n = 444,831) patients were evaluated. Frequencies of pathogenic germline variants (PGVs) and variants of uncertain significance (VUS) were compared between AA/B and NHW individuals. Changes in frequency of VUS over time were determined. Pearson's chi-squared test was used to compare categorical variables among groups. All significance tests were two-tailed, and P < .05 was considered statistically significant. RESULTS Between 2015 and 2022, rates of VUS decreased 2.3-fold in AA/B and 1.8-fold in NHW individuals; however, frequencies of VUS and PGV remained significantly higher (46% v 32%; P < .0001) and lower (9% v 13%; P < .0001) in AA/B compared with NHW individuals. Rates of VUS in ATM, BRCA1, BRCA2, PALB2, and PMS2 were significantly higher in AA/B compared with NHW individuals, whereas rates of PGV in BRCA1, BRCA2, and PALB2 were higher in AA/B compared with NHW individuals (P < .001). CONCLUSION Despite reductions in VUS frequencies over time, disparities in definitive GGT results persist. Increasing inclusion of AA/B populations in both testing and research will further increase knowledge of genetic variants across these racial groups.
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Affiliation(s)
- Rachel B Wyatt Castillo
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
| | | | | | | | | | | | - Gail E Tomlinson
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
- Mays Cancer Center, UT Health San Antonio, San Antonio, TX
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3
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Martin BE, Sands T, Bier L, Bergner A, Boehme AK, Lippa N. Comparing the frequency of variants of uncertain significance (VUS) between ancestry groups in a paediatric epilepsy cohort. J Med Genet 2024; 61:645-651. [PMID: 38453479 DOI: 10.1136/jmg-2023-109450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Studies indicate that variants of uncertain significance are more common in non-European populations due to lack of a diversity in population databases. This difference has not been explored in epilepsy, which is increasingly found to be genetic in paediatric populations, and has precision medicine applications. This study examines the differences in the frequency of uncertain next-generation sequencing (NGS) results among a paediatric epilepsy cohort between ancestral groups historically under-represented in biomedical research (UBR) and represented in biomedical research (RBR). METHODS A retrospective chart review of patients with epilepsy seen at Columbia University Irving Medical Center (CUIMC). One hundred seventy-eight cases met the following criteria: (1) visited any provider within the Pediatric Neurology Clinic at CUIMC, (2) had an ICD code indicating a diagnosis of epilepsy, (3) underwent NGS testing after March 2015 and (4) had self-reported ancestry that fit into a single dichotomous category of either historically represented or under-represented in biomedical research. RESULTS UBR cases had significantly higher rates of uncertain results when compared with RBR cases (79.2% UBR, 20.8% RBR; p value=0.002). This finding remained true after controlling for potential confounding factors, including sex, intellectual disability or developmental delay, epilepsy type, age of onset, number of genes tested and year of testing. CONCLUSION Our results add to the literature that individuals who are of ancestries historically under-represented in genetics research are more likely to receive uncertain genetic results than those of represented majority ancestral groups and establishes this finding in an epilepsy cohort.
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Affiliation(s)
- Bree E Martin
- Department of General Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tristan Sands
- Department of Neurology, Columbia University, New York, New York, USA
- Columbia University Irving Medical Center, New York, New York, USA
| | - Louise Bier
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amanda Bergner
- Genetic Counseling Graduate Program, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Amelia K Boehme
- Department of Neurology, Columbia University, New York, New York, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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4
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Brown EE, Byrne K, Michos ED, Leucker TM, Marvel F, Jones SR, Martin SS, Arvanitis M. Expanded genetic testing in familial hypercholesterolemia-A single center's experience. Am J Prev Cardiol 2024; 18:100683. [PMID: 38828125 PMCID: PMC11139767 DOI: 10.1016/j.ajpc.2024.100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/03/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024] Open
Abstract
Objective Assess the yield of genetic testing for pathogenic variants in ABCG5, ABCG8, LIPA, and APOE in individuals with personal and family histories suggestive of familial hypercholesterolemia. Methods Retrospective review of patients seen in the Advanced Lipid Disorders Clinic at Johns Hopkins. Results In the lipid clinic at a single center during the years 2015-2023, 607 patients underwent genetic testing for familial hypercholesterolemia, of which 263 underwent the expanded genetic testing for sitosterolemia. Eighty-eight patients had genetic testing which included APOE, and 22 patients had testing which included LIPA. Among these, one patient was identified to have a pathogenic variant in APOE and another patient with a pathogenic variant in ABCG5 (0.7 % yield). The frequency of a positive result was double that of a variant of uncertain significance. Conclusion These data suggest in rare cases expanded testing can provide answers for patients and families with a minimal likelihood of a variant of uncertain significance.
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Affiliation(s)
- Emily E. Brown
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Kathleen Byrne
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Erin D. Michos
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Thorsten M. Leucker
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Francoise Marvel
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Steven R. Jones
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Seth S. Martin
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
| | - Marios Arvanitis
- Division of Cardiology, School of Medicine, Johns Hopkins University, 600 N. Wolfe St Blalock 572, Baltimore, MD 21287, United States
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5
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Friedman CE, Fayer S, Pendyala S, Chien WM, Loiben A, Tran L, Chao LS, McKinstry A, Ahmed D, Farris SD, Stempien-Otero A, Jonlin EC, Murry CE, Starita LM, Fowler DM, Yang KC. Multiplexed Functional Assessments of MYH7 Variants in Human Cardiomyocytes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004377. [PMID: 38362799 PMCID: PMC11196868 DOI: 10.1161/circgen.123.004377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Pathogenic autosomal-dominant missense variants in MYH7 (myosin heavy chain 7), which encodes the sarcomeric protein (β-MHC [beta myosin heavy chain]) expressed in cardiac and skeletal myocytes, are a leading cause of hypertrophic cardiomyopathy and are clinically actionable. However, ≈75% of MYH7 missense variants are of unknown significance. While human-induced pluripotent stem cells (hiPSCs) can be differentiated into cardiomyocytes to enable the interrogation of MYH7 variant effect in a disease-relevant context, deep mutational scanning has not been executed using diploid hiPSC derivates due to low hiPSC gene-editing efficiency. Moreover, multiplexable phenotypes enabling deep mutational scanning of MYH7 variant hiPSC-derived cardiomyocytes are unknown. METHODS To overcome these obstacles, we used CRISPRa On-Target Editing Retrieval enrichment to generate an hiPSC library containing 113 MYH7 codon variants suitable for deep mutational scanning. We first established that β-MHC protein loss occurs in a hypertrophic cardiomyopathy human heart with a pathogenic MYH7 variant. We then differentiated the MYH7 missense variant hiPSC library to cardiomyocytes for multiplexed assessment of β-MHC variant abundance by massively parallel sequencing and hiPSC-derived cardiomyocyte survival. RESULTS Both the multiplexed assessment of β-MHC abundance and hiPSC-derived cardiomyocyte survival accurately segregated all known pathogenic variants from synonymous variants. Functional data were generated for 4 variants of unknown significance and 58 additional MYH7 missense variants not yet detected in patients. CONCLUSIONS This study leveraged hiPSC differentiation into disease-relevant cardiomyocytes to enable multiplexed assessments of MYH7 missense variants for the first time. Phenotyping strategies used here enable the application of deep mutational scanning to clinically actionable genes, which should reduce the burden of variants of unknown significance on patients and clinicians.
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Affiliation(s)
- Clayton E. Friedman
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Shawn Fayer
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
| | | | - Wei-Ming Chien
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
| | - Alexander Loiben
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Linda Tran
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Leslie S. Chao
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Ashley McKinstry
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Dania Ahmed
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Stephen D. Farris
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
| | - April Stempien-Otero
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
| | - Erica C. Jonlin
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
| | - Charles E. Murry
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Dept of Laboratory Medicine & Pathology, Univ of Washington; Seattle, WA
- Dept of Bioengineering, Univ of Washington; Seattle, WA
| | - Lea M. Starita
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Douglas M. Fowler
- Dept of Genome Sciences, Univ of Washington; Seattle, WA
- Dept of Bioengineering, Univ of Washington; Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Kai-Chun Yang
- Institute for Stem Cell & Regenerative Medicine, Univ of Washington, School of Medicine; Seattle, WA
- Center for Cardiovascular Biology, Univ of Washington; Seattle, WA
- Dept of Medicine/Cardiology, Univ of Washington; Seattle, WA
- Cardiology/Hospital Specialty Medicine, VA Puget Sound HCS; Seattle, WA
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Rački V, Bergant G, Papić E, Kovanda A, Hero M, Rožmarić G, Starčević Čizmarević N, Ristić S, Ostojić S, Kapović M, Maver A, Peterlin B, Vuletić V. GiOPARK Project: The Genetic Study of Parkinson's Disease in the Croatian Population. Genes (Basel) 2024; 15:255. [PMID: 38397244 PMCID: PMC10888376 DOI: 10.3390/genes15020255] [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: 01/29/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease is a neurological disorder that affects motor function, autonomic functions, and cognitive abilities. It is likely that both genetic and environmental factors, along with age, contribute to the cause. However, there is no comprehensive guideline for genetic testing for Parkinson's disease, and more research is needed to understand genetic variations in different populations. There has been no research on the genetic background of Parkinson's disease in Croatia so far. Therefore, with the GiOPARK project, we aimed to investigate the genetic variants responsible for Parkinson's disease in 153 Croatian patients with early onset, familial onset, and sporadic late-onset using whole-exome sequencing, along with multiplex ligation-dependent probe amplification and Sanger sequencing in select patients. We found causative variants in 7.84% of the patients, with GBA being the most common gene (4.58%), followed by PRKN (1.96%), ITM2B (0.65%), and MAPT (0.65%). Moreover, variants of uncertain significance were identified in 26.14% of the patients. The causative variants were found in all three subgroups, indicating that genetic factors play a role in all the analyzed Parkinson's disease subtypes. This study emphasizes the need for more inclusive research and improved guidelines to better understand the genetic basis of Parkinson's disease and facilitate more effective clinical management.
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Affiliation(s)
- Valentino Rački
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Eliša Papić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Mario Hero
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Gloria Rožmarić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Nada Starčević Čizmarević
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Smiljana Ristić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Miljenko Kapović
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (N.S.Č.); (S.R.); (S.O.); (M.K.)
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (G.B.); (A.K.); (A.M.); (B.P.)
| | - Vladimira Vuletić
- Department of Neurology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (V.R.); (E.P.); (M.H.); (G.R.)
- Department of Neurology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
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7
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Zech M, Winkelmann J. Next-generation sequencing and bioinformatics in rare movement disorders. Nat Rev Neurol 2024; 20:114-126. [PMID: 38172289 DOI: 10.1038/s41582-023-00909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
The ability to sequence entire exomes and genomes has revolutionized molecular testing in rare movement disorders, and genomic sequencing is becoming an integral part of routine diagnostic workflows for these heterogeneous conditions. However, interpretation of the extensive genomic variant information that is being generated presents substantial challenges. In this Perspective, we outline multidimensional strategies for genetic diagnosis in patients with rare movement disorders. We examine bioinformatics tools and computational metrics that have been developed to facilitate accurate prioritization of disease-causing variants. Additionally, we highlight community-driven data-sharing and case-matchmaking platforms, which are designed to foster the discovery of new genotype-phenotype relationships. Finally, we consider how multiomic data integration might optimize diagnostic success by combining genomic, epigenetic, transcriptomic and/or proteomic profiling to enable a more holistic evaluation of variant effects. Together, the approaches that we discuss offer pathways to the improved understanding of the genetic basis of rare movement disorders.
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Affiliation(s)
- Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
- DZPG, Deutsches Zentrum für Psychische Gesundheit, Munich, Germany.
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8
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Yeow D, Rudaks LI, Siow SF, Davis RL, Kumar KR. Genetic Testing of Movements Disorders: A Review of Clinical Utility. Tremor Other Hyperkinet Mov (N Y) 2024; 14:2. [PMID: 38222898 PMCID: PMC10785957 DOI: 10.5334/tohm.835] [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: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/16/2024] Open
Abstract
Currently, pathogenic variants in more than 500 different genes are known to cause various movement disorders. The increasing accessibility and reducing cost of genetic testing has resulted in increasing clinical use of genetic testing for the diagnosis of movement disorders. However, the optimal use case(s) for genetic testing at a patient level remain ill-defined. Here, we review the utility of genetic testing in patients with movement disorders and also highlight current challenges and limitations that need to be considered when making decisions about genetic testing in clinical practice. Highlights The utility of genetic testing extends across multiple clinical and non-clinical domains. Here we review different aspects of the utility of genetic testing for movement disorders and the numerous associated challenges and limitations. These factors should be weighed on a case-by-case basis when requesting genetic tests in clinical practice.
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Affiliation(s)
- Dennis Yeow
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Neurology, Prince of Wales Hospital, Randwick, NSW, Australia
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Laura I. Rudaks
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Sue-Faye Siow
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Ryan L. Davis
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Neurogenetics Research Group, Kolling Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St Leonards, NSW, Australia
| | - Kishore R. Kumar
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
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9
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McGill BC, Wakefield CE, Tucker KM, Daly RA, Donoghoe MW, Vetsch J, Warby M, Fuentes‐Bolanos NA, Barlow‐Stewart K, Kirk J, Courtney E, O’Brien TA, Marshall GM, Pinese M, Cowley MJ, Tyrrell V, Deyell RJ, Ziegler DS, Hetherington K. Parents' expectations, preferences, and recall of germline findings in a childhood cancer precision medicine trial. Cancer 2023; 129:3620-3632. [PMID: 37382186 PMCID: PMC10952780 DOI: 10.1002/cncr.34917] [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: 08/29/2022] [Revised: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Germline genome sequencing in childhood cancer precision medicine trials may reveal pathogenic or likely pathogenic variants in cancer predisposition genes in more than 10% of children. These findings can have implications for diagnosis, treatment, and the child's and family's future cancer risk. Understanding parents' perspectives of germline genome sequencing is critical to successful clinical implementation. METHODS A total of 182 parents of 144 children (<18 years of age) with poor-prognosis cancers enrolled in the Precision Medicine for Children with Cancer trial completed a questionnaire at enrollment and after the return of their child's results, including clinically relevant germline findings (received by 13% of parents). Parents' expectations of germline genome sequencing, return of results preferences, and recall of results received were assessed. Forty-five parents (of 43 children) were interviewed in depth. RESULTS At trial enrollment, most parents (63%) believed it was at least "somewhat likely" that their child would receive a clinically relevant germline finding. Almost all expressed a preference to receive a broad range of germline genomic findings, including variants of uncertain significance (88%). Some (29%) inaccurately recalled receiving a clinically relevant germline finding. Qualitatively, parents expressed confusion and uncertainty after the return of their child's genome sequencing results by their child's clinician. CONCLUSIONS Many parents of children with poor-prognosis childhood cancer enrolled in a precision medicine trial expect their child may have an underlying cancer predisposition syndrome. They wish to receive a wide scope of information from germline genome sequencing but may feel confused by the reporting of trial results.
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10
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Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
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Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
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11
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Dingemans AJM, Hinne M, Truijen KMG, Goltstein L, van Reeuwijk J, de Leeuw N, Schuurs-Hoeijmakers J, Pfundt R, Diets IJ, den Hoed J, de Boer E, Coenen-van der Spek J, Jansen S, van Bon BW, Jonis N, Ockeloen CW, Vulto-van Silfhout AT, Kleefstra T, Koolen DA, Campeau PM, Palmer EE, Van Esch H, Lyon GJ, Alkuraya FS, Rauch A, Marom R, Baralle D, van der Sluijs PJ, Santen GWE, Kooy RF, van Gerven MAJ, Vissers LELM, de Vries BBA. PhenoScore quantifies phenotypic variation for rare genetic diseases by combining facial analysis with other clinical features using a machine-learning framework. Nat Genet 2023; 55:1598-1607. [PMID: 37550531 DOI: 10.1038/s41588-023-01469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/05/2023] [Indexed: 08/09/2023]
Abstract
Several molecular and phenotypic algorithms exist that establish genotype-phenotype correlations, including facial recognition tools. However, no unified framework that investigates both facial data and other phenotypic data directly from individuals exists. We developed PhenoScore: an open-source, artificial intelligence-based phenomics framework, combining facial recognition technology with Human Phenotype Ontology data analysis to quantify phenotypic similarity. Here we show PhenoScore's ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 37 of 40 investigated syndromes against clinical features observed in individuals with other neurodevelopmental disorders and show it is an improvement on existing approaches. PhenoScore provides predictions for individuals with variants of unknown significance and enables sophisticated genotype-phenotype studies by testing hypotheses on possible phenotypic (sub)groups. PhenoScore confirmed previously known phenotypic subgroups caused by variants in the same gene for SATB1, SETBP1 and DEAF1 and provides objective clinical evidence for two distinct ADNP-related phenotypes, already established functionally.
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Affiliation(s)
- Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Max Hinne
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Kim M G Truijen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lia Goltstein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Janneke Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Illja J Diets
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joery den Hoed
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jet Coenen-van der Spek
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Noraly Jonis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Elizabeth E Palmer
- Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Gholson J Lyon
- Department of Human Genetics and George A. Jervis Clinic, Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York City, NY, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Diana Baralle
- Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marcel A J van Gerven
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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12
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Stolarova L, Kleiblova P, Zemankova P, Stastna B, Janatova M, Soukupova J, Achatz MI, Ambrosone C, Apostolou P, Arun BK, Auer P, Barnard M, Bertelsen B, Blok MJ, Boddicker N, Brunet J, Burnside ES, Calvello M, Campbell I, Chan SH, Chen F, Chiang JB, Coppa A, Cortesi L, Crujeiras-González A, De Leeneer K, De Putter R, DePersia A, Devereux L, Domchek S, Efremidis A, Engel C, Ernst C, Evans DGR, Feliubadaló L, Fostira F, Fuentes-Ríos O, Gómez-García EB, González S, Haiman C, Hansen TVO, Hauke J, Hodge J, Hu C, Huang H, Ishak NDB, Iwasaki Y, Konstantopoulou I, Kraft P, Lacey J, Lázaro C, Li N, Lim WK, Lindstrom S, Lori A, Martinez E, Martins A, Matsuda K, Matullo G, McInerny S, Michailidou K, Montagna M, Monteiro AN, Mori L, Nathanson K, Neuhausen SL, Nevanlinna H, Olson JE, Palmer J, Pasini B, Patel A, Piane M, Poppe B, Radice P, Renieri A, Resta N, Richardson ME, Rosseel T, Ruddy KJ, Santamariña M, Dos Santos ES, Teras L, Toland AE, Trentham-Dietz A, Vachon CM, Volk AE, Weber-Lassalle N, Weitzel JN, Wiesmuller L, Winham S, Yadav S, Yannoukakos D, Yao S, Zampiga V, Zethoven M, Zhang ZW, Zima T, Spurdle AB, Vega A, Rossing M, Del Valle J, De Nicolo A, Hahnen E, Claes KB, Ngeow J, Momozawa Y, James PA, Couch FJ, Macurek L, Kleibl Z. ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. Clin Cancer Res 2023; 29:3037-3050. [PMID: 37449874 PMCID: PMC10425727 DOI: 10.1158/1078-0432.ccr-23-0212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). EXPERIMENTAL DESIGN We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. RESULTS A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)-like (N = 226). We then examined their association with breast cancer risk in the case-control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35-3.41), 1.57 (95% CI, 1.41-1.75), and 1.19 (95% CI, 1.08-1.31), respectively. The meta-analysis of population-specific datasets showed similar results. CONCLUSIONS We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.
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Affiliation(s)
- Lenka Stolarova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Stastna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Maria Isabel Achatz
- A.C. Camargo Cancer Center and Oncology Center, Hospital Sirio-Libanes, Sao Paulo, Brazil
| | - Christine Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Cancer Center, Buffalo, New York
- WCHS Inc., Baltimore, Maryland
| | - Paraskevi Apostolou
- Human Molecular Genetics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- WHI, USA
| | - Mollie Barnard
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- CARRIERS, USA
| | - Joan Brunet
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Elizabeth S. Burnside
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
- WWHS, Charlotte, North Carolina
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Ian Campbell
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sock Hoai Chan
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Fei Chen
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Jian Bang Chiang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, Modena University Hospital, Modena, Italy
| | - Ana Crujeiras-González
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robin De Putter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Susan Domchek
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Efremidis
- Clinical Cancer Genetics and Family Consultants, CLINICAGENE, Athens Medical Center, Athens, Greece
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Lidia Feliubadaló
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Olivia Fuentes-Ríos
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Encarna B. Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sara González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - James Hodge
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- CPS3, Kennesaw, Georgia
| | - Chunling Hu
- CARRIERS, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hongyan Huang
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | | | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | - James Lacey
- Beckman Research Institute, City of Hope Cancer Center, Duarte, California
- CTS, USA
| | - Conxi Lázaro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Na Li
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Sara Lindstrom
- WHI, USA
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Adriana Lori
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- American Cancer Society, Atlanta, Georgia
| | - Elana Martinez
- Duke-NUS Medical School, Singapore, Singapore
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, California
| | - Alexandra Martins
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Alvaro N.A. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Luigi Mori
- Endocrine and Metabolic Disease Unit, ASST Spedali Civili of Brescia, Brescia, Italia
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Katherine Nathanson
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Janet E. Olson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- MCBCS, USA
| | - Julie Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Paolo Radice
- Department of Experimental Oncology, Molecular Bases of Genetic Risk and Genetic Testing Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Nicoletta Resta
- Department of Precision and Regenerative Medicine and Ionian Area, Medical Genetics Unit, University of Bari, Bari, Italy
| | | | - Toon Rosseel
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kathryn J. Ruddy
- MCBCS, USA
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Marta Santamariña
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | | | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Amanda E. Toland
- Department of Cancer Biology & Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Amy Trentham-Dietz
- WWHS, Charlotte, North Carolina
- University of Wisconsin, Madison, Wisconsin
| | | | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Lisa Wiesmuller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Stacey Winham
- MMHS, USA
- Department Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Siddhartha Yadav
- CARRIERS, USA
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Song Yao
- WCHS Inc., Baltimore, Maryland
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Magnus Zethoven
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ze Wen Zhang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesús Del Valle
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Joanne Ngeow
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Fergus J. Couch
- CARRIERS, USA
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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13
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De Oliveira HM, Soma A, Baker MR, Turner MR, Talbot K, Williams TL. A survey of current practice in genetic testing in amyotrophic lateral sclerosis in the UK and Republic of Ireland: implications for future planning. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:405-413. [PMID: 36458618 DOI: 10.1080/21678421.2022.2150556] [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: 07/19/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Objective: To determine the current practice in genetic testing for patients with apparently sporadic motor neurone disease/amyotrophic lateral sclerosis (MND/ALS) and asymptomatic at-risk relatives of familial MND/ALS patients seen in specialized care centers in the UK. Methods: An online survey with 10 questions distributed to specialist healthcare professionals with a role in requesting genetic testing working at MND/ALS care centers. Results: Considerable variation in practice was found. Almost 30% of respondents reported some discomfort in discussing genetic testing with MND/ALS patients and a majority (77%) did not think that all patients with apparently sporadic disease should be routinely offered genetic testing at present. Particular concerns were identified in relation to testing asymptomatic at-risk individuals and the majority view was that clinical genetics services should have a role in supporting genetic testing in MND/ALS, especially in asymptomatic individuals at-risk of carrying pathogenic variants. Conclusions: Variation in practice in genetic testing among MND/ALS clinics may be driven by differences in experience and perceived competence, compounded by the increasing complexity of the genetic underpinnings of MND/ALS. Clear and accessible guidelines for referral pathways between MND/ALS clinics and clinical genetics may be the best way to standardize and improve current practice, ensuring that patients and relatives receive optimal and geographically equitable support.
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Affiliation(s)
- Hugo M De Oliveira
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Arunachalam Soma
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mark R Baker
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne, UK, and
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences. Level 6, John Radcliffe Hospital, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences. Level 6, John Radcliffe Hospital, Oxford, UK
| | - Timothy L Williams
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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14
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Burke W, Parens E, Chung WK, Berger SM, Appelbaum PS. The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review. Ann Intern Med 2022; 175:994-1000. [PMID: 35436152 PMCID: PMC10555957 DOI: 10.7326/m21-4109] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic tests expand diagnostic and screening opportunities but also identify genetic variants of uncertain clinical significance (VUSs). Only a minority of VUSs are likely to prove pathogenic when later reassessed, but resolution of the uncertainty is rarely timely. That uncertainty adds complexity to clinical decision making and can result in harms and costs to patients and the health care system, including the time-consuming analysis required to interpret a VUS and the potential for unnecessary treatment and adverse psychological effects. Current efforts to improve variant interpretation will help reduce the scope of the problem, but the high prevalence of rare and novel variants in the human genome points to VUSs as an ongoing challenge. Additional strategies can help mitigate the potential harms of VUSs, including testing protocols that limit identification or reporting of VUSs, subclassification of VUSs according to the likelihood of pathogenicity, routine family-based evaluation of variants, and enhanced counseling efforts. All involve tradeoffs, and the appropriate balance of measures is likely to vary for different test uses and clinical settings. Cross-specialty deliberation and public input could contribute to systematic and broadly supported policies for managing VUSs.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | | | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara M. Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul S. Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
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15
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The Burden and Benefits of Knowledge: Ethical Considerations Surrounding Population-Based Newborn Genome Screening for Hearing. Int J Neonatal Screen 2022; 8:ijns8020036. [PMID: 35735787 PMCID: PMC9224714 DOI: 10.3390/ijns8020036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Recent advances in genomic sequencing technologies have expanded practitioners' utilization of genetic information in a timely and efficient manner for an accurate diagnosis. With an ever-increasing resource of genomic data from progress in the interpretation of genome sequences, clinicians face decisions about how and when genomic information should be presented to families, and at what potential expense. Presently, there is limited knowledge or experience in establishing the value of implementing genome sequencing into newborn screening. Herein we provide insight into the complexities and the burden and benefits of knowledge resulting from genome sequencing of newborns.
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16
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Cancer patients' understandings of genetic variants of uncertain significance in clinical care. J Community Genet 2022; 13:381-388. [PMID: 35616809 PMCID: PMC9134724 DOI: 10.1007/s12687-022-00594-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/20/2022] [Indexed: 11/10/2022] Open
Abstract
Genetic variants of uncertain significance (VUSs) pose a growing challenge for patient communication and care in precision genomic medicine. To better understand patient perspectives of VUSs, we draw on qualitative analysis of semi-structured interviews with 22 cancer patients and individuals with cancer family history who received a VUS result. The majority of patients did not recall receiving VUS results and those who remembered expressed few worries, while respondents who were tested because of a family history of cancer were more concerned about the VUS results. Personal characteristics, medical condition, family history, expectations prior to testing, and motivations for pursuing testing influence the ways patients came to terms with the uncertainty of the VUS result. We conclude by discussing the relevance of the findings to the debate on the responsibility of the patient in checking back for VUS reclassification and to implications for genetic counseling that emphasizes tailoring the pre- and post-test discussion of VUS as appropriate to the patients’ informational as well as emotional needs.
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17
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Arbustini E, Behr ER, Carrier L, van Duijn C, Evans P, Favalli V, van der Harst P, Haugaa KH, Jondeau G, Kääb S, Kaski JP, Kavousi M, Loeys B, Pantazis A, Pinto Y, Schunkert H, Di Toro A, Thum T, Urtis M, Waltenberger J, Elliott P. Interpretation and actionability of genetic variants in cardiomyopathies: a position statement from the European Society of Cardiology Council on cardiovascular genomics. Eur Heart J 2022; 43:1901-1916. [PMID: 35089333 DOI: 10.1093/eurheartj/ehab895] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/03/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
This document describes the contribution of clinical criteria to the interpretation of genetic variants using heritable Mendelian cardiomyopathies as an example. The aim is to assist cardiologists in defining the clinical contribution to a genetic diagnosis and the interpretation of molecular genetic reports. The identification of a genetic variant of unknown or uncertain significance is a limitation of genetic testing, but current guidelines for the interpretation of genetic variants include essential contributions from clinical family screening that can establish a de novo assignment of the variant or its segregation with the phenotype in the family. A partnership between clinicians and patients helps to solve major uncertainties and provides reliable and clinically actionable information.
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Affiliation(s)
- Eloisa Arbustini
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elijah R Behr
- Cardiology Research Section and Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St George's, University of London and St George's University Hospitals NHS Foundation Trust, London, UK
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paul Evans
- Department of Infection, Immunity and Cardiovascular Disease, and INSIGNEO Institute, University of Sheffield, Sheffield S10 2RX, UK
| | | | - Pim van der Harst
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kristina Hermann Haugaa
- ProCardio Center for Innovation, Department of Cardiology, Oslo University Hospital, Rikshospitalet, Postboks 4950 Nydalen, Oslo 0424, Norway
- University of Oslo, Boks 1072 Blindern, Oslo 0316, Norway
| | - Guillaume Jondeau
- CNMR Syndrome de Marfan et apparentés, Member of VASCERN, AP-HP Hopital Bichat, Service de Cardiologie, 46 rue Henri Huchard, Paris 75018, France
- INSERM LVTS U1148, Paris 75018, France
- Université de Paris, Paris, France
| | - Stefan Kääb
- Medizinische Klinik und Poliklinik I, LMU University Hospital Munich, Munich, Germany
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany
| | - Juan Pablo Kaski
- Institute of Cardiovascular Science, University College London, London, UK
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, UK
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bart Loeys
- Cardiogenomics, Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Antonis Pantazis
- The Royal Brompton and Harefield Hospitals, Part of Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Yigal Pinto
- Department of Experimental Cardiology, University of Amsterdam, Amsterdam University Medical Center, Meibergdreef 15, Amsterdam 1105 AZ, The Netherlands
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, München, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Alessandro Di Toro
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Mario Urtis
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Johannes Waltenberger
- Department of Cardiology and Cardiovascular Medicine, Medical Faculty, University of Münster, Münster, Germany
- Cardiovascular Medicine, Hirslanden Klinik Im Park, Seestrasse 220, Zürich 8027, Switzerland
| | - Perry Elliott
- Barts Heart Centre St Bartholomew's Hospital, London, UK
- Institute for Cardiovascular Science, University College London, London, UK
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18
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Botezatu A, Vladoiu S, Fudulu A, Albulescu A, Plesa A, Muresan A, Stancu C, Iancu IV, Diaconu CC, Velicu A, Popa OM, Badiu C, Dinu-Draganescu D. Advanced molecular approaches in male infertility diagnosis. Biol Reprod 2022; 107:684-704. [PMID: 35594455 DOI: 10.1093/biolre/ioac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
In the recent years a special attention has been given to a major health concern namely to male infertility, defined as the inability to conceive after 12 months of regular unprotected sexual intercourse, taken into account the statistics that highlight that sperm counts have dropped by 50-60% in recent decades. According to the WHO, infertility affects approximately 9% of couples globally, and the male factor is believed to be present in roughly 50% of cases, with exclusive responsibility in 30%. The aim of this manuscript is to present an evidence-based approach for diagnosing male infertility that includes finding new solutions for diagnosis and critical outcomes, retrieving up-to-date studies and existing guidelines. The diverse factors that induce male infertility generated in a vast amount of data that needed to be analysed by a clinician before a decision could be made for each individual. Modern medicine faces numerous obstacles as a result of the massive amount of data generated by the molecular biology discipline. To address complex clinical problems, vast data must be collected, analysed, and used, which can be very challenging. The use of artificial intelligence (AI) methods to create a decision support system can help predict the diagnosis and guide treatment for infertile men, based on analysis of different data as environmental and lifestyle, clinical (sperm count, morphology, hormone testing, karyotype, etc.) and "omics" bigdata. Ultimately, the development of AI algorithms will assist clinicians in formulating diagnosis, making treatment decisions, and predicting outcomes for assisted reproduction techniques.
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Affiliation(s)
- A Botezatu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - S Vladoiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - A Fudulu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Albulescu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,National Institute for Chemical pharmaceutical Research & Development
| | - A Plesa
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Muresan
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - C Stancu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - I V Iancu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - C C Diaconu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Velicu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - O M Popa
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - C Badiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
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19
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Costa A, Franková V, Robert G, Macek M, Patch C, Alexander E, Arellanesova A, Clayton-Smith J, Hunter A, Havlovicová M, Pourová R, Pritchard M, Roberts L, Zoubková V, Metcalfe A. Co-designing models for the communication of genomic results for rare diseases: a comparative study in the Czech Republic and the United Kingdom. J Community Genet 2022; 13:313-327. [PMID: 35523996 PMCID: PMC9075921 DOI: 10.1007/s12687-022-00589-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
The communication of genomic results to patients and families with rare diseases raise distinctive challenges. However, there is little evidence about optimal methods to communicate results to this group of service users. To address this gap, we worked with rare disease families and health professionals from two genetic/genomic services, one in the United Kingdom and one in the Czech Republic, to co-design that best meet their needs. Using the participatory methodology of Experience-Based Co-Design (EBCD), we conducted observations of clinical appointments (n=49) and interviews with family participants (n=23) and health professionals (n=22) to gather their experience of sharing/receiving results. The findings informed a facilitated co-design process, comprising 3 feedback events at each site and a series of meetings and remote consultations. Participants identified a total of four areas of current service models in need of improvement, and co-designed six prototypes of quality improvement interventions. The main finding was the identification of post-test care as the shared priority for improvement for both health professionals and families at the two sites. Our findings indicate the need to strengthen the link between diagnostics (whether or not a pathogenic variant is found) and post-test care, including psychosocial and community support. This raises implications for the reconfigurations of genomic service models, the redefinition of professional roles and responsibilities and the involvement of rare disease patients and families in health care research.
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Affiliation(s)
- Alessia Costa
- Engagement and Society, Wellcome Connecting Science, Hinxton, CB10 1SA, Cambridgeshire, UK. .,Faculty of Nursing, Midwifery and Palliative Care, King's College London, London, SE1 8WA, UK.
| | - Věra Franková
- Department of Paediatrics and Inherited Metabolic Disorders, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic. .,Institute for Medical Humanities, Charles University, First Faculty of Medicine, Prague, Czech Republic.
| | - Glenn Robert
- Faculty of Nursing, Midwifery and Palliative Care, King's College London, London, SE1 8WA, UK
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University, Second Faculty of Medicine, and University Hospital Motol, Prague, Czech Republic
| | - Christine Patch
- Engagement and Society, Wellcome Connecting Science, Hinxton, CB10 1SA, Cambridgeshire, UK.,Genomics England, London, EC1M 6BQ, UK
| | - Elizabeth Alexander
- Manchester Centre For Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, M13 9WL, UK
| | - Anna Arellanesova
- Česká asociace pro vzácná onemocnění (ČAVO), Rare Diseases Czech Republic, Bělohorská 19, Praha 6, 169 00, Czech Republic
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, M13 9WL, UK.,Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Amy Hunter
- Genetic Alliance UK, London, EC2A 4NE, UK
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University, Second Faculty of Medicine, and University Hospital Motol, Prague, Czech Republic
| | - Radka Pourová
- Department of Biology and Medical Genetics, Charles University, Second Faculty of Medicine, and University Hospital Motol, Prague, Czech Republic
| | | | - Lauren Roberts
- Genetic Alliance UK, London, EC2A 4NE, UK.,Syndromes Without A Name (SWAN UK), London, EC2A 4NE, UK
| | - Veronika Zoubková
- Department of Biology and Medical Genetics, Charles University, Second Faculty of Medicine, and University Hospital Motol, Prague, Czech Republic
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20
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Receiving results of uncertain clinical relevance from population genetic screening: systematic review & meta-synthesis of qualitative research. Eur J Hum Genet 2022; 30:520-531. [PMID: 35256770 PMCID: PMC9090782 DOI: 10.1038/s41431-022-01054-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic screening can be hugely beneficial, yet its expansion poses clinical and ethical challenges due to results of uncertain clinical relevance (such as ‘cystic fibrosis screen positive, inconclusive diagnosis’/CFSPID). This review systematically identifies, appraises, and synthesises the qualitative research on experiences of receiving results of uncertain clinical relevance from population genetic screening. Eight databases were systematically searched for original qualitative research using the SPIDER framework, and checked against inclusion criteria by the research team and an independent researcher. Nine papers were included (from USA, Canada, UK, New Zealand). PRISMA, ENTREQ, and EMERGE guidance were used to report. Quality was appraised using criteria for qualitative research. All papers focused on parental responses to uncertain results from newborn screening. Data were synthesised using meta-ethnography and first- and second-order constructs. Findings suggest that results of uncertain clinical relevance are often experienced in the same way as a ‘full-blown’ diagnosis. This has significant emotional and behavioural impact, for example adoption of lifestyle-altering disease-focused behaviours. Analysis suggests this may be due to the results not fitting a common medical model, leading recipients to interpret the significance of the result maladaptively. Findings suggest scope for professionals to negotiate and reframe uncertain screening results. Clearer initial communication is needed to reassure recipients there is no immediate severe health risk from these types of results. Public understanding of an appropriate medical model, that accounts for uncertain genetic screening results in a non-threatening way, may be key to maximising the benefits of genomic medicine and minimising potential psychological harm.
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21
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Tirrò E, Martorana F, Micale G, Inzerilli N, Carciotto R, Romano C, Longhitano C, Motta G, Lanzafame K, Stella S, Massimino M, Vitale SR, Salvatorelli L, Magro G, Manzella L, Vigneri P. Next generation sequencing in a cohort of patients with rare sarcoma histotypes: A single institution experience. Pathol Res Pract 2022; 232:153820. [DOI: 10.1016/j.prp.2022.153820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 10/19/2022]
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22
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Best MC, Butow P, Savard J, Jacobs C, Bartley N, Davies G, Napier CE, Ballinger ML, Thomas DM, Biesecker B, Tucker KM, Juraskova I, Meiser B, Schlub T, Newson AJ. Preferences for return of germline genome sequencing results for cancer patients and their genetic relatives in a research setting. Eur J Hum Genet 2022; 30:930-937. [PMID: 35277654 PMCID: PMC9349221 DOI: 10.1038/s41431-022-01069-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 11/09/2022] Open
Abstract
Germline genome sequencing (GS) holds great promise for cancer prevention by identifying cancer risk and guiding prevention strategies, however research evidence is mixed regarding patient preferences for receiving GS results. The aim of this study was to discern preferences for return of results by cancer patients who have actually undergone GS. We conducted a mixed methods study with a cohort of cancer probands (n = 335) and their genetic relatives (n = 199) undergoing GS in a research setting. Both groups completed surveys when giving consent. A subset of participants (n = 40) completed semi-structured interviews. A significantly higher percentage of probands thought people would like to be informed about genetic conditions for which there is prevention or treatment that can change cancer risk compared to conditions for which there is no prevention or treatment (93% [311] versus 65% [216]; p < 0.001). Similar results were obtained for relatives (91% [180] versus 61% [121]; p < 0.001). Themes identified in the analysis of interviews were: (1) Recognised benefits of GS, (2) Balancing benefits with risks, (3) Uncertain results are perceived as unhelpful and (4) Competing obligations. While utility was an important discriminator in what was seen as valuable for this cohort, there was a variety of responses. In view of varied participant preferences regarding return of results, it is important to ensure patient understanding of test validity and identify individual choices at the time of consent to GS. The nature and value of the information, and a contextual understanding of researcher obligations should guide result return.
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Affiliation(s)
- Megan C Best
- Faculty of Science, University of Sydney, Sydney, NSW, Australia. .,Institute for Ethics and Society, University of Notre Dame Australia, Sydney, WA, Australia.
| | - Phyllis Butow
- Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | | | - Chris Jacobs
- Graduate School of Health, University of Technology, Sydney, NSW, Australia
| | - Nicole Bartley
- Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Grace Davies
- Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Christine E Napier
- Cancer Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David M Thomas
- Cancer Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Katherine M Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ilona Juraskova
- Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Bettina Meiser
- Psychosocial Research Group, University of NSW, Sydney, NSW, Australia
| | - Timothy Schlub
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ainsley J Newson
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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23
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Patel HV, Henrikson NB, Ralston JD, Leppig K, Scrol A, Jarvik GP, DeVange S, Larson EB, Hartzler AL. Implementation matters: How patient experiences differ when genetic counseling accompanies the return of genetic variants of uncertain significance. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2022; 2021:950-958. [PMID: 35309003 PMCID: PMC8861684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Precision medicine presents challenges for effective return of results (ROR) to patients, particularly for variants of uncertain significance (VUS) where the need for genetic counseling and the impact of results are underexplored. We investigated patients' experiences with VUS ROR. Through interviews we compared experiences of patients who were referred to genetic counseling with those not referred. Although participants from both groups (n=16) reported curious enthusiasm and relief after ROR, the 5 referred participants reported less confusion, less disappointment, and better confidence in understanding their results than the 11 non-referred participants. Although VUS did not impact healthcare or daily lives, some participants who shared VUS fostered communication about future healthcare. Suggested ROR improvements included patient-friendly terminology, on-demand education, and ongoing consultation. Although patient experience of VUS improved when ROR involved expert consultation, scarcity of genetic counselors presents challenges. Improving the ROR process with patient-centered solutions could enhance the patient experience of receiving VUS.
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Affiliation(s)
| | - Nora B Henrikson
- Kaiser Permanente Washington Health Research Institute, Seattle Washington
| | - James D Ralston
- Kaiser Permanente Washington Health Research Institute, Seattle Washington
| | | | - Aaron Scrol
- Kaiser Permanente Washington Health Research Institute, Seattle Washington
| | | | | | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle Washington
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24
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Bokkers K, Vlaming M, Engelhardt EG, Zweemer RP, van Oort IM, Kiemeney LALM, Bleiker EMA, Ausems MGEM. The Feasibility of Implementing Mainstream Germline Genetic Testing in Routine Cancer Care-A Systematic Review. Cancers (Basel) 2022; 14:cancers14041059. [PMID: 35205807 PMCID: PMC8870548 DOI: 10.3390/cancers14041059] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Germline genetic testing for patients with cancer can have important implications for treatment, preventive options, and for family members. In a mainstream genetic testing pathway, pre-test counseling is performed by non-genetic healthcare professionals, thereby making genetic testing more accessible to all patients who might benefit from it. These mainstream genetic testing pathways are being implemented in different hospitals around the world, and for different cancer types. It is important to evaluate how a mainstream genetic testing pathway can be made sustainable and if quality of genetic care is maintained. We show in this systematic review that it is feasible to incorporate a mainstream genetic testing pathway into routine cancer care while maintaining quality of care. A training procedure for non-genetic healthcare professionals and a close collaboration between genetics and other clinical departments are highly recommended to ensure sustainability. Abstract Background: Non-genetic healthcare professionals can provide pre-test counseling and order germline genetic tests themselves, which is called mainstream genetic testing. In this systematic review, we determined whether mainstream genetic testing was feasible in daily practice while maintaining quality of genetic care. Methods: PubMed, Embase, CINAHL, and PsychINFO were searched for articles describing mainstream genetic testing initiatives in cancer care. Results: Seventeen articles, reporting on 15 studies, met the inclusion criteria. Non-genetic healthcare professionals concluded that mainstream genetic testing was possible within the timeframe of a routine consultation. In 14 studies, non-genetic healthcare professionals completed some form of training about genetics. When referral was coordinated by a genetics team, the majority of patients carrying a pathogenic variant were seen for post-test counseling by genetic healthcare professionals. The number of days between cancer diagnosis and test result disclosure was always lower in the mainstream genetic testing pathway than in the standard genetic testing pathway (e.g., pre-test counseling at genetics department). Conclusions: Mainstream genetic testing seems feasible in daily practice with no insurmountable barriers. A structured pathway with a training procedure is desirable, as well as a close collaboration between genetics and other clinical departments.
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Affiliation(s)
- Kyra Bokkers
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
| | - Michiel Vlaming
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
| | - Ellen G. Engelhardt
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (E.G.E.); (E.M.A.B.)
| | - Ronald P. Zweemer
- Department of Gynecological Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands;
| | - Inge M. van Oort
- Department of Urology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands; (I.M.v.O.); (L.A.L.M.K.)
| | - Lambertus A. L. M. Kiemeney
- Department of Urology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands; (I.M.v.O.); (L.A.L.M.K.)
- Department for Health Evidence, Radboud University Medical Center, Geert Grooteplein Zuid 21, 6525 EZ Nijmegen, The Netherlands
| | - Eveline M. A. Bleiker
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (E.G.E.); (E.M.A.B.)
- Department of Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- Family Cancer Clinic, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
- Correspondence: ; Tel.: +31-88-75-538-00
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25
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Mahecha D, Nuñez H, Lattig MC, Duitama J. Machine Learning Models for Accurate Prioritization of Variants of Uncertain Significance. Hum Mutat 2022; 43:449-460. [PMID: 35143088 DOI: 10.1002/humu.24339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/04/2022] [Accepted: 01/23/2022] [Indexed: 11/08/2022]
Abstract
The growing use of next generation sequencing technologies on genetic diagnosis has produced an exponential increase in the number of Variants of Uncertain Significance (VUS). In this manuscript we compare three machine learning methods to classify VUS as Pathogenic or No pathogenic, implementing a Random Forest (RF), a Support Vector Machine (SVM), and a Multilayer Perceptron (MLP). To train the models, we extracted high quality variants from ClinVar that were previously classified as VUS. For each variant, we retrieved 9 conservation scores, the loss of function tool and allele frequencies. For the RF and SVM models, hyperparameters were tuned using cross validation with a grid search. The three models were tested on a non-overlapping set of variants that had been classified as VUS any time along the last three years but had been reclassified in august 2020. The three models yielded superior accuracy on this set compared to the benchmarked tools. The RF based model yielded the best performance across different variant types and was used to create VusPrize, an open source software tool for prioritization of variants of uncertain significance. We believe that our model can improve the process of genetic diagnosis in research and clinical settings. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Daniel Mahecha
- SIGEN, Alianza Universidad de los Andes - Fundación Santa Fe de Bogota, Colombia.,Systems and Computing Engineering Department, Universidad de los Andes, Colombia
| | - Haydemar Nuñez
- Systems and Computing Engineering Department, Universidad de los Andes, Colombia
| | - Maria C Lattig
- SIGEN, Alianza Universidad de los Andes - Fundación Santa Fe de Bogota, Colombia.,Facultad de Ciencias, Universidad de los Andes
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Colombia
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26
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Levin Fridman A, Raz A, Timmermans S, Shkedi-Rafid S. Views of Israeli healthcare professionals regarding communication of genetic variants of uncertain significance to patients. J Genet Couns 2022; 31:912-921. [PMID: 35122362 PMCID: PMC9541910 DOI: 10.1002/jgc4.1560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 11/21/2022]
Abstract
While genomic medicine is becoming an important part of patient care with an ever‐increasing diagnostic yield, communicating variants of uncertain clinical significance (VUSs) remains a major challenge. We draw on qualitative analysis of semi‐structured interviews conducted in 2020 with 20 Israeli healthcare professionals and stakeholders involved in communicating the results of genome‐wide sequencing to patients. Respondents described four main strategies of communicating VUSs to patients: preparing the patient pre‐test for uncertainty; adapting the level of detail to the patient's needs; upgrading versus downgrading the VUS; and following up on the possible reclassification of VUSs. These strategies were expressed differently by physicians and genetic counselors, varying according to their specialty and perception of the patient's situation. We discuss the strategic management and communication of uncertain genomic test results with patients in the context of meeting patients' expectations and working toward genetic causality through genomic narration and designation.
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Affiliation(s)
- Alma Levin Fridman
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Aviad Raz
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Shiri Shkedi-Rafid
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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27
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Shahani SA, Marcotte EL. Landscape of germline cancer predisposition mutations testing and management in pediatrics: Implications for research and clinical care. Front Pediatr 2022; 10:1011873. [PMID: 36225340 PMCID: PMC9548803 DOI: 10.3389/fped.2022.1011873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
As germline genetic testing capacities have improved over the last two decades, increasingly more people are newly diagnosed with germline cancer susceptibility mutations. In the wake of this growth, there remain limitations in both testing strategies and translation of these results into morbidity- and mortality-reducing practices, with pediatric populations remaining especially vulnerable. To face the challenges evoked by an expanding diversity of germline cancer mutations, we can draw upon a model cancer-associated genetic condition for which we have developed a breadth of expertise in managing, Trisomy 21. We can additionally apply advances in other disciplines, such as oncofertility and pharmacogenomics, to enhance care delivery. Herein, we describe the history of germline mutation testing, epidemiology of known germline cancer mutations and their associations with childhood cancer, testing limitations, and future directions for research and clinical care.
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Affiliation(s)
- Shilpa A Shahani
- Department of Pediatrics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Erin L Marcotte
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
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28
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Comprehensive Genetic Testing for Pediatric Hypertrophic Cardiomyopathy Reveals Clinical Management Opportunities and Syndromic Conditions. Pediatr Cardiol 2022; 43:616-623. [PMID: 34714385 PMCID: PMC8554517 DOI: 10.1007/s00246-021-02764-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) has historically been diagnosed phenotypically. Through genetic testing, identification of a molecular diagnosis (MolDx) is increasingly common but the impact on pediatric patients is unknown. This was a retrospective study of next-generation sequencing data for 602 pediatric patients with a clinician-reported history of HCM. Diagnostic yield was stratified by gene and self-reported race/ethnicity. A MolDx of HCM was identified in 242 (40%) individuals. Sarcomeric genes were the highest yielding, but pathogenic and/or likely pathogenic (P/LP) variants in syndromic genes were found in 36% of individuals with a MolDx, often in patients without documented clinical suspicion for a genetic syndrome. Among all MolDx, 73% were in genes with established clinical management recommendations and 2.9% were in genes that conferred eligibility for clinical trial enrollment. Black patients were the least likely to receive a MolDx. In the current era, genetic testing can impact management of HCM, beyond diagnostics or prognostics, through disease-specific guidelines or clinical trial eligibility. Genetic testing frequently can help identify syndromes in patients for whom syndromes may not be suspected. These findings highlight the importance of pursuing broad genetic testing, independent of suspicion based on phenotype. Lower rates of MolDx in Black patients may contribute to health inequities. Further research is needed evaluating the genetics of HCM in underrepresented/underserved populations. Additionally, research related to the impact of genetic testing on clinical management of other diseases is warranted.
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29
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Donohue KE, Dolan SM, Watnick D, Gallagher KM, Odgis JA, Suckiel SA, Teitelman N, Gelb BD, Kenny EE, Wasserstein MP, Horowitz CR, Bauman LJ. Hope versus reality: Parent expectations of genomic testing. PATIENT EDUCATION AND COUNSELING 2021; 104:2073-2079. [PMID: 33640235 PMCID: PMC8679507 DOI: 10.1016/j.pec.2021.01.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 05/11/2023]
Abstract
OBJECTIVE Genomics is increasingly used for diagnostic testing in children. This study describes the expectations of parents whose child received genomic testing and whether or not they were met. METHODS A diverse stratified, purposive sample of parents of 22 children in New York City was interviewed using a semi-structured guide. Genomic test results were positive, negative, or uncertain. RESULTS Parents expressed their expectations in narrative and numeric fashion. Parents expected that their child's test would have a direct effect on their child's diagnosis. Some believed that results would be definitive, while others recognized testing limitations. Expectations reflected parents' hope to find a diagnosis and led to disappointment when results were uninformative or did not impact clinical management. CONCLUSION Results suggest pre-test genetic counseling emphasize the low likelihood of actionable results; however, parents' expectations of genomics' diagnostic capabilities are strongly rooted in their need to end the diagnostic odyssey and may be difficult to manage. PRACTICE IMPLICATIONS Parents' hope for a resolution and effective treatment for their child is a powerful context in which genetic counseling is heard. Clinicians who provide genomic testing should continue to acknowledge parents' preconceptions. Additional research in other settings will help understand how to best address and manage parent expectations of genomic medicine.
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Affiliation(s)
- Katherine E Donohue
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Siobhan M Dolan
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dana Watnick
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Katie M Gallagher
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nehama Teitelman
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa P Wasserstein
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Laurie J Bauman
- Department of Pediatrics, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States; Department of Psychiatry and Behavioral Sciences, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, United States.
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30
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Stiles MK, Wilde AAM, Abrams DJ, Ackerman MJ, Albert CM, Behr ER, Chugh SS, Cornel MC, Gardner K, Ingles J, James CA, Juang JMJ, Kääb S, Kaufman ES, Krahn AD, Lubitz SA, MacLeod H, Morillo CA, Nademanee K, Probst V, Saarel EV, Sacilotto L, Semsarian C, Sheppard MN, Shimizu W, Skinner JR, Tfelt-Hansen J, Wang DW. 2020 APHRS/HRS expert consensus statement on the investigation of decedents with sudden unexplained death and patients with sudden cardiac arrest, and of their families. J Arrhythm 2021; 37:481-534. [PMID: 34141003 PMCID: PMC8207384 DOI: 10.1002/joa3.12449] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
This international multidisciplinary document intends to provide clinicians with evidence-based practical patient-centered recommendations for evaluating patients and decedents with (aborted) sudden cardiac arrest and their families. The document includes a framework for the investigation of the family allowing steps to be taken, should an inherited condition be found, to minimize further events in affected relatives. Integral to the process is counseling of the patients and families, not only because of the emotionally charged subject, but because finding (or not finding) the cause of the arrest may influence management of family members. The formation of multidisciplinary teams is essential to provide a complete service to the patients and their families, and the varied expertise of the writing committee was formulated to reflect this need. The document sections were divided up and drafted by the writing committee members according to their expertise. The recommendations represent the consensus opinion of the entire writing committee, graded by Class of Recommendation and Level of Evidence. The recommendations were opened for public comment and reviewed by the relevant scientific and clinical document committees of the Asia Pacific Heart Rhythm Society (APHRS) and the Heart Rhythm Society (HRS); the document underwent external review and endorsement by the partner and collaborating societies. While the recommendations are for optimal care, it is recognized that not all resources will be available to all clinicians. Nevertheless, this document articulates the evaluation that the clinician should aspire to provide for patients with sudden cardiac arrest, decedents with sudden unexplained death, and their families.
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Affiliation(s)
- Martin K Stiles
- Waikato Clinical School Faculty of Medicine and Health Science The University of Auckland Hamilton New Zealand
| | - Arthur A M Wilde
- Heart Center Department of Clinical and Experimental Cardiology Amsterdam University Medical Center University of Amsterdam Amsterdam the Netherlands
| | | | | | | | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Molecular and Clinical Sciences Institute St George's University of London, and St George's University Hospitals NHS Foundation Trust London UK
| | | | - Martina C Cornel
- Amsterdam University Medical Center Vrije Universiteit Amsterdam Clinical Genetics Amsterdam Public Health Research Institute Amsterdam the Netherlands
| | | | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute The University of Sydney Sydney Australia
| | | | - Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology Department of Internal Medicine National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
| | - Stefan Kääb
- Department of Medicine I University Hospital LMU Munich Munich Germany
| | | | | | | | - Heather MacLeod
- Data Coordinating Center for the Sudden Death in the Young Case Registry Okemos MI USA
| | | | - Koonlawee Nademanee
- Chulalongkorn University Faculty of Medicine, and Pacific Rim Electrophysiology Research Institute at Bumrungrad Hospital Bangkok Thailand
| | | | - Elizabeth V Saarel
- Cleveland Clinic Lerner College of Cardiology at Case Western Reserve University Cleveland OH USA
- St Luke's Medical Center Boise ID USA
| | - Luciana Sacilotto
- Heart Institute University of São Paulo Medical School São Paulo Brazil
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute The University of Sydney Sydney Australia
| | - Mary N Sheppard
- Cardiovascular Clinical Academic Group, Molecular and Clinical Sciences Institute St George's University of London, and St George's University Hospitals NHS Foundation Trust London UK
| | - Wataru Shimizu
- Department of Cardiovascular Medicine Nippon Medical School Tokyo Japan
| | | | - Jacob Tfelt-Hansen
- Department of Forensic Medicine Faculty of Medical Sciences Rigshospitalet Copenhagen Denmark
| | - Dao Wu Wang
- The First Affiliated Hospital of Nanjing Medical University Nanjing China
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Huang H, Cai M, Liu L, Xu L, Lin N. Effectiveness of Chromosomal Microarray Analysis for Prenatal Diagnosis of Fetal Echogenic Intracardiac Focus: A Single-Center Experience. Int J Gen Med 2021; 14:1991-1997. [PMID: 34045891 PMCID: PMC8149271 DOI: 10.2147/ijgm.s311800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Echogenic intracardiac focus (EIF) is a common ultrasound finding during pregnancy. However, the correlation between fetal EIF and cardiac abnormality remains in dispute until now. The study aimed to examine the association of fetal EIF with chromosomal abnormality by means of chromosomal microarray analysis (CMA). MATERIALS AND METHODS A total of 192 pregnant women with fetal EIF undergoing amniocentesis or umbilical cord blood puncture were recruited and assigned into groups A (8 cases with isolated EIF alone), B (75 cases with EIF and other cardiac malformations) and C (109 cases with EIF and extracardiac malformations). All fetuses underwent karyotyping analysis and CMA simultaneously. The detection of chromosomal abnormality and copy number variations (CNVs) were compared. RESULTS Chromosomal karyotyping identified 5 fetuses with chromosomal abnormality, including 3 cases with trisomy 21, one fetus with Turner's syndrome, and one fetus with chromosome 8 mosaicism, while CMA detected 6 additional fetuses with CNVs, including 2 fetuses with pathogenic CNVs and 4 fetuses with variants of uncertain significance (VOUS). There was no significant difference among groups A (0), B (5.33%) and C (6.42%) in terms of the prevalence of chromosomal abnormality (P> 0.05). Among the 4 fetuses with VOUS, pregnancy continued in 2 fetuses, and pregnancy was terminated in other 2 fetuses. CONCLUSION An isolated EIF may not correlate with chromosomal abnormality. However, CMA is recommended in fetuses with CMA complicated by other abnormal cardiac ultrasound findings, which facilitates the prediction of fetal outcomes during the genetic counseling and precision assessment of prognosis.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Linyu Liu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
- School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People’s Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
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Dalach P, Savarirayan R, Baynam G, McGaughran J, Kowal E, Massey L, Jenkins M, Paradies Y, Kelaher M. "This is my boy's health! Talk straight to me!" perspectives on accessible and culturally safe care among Aboriginal and Torres Strait Islander patients of clinical genetics services. Int J Equity Health 2021; 20:103. [PMID: 33865398 PMCID: PMC8052687 DOI: 10.1186/s12939-021-01443-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Aboriginal and Torres Strait Islander people do not enjoy equal access to specialist health services that adequately meet their needs. Clinical genetics services are at the vanguard of realising the health benefits of genomic medicine. As the field continues to expand in clinical utility and implementation, it is critical that Aboriginal and Torres Strait Islander people are able to participate and benefit equally to avoid further widening of the existing health gap. This is the first study to explore barriers to accessing clinical genetics services among Aboriginal and Torres Strait Islander people, which has been acknowledged as a key strategic priority in Australian genomic health policy. METHODS A participatory design process engaged a majority-Aboriginal Project Reference Group and Aboriginal End-User Group. 63 semi-structured interviews were conducted with Aboriginal and/or Torres Strait Islander people who had accessed the government-funded clinical genetics service in Western Australia, Queensland or the Northern Territory between 2014 and 2018. The sample included patients, parents and carers. Participants were asked to recount their 'patient journey', from referral through to post-appointment and reflect on their perceptions of genetics and its implications for the health of themselves and their families. Analysis tracked chronological service engagement, followed by an inductive thematic approach. RESULTS Barriers to access and engagement were present at each stage of the patient journey. These included challenges in obtaining a referral, long waiting periods, limited genetic literacy, absence of Aboriginal support services, communication challenges and lack of adequate psychosocial support and follow-up after attendance. Participants' overall experiences of attending a genetic health service were varied, with positive perceptions tied closely to a diagnosis being achieved. The experience of (and expectation for) recognition of cultural identity and provision of culturally safe care was low among participants. Unaddressed concerns continued to cause significant distress in some people years after their appointment took place. CONCLUSIONS There is significant scope for improving the care provided to Aboriginal and Torres Strait Islander people at clinical genetics services. Immediate attention to minimising logistical barriers, developing relationships with Aboriginal Community Controlled Health Services and providing practical and specific cultural safety training for practitioners is required at the service-level. Our findings strongly support the development of guidelines or policies recognising the collective cultural needs of Aboriginal and Torres Strait Islander people in relation to genomic health care.
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Affiliation(s)
- Philippa Dalach
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia.
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Gareth Baynam
- Western Australian Department of Health, Genetic Services of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Australia
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Emma Kowal
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Libby Massey
- Machado Joseph Disease Foundation, Alyangula, Northern Territory, Australia
- James Cook University, Townsville, Queensland, Australia
| | - Misty Jenkins
- Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Yin Paradies
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Margaret Kelaher
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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Brown EE. The genetic counselor's role in management of patients with dyslipidemia. Curr Opin Lipidol 2021; 32:83-88. [PMID: 33492006 DOI: 10.1097/mol.0000000000000732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE OF REVIEW The role of genetic testing in diagnosis and management of dyslipidemias continues to grow. Consequently, it is increasingly important for patients to have access to clinicians who have expertise in medical genetics and the psychological implications related to this type of testing. Often a lipidologist has had limited training in this regard, and this review explores the role of the genetic counselor to fill this gap. RECENT FINDINGS Genetic counselors are key members of the healthcare team, and their specialized training in medical genetics and counseling allows them to fill this professional knowledge gap within the lipid clinic. SUMMARY With the continued emphasis on precision medicine, the utility of genetic testing for dyslipidemias will continue to grow. This will in turn increase the demand for provider expertise in medical genetics and counseling around these complex issues. Integrating a genetic counselor within the lipid clinic provides an ideal management scenario providing patients and families with access to not only medical information but also emotional support regarding their hereditary condition.
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Affiliation(s)
- Emily E Brown
- Center for Inherited Heart Disease, Division of Cardiology, Johns Hopkins University, Baltimore, Maryland, USA
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Uhlig HH, Charbit-Henrion F, Kotlarz D, Shouval DS, Schwerd T, Strisciuglio C, de Ridder L, van Limbergen J, Macchi M, Snapper SB, Ruemmele FM, Wilson DC, Travis SP, Griffiths AM, Turner D, Klein C, Muise AM, Russell RK. Clinical Genomics for the Diagnosis of Monogenic Forms of Inflammatory Bowel Disease: A Position Paper From the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology and Nutrition. J Pediatr Gastroenterol Nutr 2021; 72:456-473. [PMID: 33346580 PMCID: PMC8221730 DOI: 10.1097/mpg.0000000000003017] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND It is important to identify patients with monogenic IBD as management may differ from classical IBD. In this position statement we formulate recommendations for the use of genomics in evaluating potential monogenic causes of IBD across age groups. METHODS The consensus included paediatric IBD specialists from the Paediatric IBD Porto group of the European Society of Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) and specialists from several monogenic IBD research consortia. We defined key topics and performed a systematic literature review to cover indications, technologies (targeted panel, exome and genome sequencing), gene panel setup, cost-effectiveness of genetic screening, and requirements for the clinical care setting. We developed recommendations that were voted upon by all authors and Porto group members (32 voting specialists). RESULTS We recommend next-generation DNA-sequencing technologies to diagnose monogenic causes of IBD in routine clinical practice embedded in a setting of multidisciplinary patient care. Routine genetic screening is not recommended for all IBD patients. Genetic testing should be considered depending on age of IBD-onset (infantile IBD, very early-onset IBD, paediatric or young adult IBD), and further criteria, such as family history, relevant comorbidities, and extraintestinal manifestations. Genetic testing is also recommended in advance of hematopoietic stem cell transplantation. We developed a diagnostic algorithm that includes a gene panel of 75 monogenic IBD genes. Considerations are provided also for low resource countries. CONCLUSIONS Genomic technologies should be considered an integral part of patient care to investigate patients at risk for monogenic forms of IBD.
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Affiliation(s)
- Holm H. Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Fabienne Charbit-Henrion
- Université de Paris, INSERM UMR 1163 Immunité Intestinale, APHP, Hôpital Necker Enfants Malades, Service de Génétique moléculaire, Paris, France
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dror S. Shouval
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | | | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus University Medical Center Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Johan van Limbergen
- Amsterdam University Medical Centres, Emma Children’s Hospital, The Netherlands and Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Marina Macchi
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Frank M. Ruemmele
- Université de Paris, APHP, Hôpital Necker Enfants Malades, Service de Gastroentérologie pédiatrique, Paris, France
| | - David C. Wilson
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
| | - Simon P.L. Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Anne M. Griffiths
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Dan Turner
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Aleixo M. Muise
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Richard K. Russell
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
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Watnick D, Odgis JA, Suckiel SA, Gallagher KM, Teitelman N, Donohue KE, Gelb BD, Kenny EE, Wasserstein MP, Horowitz CR, Dolan SM, Bauman LJ. "Is that something that should concern me?": a qualitative exploration of parent understanding of their child's genomic test results. HGG ADVANCES 2021; 2. [PMID: 33884375 PMCID: PMC8057699 DOI: 10.1016/j.xhgg.2021.100027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Genetic counselors are trained to deliver complicated genomic test results to parents of pediatric patients. However, there is limited knowledge on how parents perceive this information and what they understand about the results. This research aims to qualitatively explore parents’ experiences receiving genomic test results for their children. As part of formative research for the NYCKidSeq Study, we recruited a purposive sample of parents of 22 children stratified by child race/ethnicity and test result classification (positive, uncertain, or negative) and conducted in-depth interviews using a semi-structured guide. Analysis was conducted using grounded theory’s constant comparative method across cases and themes. Parents described different elements of understanding: genetics knowledge; significance and meaning of positive, uncertain, or negative results; and implications for the health of their child and family. Parents reported challenges understanding technical details and significance of their child’s results but gladly allowed their providers to be custodians of this information. However, of the different elements of understanding described, parents cared most deeply about being able to understand implications for their child’s and family’s health. These findings suggest that a counseling approach that primarily addresses parents’ desire to understand how to best care for their child and family may be more appropriate than an information-heavy approach focused on technical details. Further research is warranted to confirm these findings in larger parent cohorts and to explore ways genetic counseling can support parents’ preferences without sacrificing important components of parent understanding and overall satisfaction with their experiences with genomic medicine.
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Affiliation(s)
- Dana Watnick
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katie M Gallagher
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nehama Teitelman
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Katherine E Donohue
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Carol R Horowitz
- Departments of Population Health Science and Policy and Medicine, Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Siobhan M Dolan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Obstetrics, Gynecology, and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laurie J Bauman
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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36
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Childerhose JE, Rich CA, East KM, Kelley WV, Simmons S, Finnila CR, Bowling KM, Amaral MD, Hiatt SM, Thompson M, Gray DE, Lawlor JMJ, Myers RM, Barsh GS, Bebin EM, Cooper GM, Brothers KB, Brothers KB. The Therapeutic Odyssey: Positioning Genomic Sequencing in the Search for a Child's Best Possible Life. AJOB Empir Bioeth 2021; 12:179-189. [PMID: 33843487 PMCID: PMC9922533 DOI: 10.1080/23294515.2021.1907475] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: The desire of parents to obtain a genetic diagnosis for their child with intellectual disability and associated symptoms has long been framed as a diagnostic odyssey, an arduous and sometimes perilous journey focused on the goal of identifying a cause for the child's condition.Methods: Semi-structured interviews (N = 60) were conducted with parents of children (N = 59, aged 2-24 years) with intellectual disability and/or developmental delay (IDD) who underwent genome sequencing at a single pediatric multispecialty clinic. Interviews were conducted after parents received their child's sequencing result (positive findings, negative findings, or variants of unknown significance). Thematic analysis was performed on all interviews.Results: Parents reported that obtaining a genetic diagnosis was one important step in their overall goal of helping their child live their best life possible life. They intended to use the result as a tool to help their child by seeking the correct school placement and obtaining benefits and therapeutic services.Conclusions: For the parents of children with IDD, the search for a genetic diagnosis is best conceptualized as a part of parents' ongoing efforts to leverage various diagnoses to obtain educational and therapeutic services for their children. Cleaving parents' search for a genetic diagnosis from these broader efforts obscures the value that some parents place on a sequencing result in finding and tailoring therapies and services beyond the clinic. Interviews with parents reveal, therefore, that genomic sequencing is best understood as one important stage of an ongoing therapeutic odyssey that largely takes place outside the clinic. Findings suggest the need to expand translational research efforts to contextualize a genetic diagnosis within parents' broader efforts to obtain educational and therapeutic services outside clinical contexts.
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Affiliation(s)
- Janet E. Childerhose
- Division of General Internal Medicine, The Ohio State University, Columbus, Ohio, USA.,Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
| | - Carla A. Rich
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
| | - Kelly M. East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Shirley Simmons
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Kevin M. Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - David E. Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - E. Martina Bebin
- The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Greg M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kyle B. Brothers
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA.,Correspondence to: Kyle B. Brothers, MD, PhD, University of Louisville School of Medicine, 231 E. Chestnut St., N-97, Louisville, KY 40202, Work Phone: 502-588-0797, Cell Phone: 502-762-8666, Fax: 502-629-5285,
| | - Kyle Bertram Brothers
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
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37
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Stiles MK, Wilde AAM, Abrams DJ, Ackerman MJ, Albert CM, Behr ER, Chugh SS, Cornel MC, Gardner K, Ingles J, James CA, Jimmy Juang JM, Kääb S, Kaufman ES, Krahn AD, Lubitz SA, MacLeod H, Morillo CA, Nademanee K, Probst V, Saarel EV, Sacilotto L, Semsarian C, Sheppard MN, Shimizu W, Skinner JR, Tfelt-Hansen J, Wang DW. 2020 APHRS/HRS expert consensus statement on the investigation of decedents with sudden unexplained death and patients with sudden cardiac arrest, and of their families. Heart Rhythm 2021; 18:e1-e50. [PMID: 33091602 PMCID: PMC8194370 DOI: 10.1016/j.hrthm.2020.10.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022]
Abstract
This international multidisciplinary document intends to provide clinicians with evidence-based practical patient-centered recommendations for evaluating patients and decedents with (aborted) sudden cardiac arrest and their families. The document includes a framework for the investigation of the family allowing steps to be taken, should an inherited condition be found, to minimize further events in affected relatives. Integral to the process is counseling of the patients and families, not only because of the emotionally charged subject, but because finding (or not finding) the cause of the arrest may influence management of family members. The formation of multidisciplinary teams is essential to provide a complete service to the patients and their families, and the varied expertise of the writing committee was formulated to reflect this need. The document sections were divided up and drafted by the writing committee members according to their expertise. The recommendations represent the consensus opinion of the entire writing committee, graded by Class of Recommendation and Level of Evidence. The recommendations were opened for public comment and reviewed by the relevant scientific and clinical document committees of the Asia Pacific Heart Rhythm Society (APHRS) and the Heart Rhythm Society (HRS); the document underwent external review and endorsement by the partner and collaborating societies. While the recommendations are for optimal care, it is recognized that not all resources will be available to all clinicians. Nevertheless, this document articulates the evaluation that the clinician should aspire to provide for patients with sudden cardiac arrest, decedents with sudden unexplained death, and their families.
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Affiliation(s)
- Martin K Stiles
- Waikato Clinical School, Faculty of Medicine and Health Science, The University of Auckland, Hamilton, New Zealand
| | - Arthur A M Wilde
- Amsterdam University Medical Center, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam, the Netherlands
| | | | | | | | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London, and St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Sumeet S Chugh
- Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Martina C Cornel
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | | | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | | | - Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
| | | | - Andrew D Krahn
- The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Heather MacLeod
- Data Coordinating Center for the Sudden Death in the Young Case Registry, Okemos, Michigan, USA
| | | | - Koonlawee Nademanee
- Chulalongkorn University, Faculty of Medicine, and Pacific Rim Electrophysiology Research Institute at Bumrungrad Hospital, Bangkok, Thailand
| | | | - Elizabeth V Saarel
- Cleveland Clinic Lerner College of Cardiology at Case Western Reserve University, Cleveland, Ohio, and St Luke's Medical Center, Boise, Idaho, USA
| | - Luciana Sacilotto
- Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Mary N Sheppard
- Cardiovascular Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London, and St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Nippon Medical School, Tokyo, Japan
| | - Jonathan R Skinner
- Cardiac Inherited Disease Group, Starship Hospital, Auckland, New Zealand
| | - Jacob Tfelt-Hansen
- Department of Forensic Medicine, Faculty of Medical Sciences, Rigshospitalet, Copenhagen, Denmark
| | - Dao Wu Wang
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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38
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Brett GR, Martyn M, Lynch F, de Silva MG, Ayres S, Gallacher L, Boggs K, Baxendale A, Schenscher S, King-Smith S, Fowles L, Springer A, Lunke S, Vasudevan A, Krzesinski E, Pinner J, Sandaradura SA, Barnett C, Patel C, Wilson M, Stark Z. Parental experiences of ultrarapid genomic testing for their critically unwell infants and children. Genet Med 2020; 22:1976-1985. [PMID: 32719395 DOI: 10.1038/s41436-020-0912-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/10/2020] [Indexed: 12/25/2022] Open
Abstract
PURPOSE To explore parental experiences of ultrarapid genomic testing for their critically unwell infants and children. METHODS Parents of critically unwell children who participated in a national ultrarapid genomic diagnosis program were surveyed >12 weeks after genomic results return. Surveys consisted of custom questions and validated scales, including the Decision Regret Scale and Genomics Outcome Scale. RESULTS With 96 survey invitations sent, the response rate was 57% (n = 55). Most parents reported receiving enough information during pretest (n = 50, 94%) and post-test (n = 44, 83%) counseling. Perceptions varied regarding benefits of testing, however most parents reported no or mild decision regret (n = 45, 82%). The majority of parents (31/52, 60%) were extremely concerned about the condition recurring in future children, regardless of actual or perceived recurrence risk. Parents whose child received a diagnostic result reported higher empowerment. CONCLUSION This study provides valuable insight into parental experiences of ultrarapid genomic testing in critically unwell children, including decision regret, empowerment, and post-test reproductive planning, to inform design and delivery of rapid diagnosis programs. The findings suggest considerations for pre- and post-test counseling that may influence parental experiences during the testing process and beyond, such as the importance of realistically conveying the likelihood for clinical and/or personal utility.
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Affiliation(s)
- Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia. .,The University of Melbourne, Melbourne, Australia.
| | - Melissa Martyn
- The University of Melbourne, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
| | - Fiona Lynch
- The University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | - Samantha Ayres
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia
| | - Kirsten Boggs
- Australian Genomics Health Alliance, Melbourne, Australia.,Sydney Children's Hospitals Network-Randwick, Sydney, Australia.,Sydney Children's Hospitals Network-Westmead, Sydney, Australia
| | - Anne Baxendale
- Australian Genomics Health Alliance, Melbourne, Australia.,Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Adelaide, Australia
| | - Sarah Schenscher
- Australian Genomics Health Alliance, Melbourne, Australia.,Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Adelaide, Australia
| | - Sarah King-Smith
- Australian Genomics Health Alliance, Melbourne, Australia.,Centre for Cancer Biology, SA Pathology, University of South Australia, Adelaide, Australia
| | - Lindsay Fowles
- Australian Genomics Health Alliance, Melbourne, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Australia.,Department of Paediatrics, Monash University, Melbourne, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | | | - Emma Krzesinski
- Monash Genetics, Monash Health, Melbourne, Australia.,Department of Paediatrics, Monash University, Melbourne, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network-Randwick, Sydney, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network-Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Adelaide, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network-Westmead, Sydney, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,The University of Melbourne, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
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Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance. Genet Med 2020; 22:1005-1014. [PMID: 32123317 PMCID: PMC7272326 DOI: 10.1038/s41436-020-0766-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Diagnosis of genetic disorders is hampered by large numbers of variants of uncertain significance (VUSs) identified through next-generation sequencing. Many such variants may disrupt normal RNA splicing. We examined effects on splicing of a large cohort of clinically identified variants and compared performance of bioinformatic splicing prediction tools commonly used in diagnostic laboratories. METHODS Two hundred fifty-seven variants (coding and noncoding) were referred for analysis across three laboratories. Blood RNA samples underwent targeted reverse transcription polymerase chain reaction (RT-PCR) analysis with Sanger sequencing of PCR products and agarose gel electrophoresis. Seventeen samples also underwent transcriptome-wide RNA sequencing with targeted splicing analysis based on Sashimi plot visualization. Bioinformatic splicing predictions were obtained using Alamut, HSF 3.1, and SpliceAI software. RESULTS Eighty-five variants (33%) were associated with abnormal splicing. The most frequent abnormality was upstream exon skipping (39/85 variants), which was most often associated with splice donor region variants. SpliceAI had greatest accuracy in predicting splicing abnormalities (0.91) and outperformed other tools in sensitivity and specificity. CONCLUSION Splicing analysis of blood RNA identifies diagnostically important splicing abnormalities and clarifies functional effects of a significant proportion of VUSs. Bioinformatic predictions are improving but still make significant errors. RNA analysis should therefore be routinely considered in genetic disease diagnostics.
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40
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Makhnoon S, Peterson SK. Variant of Uncertain Significance-Related Uncertainty in Breast Cancer Genomics. CURRENT BREAST CANCER REPORTS 2020. [DOI: 10.1007/s12609-020-00351-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Lewiecki EM, Bilezikian JP, Kagan R, Krakow D, McClung MR, Miller PD, Rush ET, Shuhart CR, Watts NB, Yu EW. Proceedings of the 2019 Santa Fe Bone Symposium: New Concepts in the Care of Osteoporosis and Rare Bone Diseases. J Clin Densitom 2020; 23:1-20. [PMID: 31685420 DOI: 10.1016/j.jocd.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023]
Abstract
The 20th annual Santa Fe Bone Symposium was held August 9-10, 2019, in Santa Fe, New Mexico, USA. This is an annual meeting devoted to clinical applications of recent advances in skeletal research that impact the care of patients with osteoporosis, metabolic bone diseases, and inherited bone diseases. Participants included practicing and academic physicians, fellows, advanced practice providers, fracture liaison service (FLS) coordinators, clinical researchers, and bone density technologists. The symposium consisted of lectures, case presentations, and panel discussions, with an emphasis on learning through interaction of all attendees. Topics included new approaches in the use of anabolic agents for the treatment osteoporosis, a review of important events in skeletal health over the past year, new and emerging treatments for rare bone diseases, the use of genetic testing for bone diseases in clinical practice, medication-associated causes of osteoporosis, new concepts in the use of estrogen therapy for osteoporosis, new Official Positions of the International Society for Clinical Densitometry, skeletal consequences of bariatric surgery, and update on the progress and potential of Bone Health TeleECHO, a virtual community of practice using videoconferencing technology to link healthcare professionals for advancing the care of osteoporosis worldwide. Sessions on rare bone diseases were developed in collaboration with the Rare Bone Disease Alliance. Symposium premeetings included an FLS workshop by the National Osteoporosis Foundation and others devoted to the use of new therapeutic agents for the care of osteoporosis and related disorders.
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Affiliation(s)
- E Michael Lewiecki
- New Mexico Clinical Research & Osteoporosis Center, Albuquerque, NM, USA.
| | - John P Bilezikian
- Columbia University College of Physicians and Surgeons, NYC, NY, USA
| | - Risa Kagan
- UCSF and Sutter East Bay Medical Foundation, Berkeley, CA, USA
| | - Deborah Krakow
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R McClung
- Oregon Osteoporosis Center, Portland, OR, USA; Mary MacKillop Center for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Paul D Miller
- University of Colorado Health Sciences Center, Denver, CO, USA
| | - Eric T Rush
- University of Kansas Medical Center, Kansas City, MO, USA; Children's Mercy Hospital, Kansas City, MO, USA; University of Missouri - Kansas City, Kansas City, MO, USA
| | | | - Nelson B Watts
- Mercy Health Osteoporosis and Bone Health Services, Cincinnati, OH, USA
| | - Elaine W Yu
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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42
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Precone V, Cannarella R, Paolacci S, Busetto GM, Beccari T, Stuppia L, Tonini G, Zulian A, Marceddu G, Calogero AE, Bertelli M. Male Infertility Diagnosis: Improvement of Genetic Analysis Performance by the Introduction of Pre-Diagnostic Genes in a Next-Generation Sequencing Custom-Made Panel. Front Endocrinol (Lausanne) 2020; 11:605237. [PMID: 33574797 PMCID: PMC7872015 DOI: 10.3389/fendo.2020.605237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/16/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Infertility affects about 7% of the general male population. The underlying cause of male infertility is undefined in about 50% of cases (idiopathic infertility). The number of genes involved in human spermatogenesis is over two thousand. Therefore, it is essential to analyze a large number of genes that may be involved in male infertility. This study aimed to test idiopathic male infertile patients negative for a validated panel of "diagnostic" genes, for a wide panel of genes that we have defined as "pre-diagnostic." METHODS We developed a next-generation sequencing (NGS) gene panel including 65 pre-diagnostic genes that were used in 12 patients who were negative to a diagnostic genetic test for male infertility disorders, including primary spermatogenic failure and central hypogonadism, consisting of 110 genes. RESULTS After NGS sequencing, variants in pre-diagnostic genes were identified in 10/12 patients who were negative to a diagnostic test for primary spermatogenic failure (n = 9) or central hypogonadism (n = 1) due to mutations of single genes. Two pathogenic variants of DNAH5 and CFTR genes and three uncertain significance variants of DNAI1, DNAH11, and CCDC40 genes were found. Moreover, three variants with high impact were found in AMELY, CATSPER 2, and ADCY10 genes. CONCLUSION This study suggests that searching for pre-diagnostic genes may be of relevance to find the cause of infertility in patients with apparently idiopathic primary spermatogenic failure due to mutations of single genes and central hypogonadism.
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Affiliation(s)
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Gian Maria Busetto
- Department of Urology, “Sapienza” University of Rome, Policlinico Umberto I, Rome, Italy
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Liborio Stuppia
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Gerolamo Tonini
- Department of Surgery, Fondazione Poliambulanza, Brescia, Italy
| | | | | | - Aldo E. Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Matteo Bertelli
- MAGI EUREGIO, Bolzano, Italy
- MAGI’S LAB, Rovereto, Italy
- EBTNA-LAB, Rovereto, Italy
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