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Chen X, Balliew J, Bauer CX, Deegan J, Gitter A, Hanson BM, Maresso AW, Tisza MJ, Troisi CL, Rios J, Mena KD, Boerwinkle E, Wu F. RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.12.24310301. [PMID: 39040200 PMCID: PMC11261926 DOI: 10.1101/2024.07.12.24310301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.
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Affiliation(s)
- Xingwen Chen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Blake M Hanson
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anthony W Maresso
- TAILOR Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Catherine L Troisi
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
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2
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Harte AJ, Ghasemian E, Pickering H, Houghton J, Chernet A, Sata E, Yismaw G, Zeru T, Tadesse Z, Callahan EK, Nash SD, Holland MJ. Unravelling Chlamydia trachomatis diversity in Amhara, Ethiopia: MLVA-ompA sequencing as a molecular typing tool for trachoma. PLoS Negl Trop Dis 2024; 18:e0012143. [PMID: 38662795 PMCID: PMC11075894 DOI: 10.1371/journal.pntd.0012143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Trachoma is the leading infectious cause of blindness worldwide and is now largely confined to around 40 low- and middle-income countries. It is caused by Chlamydia trachomatis (Ct), a contagious intracellular bacterium. The World Health Organization recommends mass drug administration (MDA) with azithromycin for treatment and control of ocular Ct infections, alongside improving facial cleanliness and environmental conditions to reduce transmission. To understand the molecular epidemiology of trachoma, especially in the context of MDA and transmission dynamics, the identification of Ct genotypes could be useful. While many studies have used the Ct major outer membrane protein gene (ompA) for genotyping, it has limitations. Our study applies a typing system novel to trachoma, Multiple Loci Variable Number Tandem Repeat Analysis combined with ompA (MLVA-ompA). Ocular swabs were collected post-MDA from four trachoma-endemic zones in Ethiopia between 2011-2017. DNA from 300 children with high Ct polymerase chain reaction (PCR) loads was typed using MLVA-ompA, utilizing 3 variable number tandem repeat (VNTR) loci within the Ct genome. Results show that MLVA-ompA exhibited high discriminatory power (0.981) surpassing the recommended threshold for epidemiological studies. We identified 87 MLVA-ompA variants across 26 districts. No significant associations were found between variants and clinical signs or chlamydial load. Notably, overall Ct diversity significantly decreased after additional MDA rounds, with a higher proportion of serovar A post-MDA. Despite challenges in sequencing one VNTR locus (CT1299), MLVA-ompA demonstrated cost-effectiveness and efficiency relative to whole genome sequencing, providing valuable information for trachoma control programs on local epidemiology. The findings suggest the potential of MLVA-ompA as a reliable tool for typing ocular Ct and understanding transmission dynamics, aiding in the development of targeted interventions for trachoma control.
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Affiliation(s)
- Anna J. Harte
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ehsan Ghasemian
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harry Pickering
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joanna Houghton
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | | | - Taye Zeru
- The Amhara Regional Health Bureau, Bahir Dar, Ethiopia
| | | | | | - Scott D. Nash
- The Carter Center, Atlanta, Georgia, United States of America
| | - Martin J. Holland
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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3
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Mead EC, Wang CA, Phung J, Fu JY, Williams SM, Merialdi M, Jacobsson B, Lye S, Menon R, Pennell CE. The Role of Genetics in Preterm Birth. Reprod Sci 2023; 30:3410-3427. [PMID: 37450251 PMCID: PMC10692032 DOI: 10.1007/s43032-023-01287-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Preterm birth (PTB), defined as the birth of a child before 37 completed weeks gestation, affects approximately 11% of live births and is the leading cause of death in children under 5 years. PTB is a complex disease with multiple risk factors including genetic variation. Much research has aimed to establish the biological mechanisms underlying PTB often through identification of genetic markers for PTB risk. The objective of this review is to present a comprehensive and updated summary of the published data relating to the field of PTB genetics. A literature search in PubMed was conducted and English studies related to PTB genetics were included. Genetic studies have identified genes within inflammatory, immunological, tissue remodeling, endocrine, metabolic, and vascular pathways that may be involved in PTB. However, a substantial proportion of published data have been largely inconclusive and multiple studies had limited power to detect associations. On the contrary, a few large hypothesis-free approaches have identified and replicated multiple novel variants associated with PTB in different cohorts. Overall, attempts to predict PTB using single "-omics" datasets including genomic, transcriptomic, and epigenomic biomarkers have been mostly unsuccessful and have failed to translate to the clinical setting. Integration of data from multiple "-omics" datasets has yielded the most promising results.
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Affiliation(s)
- Elyse C Mead
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Jason Phung
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, NSW, 2305, Australia
| | - Joanna Yx Fu
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mario Merialdi
- Maternal Newborn Health Innovations, Geneva, PBC, Switzerland
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynaecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Stephen Lye
- Lunenfeld Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, Division of Basic Science and Translational Research, University of Texas Medical Branch, Galveston, TX, USA
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia.
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia.
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, NSW, 2305, Australia.
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4
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Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [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: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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5
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Li W, Chen H, Jiang X, Harmanci A. Federated generalized linear mixed models for collaborative genome-wide association studies. iScience 2023; 26:107227. [PMID: 37529100 PMCID: PMC10387571 DOI: 10.1016/j.isci.2023.107227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/28/2023] [Accepted: 06/23/2023] [Indexed: 08/03/2023] Open
Abstract
Federated association testing is a powerful approach to conduct large-scale association studies where sites share intermediate statistics through a central server. There are, however, several standing challenges. Confounding factors like population stratification should be carefully modeled across sites. In addition, it is crucial to consider disease etiology using flexible models to prevent biases. Privacy protections for participants pose another significant challenge. Here, we propose distributed Mixed Effects Genome-wide Association study (dMEGA), a method that enables federated generalized linear mixed model-based association testing across multiple sites without explicitly sharing genotype and phenotype data. dMEGA employs a reference projection to correct for population-stratification and utilizes efficient local-gradient updates among sites, incorporating both fixed and random effects. The accuracy and efficiency of dMEGA are demonstrated through simulated and real datasets. dMEGA is publicly available at https://github.com/Li-Wentao/dMEGA.
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Affiliation(s)
- Wentao Li
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Han Chen
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
- School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Xiaoqian Jiang
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Arif Harmanci
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
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6
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Iltis AS, Rolf L, Yaeger L, Goodman MS, DuBois JM. Attitudes and beliefs regarding race-targeted genetic testing of Black people: A systematic review. J Genet Couns 2023; 32:435-461. [PMID: 36644818 PMCID: PMC10349658 DOI: 10.1002/jgc4.1653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 01/17/2023]
Abstract
Geographical ancestry has been associated with an increased risk of various genetic conditions. Race and ethnicity often have been used as proxies for geographical ancestry. Despite numerous problems associated with the crude reliance on race and ethnicity as proxies for geographical ancestry, some genetic testing in the clinical, research, and employment settings has been and continues to be race- or ethnicity-based. Race-based or race-targeted genetic testing refers to genetic testing offered only or primarily to people of particular racial or ethnic groups because of presumed differences among groups. One current example is APOL1 testing of Black kidney donors. Race-based genetic testing raises numerous ethical and policy questions. Given the ongoing reliance on the Black race in genetic testing, it is important to understand the views of people who identify as Black or are identified as Black (including African American, Afro-Caribbean, and Hispanic Black) regarding race-based genetic testing that targets Black people because of their race. We conducted a systematic review of studies and reports of stakeholder-engaged projects that examined how people who identify as or are identified as Black perceive genetic testing that specifically presumes genetic differences exist among racial groups or uses race as a surrogate for ancestral genetic variation and targets Black people. Our review identified 14 studies that explicitly studied this question and another 13 that implicitly or tacitly studied this matter. We found four main factors that contribute to a positive attitude toward race-targeted genetic testing (facilitators) and eight main factors that are associated with concerns regarding race-targeted genetic testing (barriers). This review fills an important gap. These findings should inform future genetic research and the policies and practices developed in clinical, research, public health, or other settings regarding genetic testing.
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Affiliation(s)
| | - Liz Rolf
- Washington University in St. Louis School of Medicine
| | - Lauren Yaeger
- Washington University in St. Louis School of Medicine
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7
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Rezapour A, Souresrafil A, Barzegar M, Sheikhy-Chaman M, Tatarpour P. Economic evaluation of next-generation sequencing techniques in diagnosis of genetic disorders: A systematic review. Clin Genet 2023; 103:513-528. [PMID: 36808726 DOI: 10.1111/cge.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023]
Abstract
In recent years, massively parallel sequencing or next generation sequencing (NGS) has considerably changed both the research and diagnostic fields, and rapid developments have led to the combination of NGS techniques in clinical practice, ease of analysis, and detection of genetic mutations. This article aimed at reviewing the economic evaluation studies of the NGS techniques in the diagnosis of genetic diseases. In this systematic review, scientific databases (PubMed, EMBASE, Web of Science, Cochrane, Scopus, and CEA registry) were searched from 2005 to 2022 to identify the related literature on the economic evaluation of NGS techniques in the diagnosis of genetic diseases. Full-text reviews and data extraction were all performed by two independent researchers. The quality of all the articles included in this study was evaluated using the Checklist of Quality of Health Economic Studies (QHES). Out of 20 521 screened abstracts, 36 studies met the inclusion criteria. The mean score of the QHES checklist for the studies was 0.78 (high quality). Seventeen studies were conducted based on modeling. Cost-effectiveness analysis, cost-utility analysis, and cost-minimization analysis were done in 26 studies, 13 studies, and 1 study, respectively. Based on the available evidence and findings, exome sequencing, which is one of the NGS techniques, could have the potential to be used as a cost-effective genomic test to diagnose children with suspected genetic diseases. The results of the present study support the cost-effectiveness of exome sequencing in diagnosing suspected genetic disorders. However, the use of exome sequencing as a first- or second-line diagnostic test is still controversial. Most studies have been conducted in high-income countries, and research on the cost-effectiveness of NGS methods is recommended in low- and middle-income countries.
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Affiliation(s)
- Aziz Rezapour
- Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Aghdas Souresrafil
- Department of Health Services and Health Promotion, School of Health, Occupational Environment Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Barzegar
- Department of English Language, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Sheikhy-Chaman
- Department of Health Economics, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Parvin Tatarpour
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
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8
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König P, Beier S, Mascher M, Stein N, Lange M, Scholz U. DivBrowse-interactive visualization and exploratory data analysis of variant call matrices. Gigascience 2022; 12:giad025. [PMID: 37083938 PMCID: PMC10120423 DOI: 10.1093/gigascience/giad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/23/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The sequencing of whole genomes is becoming increasingly affordable. In this context, large-scale sequencing projects are generating ever larger datasets of species-specific genomic diversity. As a consequence, more and more genomic data need to be made easily accessible and analyzable to the scientific community. FINDINGS We present DivBrowse, a web application for interactive visualization and exploratory analysis of genomic diversity data stored in Variant Call Format (VCF) files of any size. By seamlessly combining BLAST as an entry point together with interactive data analysis features such as principal component analysis in one graphical user interface, DivBrowse provides a novel and unique set of exploratory data analysis capabilities for genomic biodiversity datasets. The capability to integrate DivBrowse into existing web applications supports interoperability between different web applications. Built-in interactive computation of principal component analysis allows users to perform ad hoc analysis of the population structure based on specific genetic elements such as genes and exons. Data interoperability is supported by the ability to export genomic diversity data in VCF and General Feature Format 3 files. CONCLUSION DivBrowse offers a novel approach for interactive visualization and analysis of genomic diversity data and optionally also gene annotation data by including features like interactive calculation of variant frequencies and principal component analysis. The use of established standard file formats for data input supports interoperability and seamless deployment of application instances based on the data output of established bioinformatics pipelines.
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Affiliation(s)
- Patrick König
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Sebastian Beier
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
- Institute of Bio- and Geosciences, IBG-4, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
- Center for Integrated Breeding Research, Georg-August University, 37075 Göttingen, Germany
| | - Matthias Lange
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Uwe Scholz
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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9
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Kiflen M, Le A, Mao S, Lali R, Narula S, Xie F, Paré G. Cost-Effectiveness of Polygenic Risk Scores to Guide Statin Therapy for Cardiovascular Disease Prevention. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003423. [PMID: 35904973 DOI: 10.1161/circgen.121.003423] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Atherosclerotic cardiovascular diseases (CVDs) are leading causes of death despite effective therapies and result in unnecessary morbidity and mortality throughout the world. We aimed to investigate the cost-effectiveness of polygenic risk scores (PRS) to guide statin therapy for Canadians with intermediate CVD risk and model its economic outlook. METHODS This cost-utility analysis was conducted using UK Biobank prospective cohort study participants, with recruitment from 2006 to 2010, and at least 10 years of follow-up. We included nonrelated white British-descent participants (n=96 116) at intermediate CVD risk with no prior lipid lowering medication or statin-indicated conditions. A coronary artery disease PRS was used to inform decision to use statins. The effects of statin therapy with and without PRS, as well as CVD events were modelled to determine the incremental cost-effectiveness ratio from a Canadian public health care perspective. We discounted future costs and quality-adjusted life-years by 1.5% annually. RESULTS The optimal economic strategy was when intermediate risk individuals with a PRS in the top 70% are eligible for statins while the lowest 1% are excluded. Base-case analysis at a genotyping cost of $70 produced an incremental cost-effectiveness ratio of $172 906 (143 685 USD) per quality-adjusted life-year. In the probabilistic sensitivity analysis, the intervention has approximately a 50% probability of being cost-effective at $179 100 (148 749 USD) per quality-adjusted life-year. At a $0 genotyping cost, representing individuals with existing genotyping information, PRS-guided strategies dominated standard care when 12% of the lowest PRS individuals were withheld from statins. With improved PRS predictive performance and lower genotyping costs, the incremental cost-effectiveness ratio demonstrates possible cost-effectiveness under thresholds of $150 000 and possibly $50 000 per quality-adjusted life-year. CONCLUSIONS This study suggests that using PRS alongside existing guidelines might be cost-effective for CVD. Stronger predictiveness combined with decreased cost of PRS could further improve cost-effectiveness, providing an economic basis for its inclusion into clinical care.
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Affiliation(s)
- Michel Kiflen
- Department of Medicine, University of Toronto, Toronto (M.K.).,Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada
| | - Ann Le
- Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada.,Department of Medical Sciences (A.L.), McMaster University, Hamilton, Ontario, Canada
| | - Shihong Mao
- Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada
| | - Ricky Lali
- Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada.,Department of Health Research Methods, Evidence, and Impact (R.L., S.N., F.X., G.P.), McMaster University, Hamilton, Ontario, Canada
| | - Sukrit Narula
- Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada.,Department of Internal Medicine, Yale University, New Haven, CT (S.N.)
| | - Feng Xie
- Department of Health Research Methods, Evidence, and Impact (R.L., S.N., F.X., G.P.), McMaster University, Hamilton, Ontario, Canada
| | - Guillaume Paré
- Population Health Research Institute (M.K., A.L., S.M., R.L., S.N., G.P.), McMaster University, Hamilton, Ontario, Canada.,Department of Health Research Methods, Evidence, and Impact (R.L., S.N., F.X., G.P.), McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada.,Thrombosis & Atherosclerosis Research Institute (G.P.), McMaster University, Hamilton, Ontario, Canada.,McMaster University, Hamilton, Ontario, Canada (G.P.)
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10
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Poon SHL, Cheung JJC, Shih KC, Chan YK. A systematic review of multimodal clinical biomarkers in the management of thyroid eye disease. Rev Endocr Metab Disord 2022; 23:541-567. [PMID: 35066781 DOI: 10.1007/s11154-021-09702-9] [Citation(s) in RCA: 3] [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] [Accepted: 12/07/2021] [Indexed: 12/25/2022]
Abstract
Thyroid Eye Disease (TED) is an autoimmune disease that affects the extraocular muscles and periorbital fat. It most commonly occurs with Graves' Disease (GD) as an extrathyroidal manifestation, hence, it is also sometimes used interchangeably with Graves' Ophthalmopathy (GO). Well-known autoimmune markers for GD include thyroid stimulating hormone (TSH) receptor antibodies (TSH-R-Ab) which contribute to hyperthyroidism and ocular signs. Currently, apart from radiological investigations, detection of TED is based on clinical signs and symptoms which is largely subjective, with no established biomarkers which could differentiate TED from merely GD. We evaluated a total of 28 studies on potential biomarkers for diagnosis of TED. Articles included were published in English, which investigated clinical markers in tear fluid, orbital adipose-connective tissues, orbital fibroblasts and extraocular muscles, serum, thyroid tissue, as well as imaging biomarkers. Results demonstrated that biomarkers with reported diagnostic power have high sensitivity and specificity for TED, including those using a combination of biomarkers to differentiate between TED and GD, as well as the use of magnetic resonance imaging (MRI). Other biomarkers which were upregulated include cytokines, proinflammatory markers, and acute phase reactants in subjects with TED, which are however, deemed less specific to TED. Further clinical investigations for these biomarkers, scrutinising their specificity and sensitivity on a larger sample of patients, may point towards selection of suitable biomarkers for aiding detection and prognosis of TED in the future.
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Affiliation(s)
- Stephanie Hiu Ling Poon
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 301B Cyberport 4, 100 Cyberport Road, Pokfulam, Hong Kong SAR
| | | | - Kendrick Co Shih
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 301B Cyberport 4, 100 Cyberport Road, Pokfulam, Hong Kong SAR.
| | - Yau Kei Chan
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 301B Cyberport 4, 100 Cyberport Road, Pokfulam, Hong Kong SAR
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11
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Granger MJ, Eck PK, Vazquez-Vidal I, Shamloo M, House JD, Mackay DS. Genosets for APOE and CYP7A1-rs3808607 variants do not predict LDL cholesterol lowering upon intervention with plant sterols in a randomized, double-blind, placebo-controlled trial. Am J Clin Nutr 2022; 115:717-723. [PMID: 34791009 DOI: 10.1093/ajcn/nqab378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/15/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The consumption of 2 g/d plant sterols (PSs) reduces circulating LDL cholesterol by ≤10%. The degree of LDL cholesterol lowering was associated with specific apolipoprotein E [APOE, Reference SNP (rs)429358] and cholesterol 7α-hydroxylase (CYP7A1, rs3808607) genosets in previous post hoc analyses of randomized controlled trials. However, because post hoc analyses do not conform to the randomization model, there is a greater potential that the findings could be due to type I error, thus warranting validation through an a priori-designed intervention trial. OBJECTIVES The GenePredict Plant Sterol study (GPS) was designed to validate associations of LDL cholesterol lowering with specific APOE and CYP7A1 genosets through a priori recruitment of individuals carrying prespecified genosets. METHODS A 2-center, double-blind, placebo-controlled, randomized 2-period crossover dietary intervention with 2 g/d PS for 28 d with a minimum 28-d washout was undertaken from July 2017 to December 2019. A priori recruitment of individuals with slightly elevated LDL cholesterol was based on genosets of APOE isoforms and CYP7A1 rs3808607. Randomization was performed with stratification by sex and genoset. RESULTS The recruitment target of 64 participants with prespecified genosets could not be reached, despite the screening of 477 individuals; 42 participants completed the intervention trial. Reductions in LDL cholesterol were similar across all 3 genosets (-0.298 ± 0.164, -0.357 ± 0.115, -0.293 ± 0.109 mmol/L; P = 0.0002 overall; P = 0.9126 for treatment × genoset), providing evidence that the shortfall in recruitment might not have stopped the trial from meeting the objective. CONCLUSIONS APOE and CYP7A1 genotypes did not influence the efficacy of LDL cholesterol reductions upon dietary intervention with PSs. Findings of previous post hoc analyses could not be validated in a trial using a priori genotype-based recruitment. Obtaining adequate numbers of participants is challenging in trials using genoset-based recruitment, even for common variants.
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Affiliation(s)
- Matthew J Granger
- Department of Food and Human Nutritional Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peter K Eck
- Department of Food and Human Nutritional Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Itzel Vazquez-Vidal
- Richardson Centre for Functional Foods and Nutraceuticals, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maryam Shamloo
- Department of Food and Human Nutritional Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James D House
- Richardson Centre for Functional Foods and Nutraceuticals, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dylan S Mackay
- Department of Food and Human Nutritional Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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12
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Dalton DL, Pretorius C, de Klerk-Lorist LM, Reininghaus B, Buss P, Mitchell EP. Absence of 2899C<T Mutation in the WNK4 Gene in a Free-Ranging Lion (Panthera leo) with Polymyopathy. Animals (Basel) 2022; 12:ani12030389. [PMID: 35158718 PMCID: PMC8833707 DOI: 10.3390/ani12030389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Samples from an African lion cub in the Greater Kruger National Park area (South Africa), which could not walk, were tested for a gene mutation that causes one type of muscle weakness in domestic cats. The cause of the muscle weakness is believed to be genetic, but our study showed that the mutation that is found in similarly affected domestic cats was not present in the cub. Genetic diseases are more common in inbred animal populations, so this condition needs to be further evaluated to assist in the conservation of these magnificent creatures. Abstract Polyphasic skeletal muscle degeneration, necrosis and mineralization of skeletal muscle was diagnosed in eight juvenile free-ranging lions (Panthera leo), from five different litters in the Greater Kruger National Park area that were unable to walk properly. A detailed investigation was not possible in free-ranging lions, so the cause could not be determined. The cases resembled hypokalemic polymyopathy in domestic cats with muscle weakness. A candidate-gene approach previously identified a nonsense mutation in the gene coding for the enzyme lysine-deficient 4 protein kinase (WNK4) associated with the disease in Burmese and Tonkinese cats. In this study, we sequenced all 19 exons of the gene in one case, and two control samples, to identify possible mutations that may be associated with polymyopathy in free-ranging lions. Here, no mutations were detected in any of the exons sequenced. Our findings indicate that the WNK4 gene is not a major contributor to the condition in these lions. Further studies into the pathogenesis of this condition are needed to inform conservation policies for this vulnerable, iconic African species.
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Affiliation(s)
- Desiré L. Dalton
- South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa; (D.L.D.); (C.P.)
| | - Chantelle Pretorius
- South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa; (D.L.D.); (C.P.)
| | - Lin-Mari de Klerk-Lorist
- Skukuza State Veterinary Office & Laboratory, Directorate Animal Health, Department of Agriculture, Land Reform and Rural Development, Kruger National Park, P.O. Box 12, Skukuza 1350, South Africa;
| | - Bjorn Reininghaus
- Mpumulanga Veterinary Services, Thulamahashe, P/Bag X11309, Mbombela 1200, South Africa;
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, P.O. Box 86, Skukuza 1350, South Africa;
| | - Emily P. Mitchell
- South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa; (D.L.D.); (C.P.)
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, P/Bag X01, Onderstepoort 0110, South Africa
- Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, P/Bag X01, Onderstepoort 0110, South Africa
- Correspondence:
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13
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Current Trends in Genetics and Neonatal Care. Adv Neonatal Care 2021; 21:473-481. [PMID: 33538495 DOI: 10.1097/anc.0000000000000834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Genetic and genomic health applications are rapidly changing. A clear and updated description of these applications for the neonatal population is needed to guide current nursing practice. PURPOSE To provide scientific evidence and guidance on the current genetic and genomic applications pertinent to neonatal care. METHODS A search of CINAHL and PubMed was conducted using the search terms "newborn/neonatal" and "genetics," "genomics," "newborn screening," "pharmacogenomics," "ethical," and "legal." Google searches were also conducted to synthesize professional guidelines, position statements, and current genetic practices. FINDINGS/RESULTS Components of the newborn genetic assessment, including details on the newborn physical examination, family history, and laboratory tests pertinent to the newborn, are reported. The history and process of newborn screening are described, in addition to the impact of advancements, such as whole exome and genome sequencing, on newborn screening. Pharmacogenomics, a genomic application that is currently utilized primarily in the research context for neonates, is described and future implications stated. Finally, the specific ethical and legal implications for these genetic and genomic applications are detailed, along with genetic/genomic resources for nurses. IMPLICATIONS FOR PRACTICE Providing nurses with the most up-to-date evidence on genetic and genomic applications ensures their involvement and contributions to quality neonatal care. IMPLICATIONS FOR RESEARCH Ongoing genetic/genomic research is needed to understand the implications of genetic/genomic applications on the neonatal population and how these new applications will change neonatal care.
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14
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Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding. Genomics 2021; 113:3083-3091. [PMID: 34237377 DOI: 10.1016/j.ygeno.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/23/2022]
Abstract
Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.
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15
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Bean LJH, Scheuner MT, Murray MF, Biesecker LG, Green RC, Monaghan KG, Palomaki GE, Sharp RR, Trotter TL, Watson MS, Powell CM. DNA-based screening and personal health: a points to consider statement for individuals and health-care providers from the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:979-988. [PMID: 33790423 DOI: 10.1038/s41436-020-01083-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023] Open
Affiliation(s)
- Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Maren T Scheuner
- Division of Medical Genetics, Department of Pediatrics, and Division of Hematology-Oncology, Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA.,Clinical Genetics Program, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Michael F Murray
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI, USA.,Women and Infants Hospital, Providence, RI, USA
| | | | - Tracy L Trotter
- San Ramon Valley Primary Care Medical Group, San Ramon, CA, USA
| | | | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Genetics and Metabolism, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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16
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Sebate B, Cuttler K, Cloete R, Britz M, Christoffels A, Williams M, Carr J, Bardien S. Prioritization of candidate genes for a South African family with Parkinson's disease using in-silico tools. PLoS One 2021; 16:e0249324. [PMID: 33770142 PMCID: PMC7997022 DOI: 10.1371/journal.pone.0249324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 11/19/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder exhibiting Mendelian inheritance in some families. Next-generation sequencing approaches, including whole exome sequencing (WES), have revolutionized the field of Mendelian disorders and have identified a number of PD genes. We recruited a South African family with autosomal dominant PD and used WES to identify a possible pathogenic mutation. After filtration and prioritization, we found five potential causative variants in CFAP65, RTF1, NRXN2, TEP1 and CCNF. The variant in NRXN2 was selected for further analysis based on consistent prediction of deleteriousness across computational tools, not being present in unaffected family members, ethnic-matched controls or public databases, and its expression in the substantia nigra. A protein model for NRNX2 was created which provided a three-dimensional (3D) structure that satisfied qualitative mean and global model quality assessment scores. Trajectory analysis showed destabilizing effects of the variant on protein structure, indicated by high flexibility of the LNS-6 domain adopting an extended conformation. We also found that the known substrate N-acetyl-D-glucosamine (NAG) contributed to restoration of the structural stability of mutant NRXN2. If NRXN2 is indeed found to be the causal gene, this could reveal a new mechanism for the pathobiology of PD.
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Affiliation(s)
- Boiketlo Sebate
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Katelyn Cuttler
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Marcell Britz
- Greenacres Medical Centre, Port Elizabeth, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Monique Williams
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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17
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Smith HS, McGuire AL, Wittenberg E, Lavelle TA. Family-level impact of genetic testing: integrating health economics and ethical, legal, and social implications. Per Med 2021; 18:209-212. [PMID: 33728981 DOI: 10.2217/pme-2021-0016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tweetable abstract Health economics and ELSI can be better integrated to consider the family impacts of genetic and genomic testing.
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Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy L McGuire
- Center for Medical Ethics & Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eve Wittenberg
- Center for Health Decision Science, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Tara A Lavelle
- Center for the Evaluation of Value & Risk in Health (CEVR), Institute for Clinical Research & Health Policy Studies, Tufts Medical Center, Boston, MA 02111, USA
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18
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Fontes Marx M, Ataguba JE, de Vries J, Wonkam A. Systematic Review of the Economic Evaluation of Returning Incidental Findings in Genomic Research. Front Public Health 2021; 9:697381. [PMID: 34277554 PMCID: PMC8281014 DOI: 10.3389/fpubh.2021.697381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Objectives: Discussions regarding who and how incidental findings (IFs) should be returned and the ethics behind returning IFs have increased dramatically over the years. However, information on the cost and benefits of returning IFs to patients remains scanty. Design: This study systematically reviews the economic evaluation of returning IFs in genomic sequencing. We searched for published articles on the cost-effectiveness, cost-benefit, and cost-utility of IFs in Medline, Scopus, PubMed, and Google Scholar. Results: We found six published articles that met the eligibility criteria of this study. Two articles used cost analysis only, one used cost-benefit analysis only, two used both cost analysis and cost-effectiveness, and one used both cost-benefit analysis and cost-utility to describe the cost of returning IFs in genomic sequencing. Conclusion: While individuals value the IF results and are willing to pay for them, the cost of returning IFs depends on the primary health condition of the patient. Although patients were willing to pay, there was no clear evidence that returning IFs might be cost-effective. More rigorous economic evaluation studies of IFs are needed to determine whether or not the cost of returning IFs is beneficial to the patient.
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Affiliation(s)
- Mayara Fontes Marx
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - John E Ataguba
- Health Economics Unit, School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina de Vries
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute to Infectious Disease and Molecular Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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19
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Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni S, Grove ME, Taylor SL, Ashley E. Clinical utility of genomic sequencing: a measurement toolkit. NPJ Genom Med 2020; 5:56. [PMID: 33319814 PMCID: PMC7738524 DOI: 10.1038/s41525-020-00164-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Whole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder's perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.
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Affiliation(s)
- Robin Z Hayeems
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children and the Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada.
| | - David Dimmock
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, CA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Robert C Green
- Brigham and Women's Hospital Broad Institute and Harvard Medical School, Boston, MA, USA
| | | | - Vaidehi Jobanputra
- New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology Columbia University Medical Center, New York, NY, USA
| | - Roberto Mendoza
- The Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shashi Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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20
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Vu M, Degeling K, Martyn M, Lynch E, Chong B, Gaff C, IJzerman MJ. Evaluating the resource implications of different service delivery models for offering additional genomic findings. Genet Med 2020; 23:606-613. [PMID: 33214711 DOI: 10.1038/s41436-020-01030-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To evaluate the resource implications of different delivery models for the provision of additional findings (AF) in genomics from a health-care purchaser perspective. METHODS Data from the Additional Findings study were used to develop and validate a discrete event simulation model that represented the pathway of delivering AF. Resource implications were estimated by microcosting the consultations, sample verifications, bioinformatics, curation, and multidisciplinary case review meetings. A proof-of-concept model was used to generate costing, and then the simulation model was varied to assess the impact of an automated analysis pipeline, use of telehealth consultation, full automation with electronic decision support, and prioritizing case review for cases with pathogenic variants. RESULTS For the proof-of-concept delivery model, the average total cost to report AF was US$430 per patient irrespective of result pathogenicity (95% confidence interval [CI] US$375-US$489). However, the cost of per AF diagnosis was US$4349 (95% CI US$3794-US$4953). Alternative approaches to genetic counseling (telehealth, decision support materials) and to multidisciplinary case review (pathogenic AF cases only) lowered the total per patient cost of AF analysis and reporting by 41-51%. CONCLUSION Resources required to provide AF can be reduced substantially by implementing alternative approaches to counseling and multidisciplinary case review.
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Affiliation(s)
- Martin Vu
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Koen Degeling
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Elly Lynch
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Belinda Chong
- Murdoch Children's Research Institute, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Maarten J IJzerman
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia. .,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia. .,Department of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia.
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21
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Tegally H, San JE, Giandhari J, de Oliveira T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics 2020; 21:729. [PMID: 33081689 PMCID: PMC7576741 DOI: 10.1186/s12864-020-07137-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/11/2020] [Indexed: 02/08/2023] Open
Abstract
In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laboratories are now considering liquid-handling automation to make the sequencing workflow more efficient and cost effective. The question remains as to its suitability and return on investment. A number of points need to be carefully considered before introducing robots into biological laboratories. Here, we describe the state-of-the-art technology of both sophisticated and do-it-yourself (DIY) robotic liquid-handlers and provide a practical review of the motivation, implications and requirements of laboratory automation for genome sequencing experiments.
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Affiliation(s)
- Houriiyah Tegally
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
| | - James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Jennifer Giandhari
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
- Department of Global Health, University of Washington, 908 Jefferson Street, 13th Floor, Seattle, WA, 98104, USA.
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22
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Patient reactions to receiving negative genomic screening results by mail. Genet Med 2020; 22:1994-2002. [PMID: 32669678 DOI: 10.1038/s41436-020-0906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/09/2023] Open
Abstract
PURPOSE As genomic screening is incorporated into a wider array of clinical settings, it is critical that we understand how patients may respond to a various screening results. Although multiple studies have examined how patients understand positive genomic screening results, few data exist regarding patient engagement with negative screening results. METHODS An 82-item survey was administered to 1712 individuals who received negative genomic screening results by mail following evaluation of 109 medically actionable genes. Genetic counselors were available to assist with the interpretation of screening results. RESULTS One thousand four hundred forty-two participants completed the survey (84.2%). The vast majority of respondents valued the information they received, with 98% of respondents reporting that negative genomic screening results were valuable and 72% indicating they would recommend genomic screening to others. Nonetheless, many respondents had questions about their genomic screening results (28%) and would have preferred to receive their screening results in person (18%). CONCLUSION These data suggest most patients value receiving negative genomic screening results and are comfortable receiving their results by mail. Nevertheless, a significant proportion of patients also reported difficulty understanding some aspects of their results. This finding challenges the idea that communicating genomic screening results by mail alone is sufficient to meet patients' needs.
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23
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Etchegary H, Wilson B, Rahman P, Simmonds C, Pullman D. Public interest in whole genome sequencing and information needs: an online survey study. Per Med 2020; 17:283-293. [DOI: 10.2217/pme-2019-0136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aim: To survey the general public about whole genome sequencing interest, including pharmacogenomic testing, and to identify information important for sequencing decisions. Patients & methods: An online survey of 901 members of the general public in an eastern Canadian province. Results: Interest in whole genome sequencing, including pharmacogenomic testing, was high with few differences among demographic variables. Issues identified as very important to sequencing decisions included familial implications of testing, whether treatment was available for conditions tested and knowing who could access genomic information. Most respondents would value support when interpreting sequencing results. Conclusion: Findings reveal the kind of information and support users of sequencing services would value and could inform the implementation of sequencing into care in ways that accord with public preferences and needs.
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Affiliation(s)
- Holly Etchegary
- Faculty of Medicine, Memorial University, St John's, NL, Canada; Craig L. Dobbin Centre for Genetics, Rm 4M210, St John's, NL, A1B 3V6
| | - Brenda Wilson
- Professor of Medicine and Associate Dean, Community Health and Humanities, Memorial University, St John’s, NL A1B 3V6, Canada
| | - Proton Rahman
- Professor of Medicine (Rheumatology), Memorial University and Rheumatologist, Eastern Regional Health Authority, St John’s, NL A1B 3V6, Canada
| | - Charlene Simmonds
- Manager, Health Research Unit, Faculty of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
| | - Daryl Pullman
- Professor of Medicine (Bioethics), Faculty of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
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Joshi E, Mighton C, Clausen M, Casalino S, Kim THM, Kowal C, Birken C, Maguire JL, Bombard Y. Primary care provider perspectives on using genomic sequencing in the care of healthy children. Eur J Hum Genet 2020; 28:551-557. [PMID: 31804631 PMCID: PMC7171087 DOI: 10.1038/s41431-019-0547-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Genome sequencing (GS) studies involving healthy children can advance scientific knowledge of genetic variation. Little research has examined primary care providers' views on using GS in this context. This study explored primary care provider perspectives on the use of GS in research and the care of healthy children. We conducted semi-structured interviews with 16 providers discussing their views on GS research and receiving results. Interviews were analyzed by thematic analysis and constant comparison. Participants were family physicians (11/16) and primary care pediatricians (5/16) in practice for >10 years (11/16). Participants valued GS in healthy children for research purposes; however, opinions diverged on using the results in primary care. Proponents valued using results for surveillance and prevention in healthy children. Skeptics questioned the clinical utility of results and the appropriateness of applying research data in primary care. Both groups shared concerns over opportunistic screening, validity, and interpretation of results, increased health system costs and inequities, and genetic discrimination. Primary care providers were ambivalent about the appropriateness and utility of GS in the care of healthy children. Providers feel unprepared and unsure of their obligations in disclosing these results. Providers do not feel they are equipped with the necessary resources and training to support their patients in using GS results in their care.
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Affiliation(s)
- Esha Joshi
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Marc Clausen
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Selina Casalino
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Theresa H M Kim
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Catherine Birken
- University of Toronto, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Jonathon L Maguire
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.
- University of Toronto, Toronto, ON, Canada.
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Johnson KB, Clayton EW, Starren J, Peterson J. The Implementation Chasm Hindering Genome-informed Health Care. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2020; 48:119-125. [PMID: 32342791 PMCID: PMC7395963 DOI: 10.1177/1073110520916999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The promises of precision medicine are often heralded in the medical and lay literature, but routine integration of genomics in clinical practice is still limited. While the "last mile' infrastructure to bring genomics to the bedside has been demonstrated in some healthcare settings, a number of challenges remain - both in the receptivity of today's health system and in its technical and educational readiness to respond to this evolution in care. To improve the impact of genomics on health and disease management, we will need to integrate both new knowledge and new care processes into existing workflows. This change will be onerous and time-consuming, but hopefully valuable to the provision of high quality, economically feasible care worldwide.
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Affiliation(s)
- Kevin B Johnson
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Ellen Wright Clayton
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Justin Starren
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
| | - Josh Peterson
- Kevin B. Johnson, M.D., M.S., is Cornelius Vanderbilt Professor and Chair of Biomedical Informatics, with a joint appointment in the Department of Pediatrics at Vanderbilt University Medical Center. He received his M.D. from Johns Hopkins Hospital in Baltimore and his M.S. in Medical Informatics from Stanford University in 1992. Ellen Wright Clayton, M.D., J.D., is the Craig-Weaver Professor of Pediatrics, Professor of Health Policy in the Center for Biomedical Ethics and Society at Vanderbilt University Medical Center, and Professor of Law at Vanderbilt University. She has been studying the ethical, legal, and social implications of genetics research and its translation to the clinic for many years. She is currently a PI of LawSeq as well as GetPreCiSe, a Center of Excellence in ELSI Research focused on genetic privacy and identity, and has been an investigator in the eMERGE Network since its inception. Justin Starren, M.D., M.S., Ph.D., is Professor of Preventive Medicine and Medical Social Sciences and Chief of the Division of Health and Biomedical Informatics at the Northwestern University Feinberg School of Medicine. He received his M.D. and M.S. in Immunogenetics from Washington University in St. Louis in 1987, and his Ph.D. in Biomedical Informatics from Columbia University in 1997. Josh Peterson, M.D., M.P.H., is an Associate Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He received his M.D. from Vanderbilt University in 1997 and his M.P.H. from Harvard University School of Public Health in 2002
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Ontiveros ES, Ueda Y, Harris SP, Stern JA. Precision medicine validation: identifying the MYBPC3 A31P variant with whole-genome sequencing in two Maine Coon cats with hypertrophic cardiomyopathy. J Feline Med Surg 2019; 21:1086-1093. [PMID: 30558461 PMCID: PMC10814263 DOI: 10.1177/1098612x18816460] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVES The objective of this study was to perform a proof-of-concept experiment that validates a precision medicine approach to identify variants associated with hypertrophic cardiomyopathy (HCM). We hypothesized that whole-genome sequencing would identify variant(s) associated with HCM in two affected Maine Coon/Maine Coon cross cats when compared with 79 controls of various breeds. METHODS Two affected and two control Maine Coon/Maine Coon cross cats had whole-genome sequencing performed at approximately × 30 coverage. Variants were called in these four cats and 77 cats of various breeds as part of the 99 Lives Cat Genome Sequencing Initiative ( http://felinegenetics.missouri.edu/99lives ) using Platypus v0.7.9.1, annotated with dbSNP ID, and variants' effect predicted by SnpEff. Strict filtering criteria (alternate allele frequency >49%) were applied to identify homozygous-alternate or heterozygous variants in the two HCM-affected samples when compared with 79 controls of various breeds. RESULTS A total of four variants were identified in the two Maine Coon/Maine Coon cross cats with HCM when compared with 79 controls after strict filtering. Three of the variants identified in genes MFSD12, BTN1A1 and SLITRK5 did not segregate with disease in a separate cohort of seven HCM-affected and five control Maine Coon/Maine Coon cross cats. The remaining variant MYBPC3 segregated with disease status. Furthermore, this gene was previously associated with heart disease and encodes for a protein with sarcomeric function. CONCLUSIONS AND RELEVANCE This proof-of-concept experiment identified the previously reported MYBPC3 A31P Maine Coon variant in two HCM-affected cases. This result validates and highlights the power of whole-genome sequencing for feline precision medicine.
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Affiliation(s)
- Eric S Ontiveros
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Yu Ueda
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Samantha P Harris
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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28
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Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res 2019; 46:D1190-D1196. [PMID: 29069403 PMCID: PMC5753339 DOI: 10.1093/nar/gkx1002] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/12/2017] [Indexed: 11/14/2022] Open
Abstract
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.
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Affiliation(s)
- Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 331 3822; Fax: +32 9 331 3809;
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Chen J. A fully-automated event-based variant prioritizing solution to the CAGI5 intellectual disability gene panel challenge. Hum Mutat 2019; 40:1364-1372. [PMID: 31066479 DOI: 10.1002/humu.23781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/28/2019] [Accepted: 05/02/2019] [Indexed: 11/07/2022]
Abstract
Recent applications of gene panel sequencing analysis have significantly helped with identifying genetic causes for inherited diseases. However, large amounts of candidate variants remain a major challenge for prioritizing, often requiring arbitrary cutoffs in multiple steps. In addition, existing tools often prioritize a list of promising candidates that require much manual work to evaluate. To this end, we designed an automated, basically cutoff-free scoring scheme named Context and Hereditary Event based Scoring Scheme (CHESS), that scores all possible inheritance events in each gene, by taking into consideration phenotypes, genotypes, and how the manual prioritization works. We applied CHESS to the Critical Assessment of Genome Interpretation 5 intellectual disability panel challenge, to assign clinical phenotypes to patients based on gene panel sequencing data. Through this blind testing, CHESS proved to be a leading and useful tool for genetic diagnosis in a research setting. Further analyses showed that precise phenotype terms played an important role in variant prioritization and that multiple etiologies may exist for some patients. CHESS also successfully identified many of the causal, putative and contributing variants. In the postchallenge analysis, we showed that our best submission performed slightly better than the predictions made by a state-of-the-art tool. We believe that CHESS can provide aid to this and many other diagnostic scenarios.
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Affiliation(s)
- Jingqi Chen
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China.,Department of Plant & Microbial Biology, University of California, Berkeley, California, USA
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30
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Lee HCH, Lau WL, Ko CH, Lee KC, Cheng FY, Wong S, Woo YH, Mak CM. Flexi-Myo Panel Strategy: Genomic Diagnoses of Myopathies and Muscular Dystrophies by Next-Generation Sequencing. Genet Test Mol Biomarkers 2019; 24:99-104. [PMID: 30907627 DOI: 10.1089/gtmb.2018.0185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aims: Muscle disorders are clinically and genetically heterogeneous. Investigations, including plasma creatine kinase, electromyography, and nerve conduction velocity studies are often nonspecific, whereas muscle biopsy might be limited by sampling bias and variable histopathology. Next-generation sequencing is now generally considered an important diagnostic tool for muscle disorders, with decreased costs and improved diagnostic yield. Inclusion of a large number of genes in the analysis might, however, generate a large number of ambiguous results and create unnecessary confusion for clinicians and patients. Methods: An ethnic Chinese patient presented at age 10 with tip-toe walking. Upon examination the patient had a waddling gait, a tight Achilles tendon with pes cavus. A muscle biopsy showed the presence of minicores with disruption of the myofibrillary network and Z-bands. Sequencing was performed using the Flexi-Myo panel, which provides coverage for 85 myopathic genes. Reporting of sequencing results was decided by the responsible chemical pathologists based on the available clinical and genetic information. Results: A previously identified heterozygous in-frame deletion was detected in MYH7, which confirmed the diagnosis of Laing myopathy. No variants of uncertain significance required reporting. Conclusion: We describe the effectiveness of our Flexi-Myo panel approach for the diagnosis of muscle disorders, which confirmed diagnosis of Laing myopathy in what had been a clinically ambiguous presentation. This approach enables efficient genomic testing for muscle diseases in adults and children with satisfactory diagnostic yield and sufficient sensitivity, whereas avoiding the reporting of ambiguous results. Similar strategies might also be implemented for other groups of disorders.
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Affiliation(s)
| | - Wai-Ling Lau
- Department of Paediatrics and Adolescent Medicine, Caritas Medical Centre, Hong Kong, China
| | - Chun-Hung Ko
- Department of Paediatrics and Adolescent Medicine, Caritas Medical Centre, Hong Kong, China
| | - Kam-Cheong Lee
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Fung-Yip Cheng
- Department of Clinical Pathology, Caritas Medical Centre, Hong Kong, China
| | - Shun Wong
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China.,Pathology Department, St. Paul's Hospital, Hong Kong, China
| | - Yip-Hin Woo
- Department of Radiology, Caritas Medical Centre, Hong Kong, China
| | - Chloe Miu Mak
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
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Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, Leonard DGB, Pereira S, McGuire AL, Caskey CT, Sanderson SC, Schadt EE, Nielsen DE, Crawford SD, Green RC. Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium. Genome Med 2019; 11:10. [PMID: 30808425 PMCID: PMC6391825 DOI: 10.1186/s13073-019-0619-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/05/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Increasing numbers of healthy individuals are undergoing predispositional personal genome sequencing. Here we describe the design and early outcomes of the PeopleSeq Consortium, a multi-cohort collaboration of predispositional genome sequencing projects, which is examining the medical, behavioral, and economic outcomes of returning genomic sequencing information to healthy individuals. METHODS Apparently healthy adults who participated in four of the sequencing projects in the Consortium were included. Web-based surveys were administered before and after genomic results disclosure, or in some cases only after results disclosure. Surveys inquired about sociodemographic characteristics, motivations and concerns, behavioral and medical responses to sequencing results, and perceived utility. RESULTS Among 1395 eligible individuals, 658 enrolled in the Consortium when contacted and 543 have completed a survey after receiving their genomic results thus far (mean age 53.0 years, 61.4% male, 91.7% white, 95.5% college graduates). Most participants (98.1%) were motivated to undergo sequencing because of curiosity about their genetic make-up. The most commonly reported concerns prior to pursuing sequencing included how well the results would predict future risk (59.2%) and the complexity of genetic variant interpretation (56.8%), while 47.8% of participants were concerned about the privacy of their genetic information. Half of participants reported discussing their genomic results with a healthcare provider during a median of 8.0 months after receiving the results; 13.5% reported making an additional appointment with a healthcare provider specifically because of their results. Few participants (< 10%) reported making changes to their diet, exercise habits, or insurance coverage because of their results. Many participants (39.5%) reported learning something new to improve their health that they did not know before. Reporting regret or harm from the decision to undergo sequencing was rare (< 3.0%). CONCLUSIONS Healthy individuals who underwent predispositional sequencing expressed some concern around privacy prior to pursuing sequencing, but were enthusiastic about their experience and not distressed by their results. While reporting value in their health-related results, few participants reported making medical or lifestyle changes.
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Affiliation(s)
- Emilie S Zoltick
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA, 02115, USA.,Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, 801 Massachusetts Avenue, Suite 470, Boston, MA, 02118, USA
| | - Michael D Linderman
- Department of Computer Science, Middlebury College, McCardell Bicentennial Hall, Middlebury, VT, 05753, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA
| | | | - Erica Ramos
- Geisinger National Precision Health, Geisinger, 6101 Executive Blvd, Suite 110, North Bethesda, MD, 20852, USA
| | | | - George M Church
- Open Humans Foundation, Boston, MA, USA.,Harvard Personal Genome Project, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Room 238, Boston, MA, 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Debra G B Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D, College of Medicine of the University of Vermont, 89 Beaumont Avenue, Courtyard at Given S269, Burlington, VT, 05405, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Suite 310D, Houston, TX, 77030, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Suite 310D, Houston, TX, 77030, USA
| | - C Thomas Caskey
- Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop BCM225, Houston, TX, 77030, USA
| | - Saskia C Sanderson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA.,Department of Behavioural Science and Health, University College London, Gower Street, London, WC1E 6BT, UK
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA
| | - Daiva E Nielsen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA, 02115, USA.,School of Human Nutrition, McGill University, 21111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Scott D Crawford
- SoundRocket, 950 Victors Way, Suite 50, Ann Arbor, MI, 48108, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. .,Harvard Medical School, Boston, MA, USA. .,Partners HealthCare Personalized Medicine, Boston, MA, 02115, USA.
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Cooperation between non-essential DNA polymerases contributes to genome stability in Saccharomyces cerevisiae. DNA Repair (Amst) 2019; 76:40-49. [PMID: 30818168 DOI: 10.1016/j.dnarep.2019.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 11/21/2022]
Abstract
DNA polymerases influence genome stability through their involvement in DNA replication, response to DNA damage, and DNA repair processes. Saccharomyces cerevisiae possess four non-essential DNA polymerases, Pol λ, Pol η, Pol ζ, and Rev1, which have varying roles in genome stability. In order to assess the contribution of the non-essential DNA polymerases in genome stability, we analyzed the pol4Δ rev1Δ rev3Δ rad30Δ quadruple mutant in microhomology mediated repair, due to recent studies linking some of these DNA polymerases to this repair pathway. Our results suggest that the length and quality of microhomology influence both the overall efficiency of repair and the involvement of DNA polymerases. Furthermore, the non-essential DNA polymerases demonstrate overlapping and redundant functions when repairing double-strand breaks using short microhomologies containing mismatches. Then, we examined genome-wide mutation accumulation in the pol4Δ rev1Δ rev3Δ rad30Δ quadruple mutant compared to wild type cells. We found a significant decrease in the overall rate of mutation accumulation in the quadruple mutant cells compared to wildtype, but an increase in frameshift mutations and a shift towards transversion base-substitution with a preference for G:C to T:A or C:G. Thus, the non-essential DNA polymerases have an impact on the nature of the mutational spectrum. The sequence and functional homology shared between human and S. cerevisiae non-essential DNA polymerases suggest these DNA polymerases may have a similar role in human cells.
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Grubb AL, McDonald TJ, Rutters F, Donnelly LA, Hattersley AT, Oram RA, Palmer CNA, van der Heijden AA, Carr F, Elders PJM, Weedon MN, Slieker RC, 't Hart LM, Pearson ER, Shields BM, Jones AG. A Type 1 Diabetes Genetic Risk Score Can Identify Patients With GAD65 Autoantibody-Positive Type 2 Diabetes Who Rapidly Progress to Insulin Therapy. Diabetes Care 2019; 42:208-214. [PMID: 30352895 PMCID: PMC6828553 DOI: 10.2337/dc18-0431] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/08/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Progression to insulin therapy in clinically diagnosed type 2 diabetes is highly variable. GAD65 autoantibodies (GADA) are associated with faster progression, but their predictive value is limited. We aimed to determine if a type 1 diabetes genetic risk score (T1D GRS) could predict rapid progression to insulin treatment over and above GADA testing. RESEARCH DESIGN AND METHODS We examined the relationship between T1D GRS, GADA (negative or positive), and rapid insulin requirement (within 5 years) using Kaplan-Meier survival analysis and Cox regression in 8,608 participants with clinical type 2 diabetes (onset >35 years and treated without insulin for ≥6 months). T1D GRS was both analyzed continuously (as standardized scores) and categorized based on previously reported centiles of a population with type 1 diabetes (<5th [low], 5th-50th [medium], and >50th [high]). RESULTS In GADA-positive participants (3.3%), those with higher T1D GRS progressed to insulin more quickly: probability of insulin requirement at 5 years (95% CI): 47.9% (35.0%, 62.78%) (high T1D GRS) vs. 27.6% (20.5%, 36.5%) (medium T1D GRS) vs. 17.6% (11.2%, 27.2%) (low T1D GRS); P = 0.001. In contrast, T1D GRS did not predict rapid insulin requirement in GADA-negative participants (P = 0.4). In Cox regression analysis with adjustment for age of diagnosis, BMI, and cohort, T1D GRS was independently associated with time to insulin only in the presence of GADA: hazard ratio per SD increase was 1.48 (1.15, 1.90); P = 0.002. CONCLUSIONS A T1D GRS alters the clinical implications of a positive GADA test in patients with clinical type 2 diabetes and is independent of and additive to clinical features.
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Affiliation(s)
- Anita L Grubb
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K
| | - Timothy J McDonald
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K.,Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Femke Rutters
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Louise A Donnelly
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, U.K
| | - Andrew T Hattersley
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K.,Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Richard A Oram
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K.,Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Colin N A Palmer
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, U.K
| | - Amber A van der Heijden
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Fiona Carr
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, U.K
| | - Petra J M Elders
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Mike N Weedon
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K
| | - Roderick C Slieker
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Leen M 't Hart
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ewan R Pearson
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, U.K
| | - Beverley M Shields
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K
| | - Angus G Jones
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, U.K. .,Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
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34
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Hull LE, Vassy JL. Toward greater understanding of patient decision-making around genome sequencing. Per Med 2018; 15:57-66. [PMID: 29714114 DOI: 10.2217/pme-2017-0037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the era of next-generation sequencing, it is essential to collect and understand the patient outcomes that result from this new technology. One critical determinant of these is the process by which individuals first decide whether and how to pursue genome sequencing. In this perspective article, we examine the literature on adult patient decision-making in genome sequencing and identify current research gaps to address. Several studies have explored the motivations and concerns of patients undergoing sequencing; less attention has been paid to those who decline sequencing or to individuals from lower socioeconomic groups. Many factors that might play a role in the decision to pursue or decline sequencing, including trust, family dynamics and barriers to access, have yet to be explored fully. Future research that captures the experience of the wider population will produce a more generalizable understanding of the clinical, psychosocial, and economic outcomes of pursuing or declining sequencing.
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Affiliation(s)
- Leland E Hull
- Center for Healthcare Organization and Implementation Research, VA Boston Healthcare System, Boston, MA, 02130, USA.,Section of General Internal Medicine, VA Boston Healthcare System, Boston, MA, 02130, USA
| | - Jason L Vassy
- Section of General Internal Medicine, VA Boston Healthcare System, Boston, MA, 02130, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Division of General Medicine & Primary Care, Brigham & Women's Hospital, Boston, MA, 02115, USA
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35
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Schoenberger SP. Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome? Targeting the Right Antigens in the Right Patients. Cold Spring Harb Perspect Biol 2018; 10:a028837. [PMID: 29254974 PMCID: PMC6211387 DOI: 10.1101/cshperspect.a028837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Recent advances in genomic sequencing and bioinformatics have empowered a revolution in immuno-oncology that has led to numerous unambiguous demonstrations of spontaneous and therapy-induced T-cell responses in patients against a subset of immunogenic tumor-specific somatic mutations known as neoantigens. These findings raise the exciting possibility that patients could be therapeutically treated with personalized vaccines against the mutations expressed by their own tumor. A central challenge for the broader clinical application of this approach will be to define the best antigens to target, to determine the subset of patients most likely to derive significant clinical benefit, and, finally, to discover both the best method of vaccine delivery and the optimal time in the disease course to do so. A growing number of translational immunologists believe that these challenges can be overcome and this perspective will discuss strategies to achieve this.
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Affiliation(s)
- Stephen P Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037; Division of Hematology and Oncology, UCSD Moores Cancer Center, San Diego, California 92123; and Cancer Vaccines Group, Human Longevity Inc., San Diego, California 92121
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36
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Lee HCH, Lau NKC, Yeung CW, Ng SFG, Yau KCE, Mak CM. Successful Adaptation of Targeted Gene Panel Next-Generation Sequencing in Regional Hospital in Hong Kong: Genomic Diagnosis of SCN2A-Related Seizure Disorder. Chin Med J (Engl) 2018; 131:2262-2264. [PMID: 30203812 PMCID: PMC6144848 DOI: 10.4103/0366-6999.240812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
| | | | - Chun-Wing Yeung
- Department of Pathology, Princess Margaret Hospital, Hong Kong N-3730, China
| | - Sui-Fun Grace Ng
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong N-3730, China
| | - Kin-Cheong Eric Yau
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong N-3730, China
| | - Chloe Miu Mak
- Department of Pathology, Princess Margaret Hospital, Hong Kong N-3730, China
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37
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Phillips KA, Deverka PA, Marshall DA, Wordsworth S, Regier DA, Christensen KD, Buchanan J. Methodological Issues in Assessing the Economic Value of Next-Generation Sequencing Tests: Many Challenges and Not Enough Solutions. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:1033-1042. [PMID: 30224106 PMCID: PMC6159915 DOI: 10.1016/j.jval.2018.06.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/11/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Clinical use of next-generation sequencing (NGS) tests has been increasing, but few studies have examined their economic value. Several studies have noted that there are methodological challenges to conducting economic evaluations of NGS tests. OBJECTIVE Our objective was to examine key methodological challenges for conducting economic evaluations of NGS tests, prioritize these challenges for future research, and identify how studies have attempted solutions to address these challenges. METHODS We identified challenges for economic evaluations of NGS tests using prior literature and expert judgment of the co-authors. We used a modified Delphi assessment to prioritize challenges, based on importance and probability of resolution. Using a structured literature review and article extraction we then assessed whether published economic evaluations had addressed these challenges. RESULTS We identified 11 challenges for conducting economic evaluations of NGS tests. The experts identified three challenges as the top priorities for future research: complex model structure, timeframe, and type of analysis and comparators used. Of the 15 published studies included in our literature review, four studies described specific solutions relevant to five of the 11 identified challenges. CONCLUSIONS Major methodological challenges to economic evaluations of NGS tests remain to be addressed. Our results can be used to guide future research and inform decision-makers on how to prioritize research on the economic assessment of NGS tests.
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Affiliation(s)
- Kathryn A Phillips
- Department of Clinical Pharmacy; Center for Translational and Policy Research on Personalized Medicine (TRANSPERS); UCSF Philip R. Lee Institute for Health Policy; and UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | | | - Deborah A Marshall
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sarah Wordsworth
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Dean A Regier
- Cancer Control BC, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - James Buchanan
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK
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38
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Jose R, Rooney R, Nagisetty N, Davis R, Hains D. Biorepository and integrative genomics initiative: designing and implementing a preliminary platform for predictive, preventive and personalized medicine at a pediatric hospital in a historically disadvantaged community in the USA. EPMA J 2018; 9:225-234. [PMID: 30174759 PMCID: PMC6107450 DOI: 10.1007/s13167-018-0141-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Current healthcare is evolving to emphasize cost-effective care by leveraging results and outcomes of genomic and other advanced research efforts in clinical care and preventive health planning. Through a collaborative effort between the University of Tennessee Health Science Center (UTHSC) and Le Bonheur Children's Hospital (LBCH), the Biorepository and Integrative Genomics (BIG) Initiative was established to set up a pediatric-based DNA biorepository that can serve as a foundation for successful development of delivery platforms for predictive, preventive, and personalized medical services in Memphis, Tennessee, a historically disadvantaged community in the USA. In this paper, we describe the steps that were followed to establish the biorepository. We focused on domains that are essential for implementation of a biorepository for genomic research as an initial goal and identified patient consent, DNA extraction, storage and dissemination, and governance as essential components. Specific needs in each of these domains were addressed by respective solutions developed by multidisciplinary teams under the guidance of a governance model that involved experts from multiple hospital arenas and community members. The end result was the successful launch of a large-scale DNA biorepository, with patient consent greater than 75% in the first year. Our experience highlights the importance of performing pre-design research, needs assessment, and designing an ethically vetted plan that is cost-effective, easy to implement, and inclusive of the community that is served. We believe this biorepository model, with appropriate tailoring according to organizational needs and available resources, can be adopted and successfully applied by other small- to mid-sized healthcare organizations.
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Affiliation(s)
- Rony Jose
- Center for Biomedical Informatics, Department of Pediatrics, University of Tennessee Health Science Center, 50 N Dunlap, Room 487R, Memphis, TN 38103 USA
| | - Robert Rooney
- Department of Pediatrics, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 50 N. Dunlap, Room 366R, Memphis, TN 38103 USA
| | - Naga Nagisetty
- Department of Pediatrics, University of Tennessee Health Science Center, 50 N Dunlap, Room 301R, Memphis, TN 38103 USA
| | - Robert Davis
- Center for Biomedical Informatics, Department of Pediatrics, University of Tennessee Health Science Center, 50 N Dunlap, Room 487R, Memphis, TN 38103 USA
| | - David Hains
- Department of Pediatrics, University of Tennessee Health Science Center, Center for Innate Immunity Translational Research, Children’s Foundation Research Institute at Le Bonheur Children’s Hospital, 50 N Dunlap, Room 365R, Memphis, TN 38103 USA
- Present Address: Division of Pediatric Nephrology, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202 USA
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39
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Christensen KD, Phillips KA, Green RC, Dukhovny D. Cost Analyses of Genomic Sequencing: Lessons Learned from the MedSeq Project. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:1054-1061. [PMID: 30224109 PMCID: PMC6444358 DOI: 10.1016/j.jval.2018.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To summarize lessons learned while analyzing the costs of integrating whole genome sequencing into the care of cardiology and primary care patients in the MedSeq Project by conducting the first randomized controlled trial of whole genome sequencing in general and specialty medicine. METHODS Case study that describes key methodological and data challenges that were encountered or are likely to emerge in future work, describes the pros and cons of approaches considered by the study team, and summarizes the solutions that were implemented. RESULTS Major methodological challenges included defining whole genome sequencing, structuring an appropriate comparator, measuring downstream costs, and examining clinical outcomes. Discussions about solutions addressed conceptual and practical issues that arose because of definitions and analyses around the cost of genomic sequencing in trial-based studies. CONCLUSIONS The MedSeq Project provides an instructive example of how to conduct a cost analysis of whole genome sequencing that feasibly incorporates best practices while being sensitive to the varied applications and diversity of results it may produce. Findings provide guidance for researchers to consider when conducting or analyzing economic analyses of whole genome sequencing and other next-generation sequencing tests, particularly regarding costs.
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Affiliation(s)
- Kurt D Christensen
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Philip R. Lee Institute for Health Policy and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Partners HealthCare Personalized Medicine, Boston, MA, USA
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
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40
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Presley CJ, Tang D, Soulos PR, Chiang AC, Longtine JA, Adelson KB, Herbst RS, Zhu W, Nussbaum NC, Sorg RA, Agarwala V, Abernethy AP, Gross CP. Association of Broad-Based Genomic Sequencing With Survival Among Patients With Advanced Non-Small Cell Lung Cancer in the Community Oncology Setting. JAMA 2018; 320:469-477. [PMID: 30088010 PMCID: PMC6142984 DOI: 10.1001/jama.2018.9824] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE Broad-based genomic sequencing is being used more frequently for patients with advanced non-small cell lung cancer (NSCLC). However, little is known about the association between broad-based genomic sequencing and treatment selection or survival among patients with advanced NSCLC in a community oncology setting. OBJECTIVE To compare clinical outcomes between patients with advanced NSCLC who received broad-based genomic sequencing vs a control group of patients who received routine testing for EGFR mutations and/or ALK rearrangements alone. DESIGN, SETTING, AND PARTICIPANTS Retrospective cohort study of patients with chart-confirmed advanced NSCLC between January 1, 2011, and July 31, 2016, and who received care at 1 of 191 oncology practices across the United States using the Flatiron Health Database. Patients were diagnosed with stage IIIB/IV or unresectable nonsquamous NSCLC who received at least 1 line of antineoplastic treatment. EXPOSURES Receipt of either broad-based genomic sequencing or routine testing (EGFR and/or ALK only). Broad-based genomic sequencing included any multigene panel sequencing assay examining more than 30 genes prior to third-line treatment. MAIN OUTCOMES AND MEASURES Primary outcomes were 12-month mortality and overall survival from the start of first-line treatment. Secondary outcomes included frequency of genetic alterations and treatments received. RESULTS Among 5688 individuals with advanced NSCLC (median age, 67 years [interquartile range, 41-85], 63.6% white, 80% with a history of smoking); 875 (15.4%) received broad-based genomic sequencing and 4813 (84.6%) received routine testing. Among patients who received broad-based genomic sequencing, 4.5% received targeted treatment based on testing results, 9.8% received routine EGFR/ALK targeted treatment, and 85.1% received no targeted treatment. Unadjusted mortality rates at 12 months were 49.2% for patients undergoing broad-based genomic sequencing and 35.9% for patients undergoing routine testing. Using an instrumental variable analysis, there was no significant association between broad-based genomic sequencing and 12-month mortality (predicted probability of death at 12 months, 41.1% for broad-based genomic sequencing vs 44.4% for routine testing; difference -3.6% [95% CI, -18.4% to 11.1%]; P = .63). The results were consistent in the propensity score-matched survival analysis (42.0% vs 45.1%; hazard ratio, 0.92 [95% CI, 0.73 to 1.11]; P = .40) vs unmatched cohort (hazard ratio, 0.69 [95% CI, 0.62 to 0.77]; log-rank P < .001). CONCLUSIONS AND RELEVANCE Among patients with advanced non-small cell lung cancer receiving care in the community oncology setting, broad-based genomic sequencing directly informed treatment in a minority of patients and was not independently associated with better survival.
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Affiliation(s)
| | - Daiwei Tang
- Yale School of Public Health, New Haven, Connecticut
| | | | | | | | | | | | - Weiwei Zhu
- Yale School of Medicine, New Haven, Connecticut
| | - Nathan C. Nussbaum
- Flatiron Health, New York, New York
- New York University School of Medicine, New York
| | | | - Vineeta Agarwala
- Flatiron Health, New York, New York
- Stanford University School of Medicine, Stanford, California
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41
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Cirino AL, Lakdawala NK, McDonough B, Conner L, Adler D, Weinfeld M, O'Gara P, Rehm HL, Machini K, Lebo M, Blout C, Green RC, MacRae CA, Seidman CE, Ho CY. A Comparison of Whole Genome Sequencing to Multigene Panel Testing in Hypertrophic Cardiomyopathy Patients. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001768. [PMID: 29030401 DOI: 10.1161/circgenetics.117.001768] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS. Results from panel genetic testing and WGS were compared. In 20 of 41 participants, panel genetic testing identified variants classified as pathogenic, likely pathogenic, or uncertain significance. WGS identified 19 of these 20 variants, but the variant detection algorithm missed a pathogenic 18 bp duplication in myosin binding protein C (MYBPC3) because of low coverage. In 3 individuals, WGS identified variants in genes implicated in cardiomyopathy but not included in prior panel testing: a pathogenic protein tyrosine phosphatase, non-receptor type 11 (PTPN11) variant and variants of uncertain significance in integrin-linked kinase (ILK) and filamin-C (FLNC). WGS also identified 84 secondary findings (mean=2 per person, range=0-6), which mostly defined carrier status for recessive conditions. CONCLUSIONS WGS detected nearly all variants identified on panel testing, provided 1 new diagnostic finding, and allowed interrogation of posited disease genes. Several variants of uncertain clinical use and numerous secondary genetic findings were also identified. Whereas panel testing and WGS provided similar diagnostic yield, WGS offers the advantage of reanalysis over time to incorporate advances in knowledge, but requires expertise in genomic interpretation to appropriately incorporate WGS into clinical care. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov. Unique identifier: NCT01736566.
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Affiliation(s)
- Allison L Cirino
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Neal K Lakdawala
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Barbara McDonough
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Lauren Conner
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Dale Adler
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Mark Weinfeld
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Patrick O'Gara
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Heidi L Rehm
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Kalotina Machini
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Matthew Lebo
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carrie Blout
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Robert C Green
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Calum A MacRae
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Christine E Seidman
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
| | - Carolyn Y Ho
- From the Cardiovascular Division (A.L.C., N.K.L., B.M., D.A., M.W., P.O., C.A.M., C.E.S., C.Y.H.), Department of Pathology (H.L.R.), and Division of Genetics (C.B., R.C.G., C.A.M.), Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA (N.K.L., B.M., D.A., M.W., P.O., H.L.R., R.C.G., C.A.M., C.E.S., C.Y.H.); Albany Medical College, NY (L.C.); Broad Institute of Harvard and MIT, Cambridge, MA (H.L.R., R.C.G., C.A.M.); Laboratory for Molecular Medicine (H.L.R., K.M., M.L.), Leadership Team (R.C.G.), Partners HealthCare Personalized Medicine, Cambridge, MA; and Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.).
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Economic evaluation of genomic sequencing in the paediatric population: a critical review. Eur J Hum Genet 2018; 26:1241-1247. [PMID: 29795475 DOI: 10.1038/s41431-018-0175-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/06/2018] [Accepted: 04/26/2018] [Indexed: 11/08/2022] Open
Abstract
Systematic evidence is critical to the formulation of national health policy to provide public funding for the integration of genomic sequencing into routine clinical care. The purpose of this review is to present systematic evidence on the economic evaluation of genomic sequencing conducted for paediatric patients in clinical care, and to identify any gaps in the methodology of economic evaluations. We undertook a critical review of the empirical evidence from economic evaluations of genomic sequencing among paediatric patients searching five electronic databases. Our inclusion criteria were limited to literature published in the English language between 2010 and 2017 in OECD countries. Articles that met our inclusion criteria were assessed using a recognised checklist for a well-designed economic evaluation. We found 11 full-text articles that met our inclusion criteria. Our analysis found that genomic sequencing markedly increased the diagnostic rate to 16-79%, but lowered the cost by 11-64% compared to the standard diagnostic pathway. Only five recent studies in paediatric clinical cohorts met most of the criteria for a well-designed economic evaluation and demonstrated cost-effectiveness of genomic sequencing in paediatric clinical cohorts of patients. Our review identified the need for improvement in the rigour of the methodologies used to provide robust evidence for the formulation of health policy on public funding to integrate genomic sequencing into routine clinical care. Nonetheless, there is emerging evidence of the cost-effectiveness of genomic sequencing over usual care for paediatric patients.
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43
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Dragojlovic N, Kim E, Elliott AM, Friedman JM, Lynd LD. Evaluating the use of parental reports to estimate health care resource utilization in children with suspected genetic disorders. J Eval Clin Pract 2018; 24:416-422. [PMID: 29603523 DOI: 10.1111/jep.12876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE A key step in evaluating the cost-effectiveness of diagnostic genome-wide sequencing (GWS) services is to measure the cost of prior and subsequent diagnosis-related health care resource utilization by patients. The majority of patients using diagnostic GWS services are children, and parental surveys are often used to complement utilization data abstracted from medical records. The objective of this study was to evaluate the validity of parental reports for children with very high levels of resource utilization. METHOD Primary caregivers of children enrolled in the CAUSES Research Clinic, a diagnostic GWS programme at B.C. Children's Hospital, completed an online survey. Parent-reported health care encounters for the 6-month period prior to survey completion were compared to utilization data abstracted from electronic medical records (EMR). The association between demographic characteristics and the probability of survey completion was tested using logistic regression. Agreement between parent-reported and EMR data was evaluated using Cohen's kappa, prevalence- and bias-adjusted kappa (PABAK), and the intraclass correlation coefficient (ICC). RESULTS There were no major differences in demographic characteristics or resource utilization levels between families that completed the survey and those who did not. Agreement between parental reports and EMR data was high for hospitalizations (κ = 0.71; PABAK = 0.89; ICC = 0.77) but lower for outpatient physician visits (κ = 0.21; PABAK = 0.48; ICC = 0.27). CONCLUSIONS Parental surveys are a valuable tool for estimating health care resource utilization during a 6-month recall period for children with suspected genetic disorders but are best used to complement utilization data collected from other sources.
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Affiliation(s)
- Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ellen Kim
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
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- British Columbia Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, BC, Canada
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44
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Patients Express Satisfaction, Understanding of Whole‐Genome Sequencing: In primary care and cardiology, patients were generally satisfied with their physicians' communication of WGS results, but expectations about its clinical benefits were not met. Am J Med Genet A 2018; 176:754-755. [DOI: 10.1002/ajmg.a.38669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Loubière S, Drezet A, Beau-Faller M, Moro-Sibilot D, Friard S, Wislez M, Blons H, Daniel C, Westeel V, Madroszyk A, Léna H, Merle P, Mazières J, Zalcman G, Lacave R, Antoine M, Morin F, Missy P, Barlesi F, Auquier P, Cadranel J. Cost-effectiveness of KRAS, EGFR and ALK testing for decision making in advanced nonsmall cell lung carcinoma: the French IFCT-PREDICT.amm study. Eur Respir J 2018; 51:13993003.01467-2017. [DOI: 10.1183/13993003.01467-2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/31/2018] [Indexed: 11/05/2022]
Abstract
ALK rearrangement and EGFR/KRAS mutations constitute the primary biomarkers tested to provide targeted or nontargeted therapies in advanced nonsmall cell lung cancer (NSCLC) patients. Our objective was to assess the cost-effectiveness of biomarker testing for NSCLC.Between 2013 and 2014, 843 treatment-naive patients were prospectively recruited at 19 French hospitals into a longitudinal observational cohort study. Two testing strategies were compared, i.e. with “at least one biomarker status known” and “at least KRAS status known”, in addition to “no biomarker testing” as the reference strategy. The Kaplan–Meier approach was employed to assess restricted mean survival time. Direct medical costs incurred by hospitals were estimated with regard to treatment, inpatient care and biomarker testing.Compared with “no biomarker testing”, the “at least one biomarker status known” strategy yielded an incremental cost-effectiveness ratio of EUR13 230 per life-year saved, which decreased to EUR7444 per life-year saved with the “at least KRAS status known” testing strategy. In sensitivity analyses, biomarker testing strategies were less costly and more effective in 41% of iterations.In summary, molecular testing prior to treatment initiation proves to be cost-effective in advanced NSCLC management and may assist decision makers in defining conditions for further implementation of these innovations in general practice.
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Marino P, Touzani R, Perrier L, Rouleau E, Kossi DS, Zhaomin Z, Charrier N, Goardon N, Preudhomme C, Durand-Zaleski I, Borget I, Baffert S. Cost of cancer diagnosis using next-generation sequencing targeted gene panels in routine practice: a nationwide French study. Eur J Hum Genet 2018; 26:314-323. [PMID: 29367707 PMCID: PMC5838982 DOI: 10.1038/s41431-017-0081-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 12/25/2022] Open
Abstract
It is currently unclear if next-generation sequencing (NGS) technologies can be implemented in the diagnosis setting at an affordable cost. The aim of this study was to measure the total cost of performing NGS in clinical practice in France, in both germline and somatic cancer genetics.The study was performed on 15 French representative cancer molecular genetics laboratories performing NGS panels' tests. The production cost was estimated using a micro-costing method with resources consumed collected in situ in each laboratory from a healthcare provider perspective. In addition, we used a top-down methodology for specific post-sequencing steps including bioinformatics, technical validation, and biological validation. Additional non-specific costs were also included. Costs were detailed per step of the process (from the pre-analytical phase to delivery of results), and per cost driver (consumables, staff, equipment, maintenance, overheads). Sensitivity analyses were performed.The mean total cost of NGS for targeted gene panels was estimated to 607€ (±207) in somatic genetics and 550€ (±140) in germline oncogenetic analysis. Consumables were the highest cost driver of the sequencing process. The sensitivity analysis showed that a 25% reduction of consumables resulted in a 15% decrease in total NGS cost in somatic genetics, and 13% in germline analysis. Additional costs accounted for 30-32% of the total NGS costs.Beyond cost assessment considerations, the diffusion of NGS technologies will raise questions about their efficiency when compared to more targeted approaches, and their added value in a context of routine diagnosis.
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Affiliation(s)
- Patricia Marino
- Institut Paoli Calmettes, SESSTIM, Marseille, France.
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Aix Marseille Univ, Marseille, France.
| | - Rajae Touzani
- Institut Paoli Calmettes, SESSTIM, Marseille, France
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Aix Marseille Univ, Marseille, France
| | - Lionel Perrier
- Léon Berard Cancer Centre, GATE L-SE, UMR-CNRS 5824, Lyon, France
| | - Etienne Rouleau
- Department of Pathology and Medical Biology, Gustave Roussy, Villejuif, France
| | | | - Zou Zhaomin
- Gustave Roussy, Etudes et Recherche en économie de la santé, Villejuif, France
| | | | - Nicolas Goardon
- Cancer Comprehensive Center François Baclesse, Cancer Biology and Genetics Laboratory, Caen, France
| | - Claude Preudhomme
- CHRU of Lille, Biology & Pathology Center, Laboratory of Hematology, Lille, France
| | | | - Isabelle Borget
- Gustave Roussy, Etudes et Recherche en économie de la santé, Villejuif, France
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Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Front Genet 2018; 9:20. [PMID: 29467791 PMCID: PMC5808353 DOI: 10.3389/fgene.2018.00020] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS). For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.
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Affiliation(s)
- Paul Dunn
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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Wang S, Qian F, Zheng Y, Ogundiran T, Ojengbede O, Zheng W, Blot W, Nathanson KL, Hennis A, Nemesure B, Ambs S, Olopade OI, Huo D. Genetic variants demonstrating flip-flop phenomenon and breast cancer risk prediction among women of African ancestry. Breast Cancer Res Treat 2018; 168:703-712. [PMID: 29302764 DOI: 10.1007/s10549-017-4638-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/23/2017] [Indexed: 01/19/2023]
Abstract
BACKGROUND Few studies have evaluated the performance of existing breast cancer risk prediction models among women of African ancestry. In replication studies of genetic variants, a change in direction of the risk association is a common phenomenon. Termed flip-flop, it means that a variant is risk factor in one population but protective in another, affecting the performance of risk prediction models. METHODS We used data from the genome-wide association study (GWAS) of breast cancer in the African diaspora (The Root consortium), which included 3686 participants of African ancestry from Nigeria, USA, and Barbados. Polygenic risk scores (PRSs) were constructed from the published odds ratios (ORs) of four sets of susceptibility loci for breast cancer. Discrimination capacity was measured using the area under the receiver operating characteristic curve (AUC). RESULTS Flip-flop phenomenon was observed among 30~40% of variants across studies. Using the 34 variants with consistent directionality among previous studies, we constructed a PRS with AUC of 0.531 (95% confidence interval [CI]: 0.512-0.550), which is similar to the PRS using 93 variants and ORs from European ancestry populations (AUC = 0.525, 95% CI: 0.506-0.544). Additionally, we found the 34-variant PRS has good discriminative accuracy in women with family history of breast cancer (AUC = 0.586, 95% CI: 0.532-0.640). CONCLUSIONS We found that PRS based on variants identified from prior GWASs conducted in women of European and Asian ancestries did not provide a comparable degree of risk stratification for women of African ancestry. Further large-scale fine-mapping studies in African ancestry populations are desirable to discover population-specific genetic risk variants.
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Affiliation(s)
- Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China.,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., MC 2020, Chicago, IL, 60637, USA
| | - Frank Qian
- Department of Medicine, University of Chicago, Chicago, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., MC 2020, Chicago, IL, 60637, USA
| | - Temidayo Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | | | - Anselm Hennis
- Chronic Disease Research Centre, Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York, Stony Brook, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Rockville, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., MC 2020, Chicago, IL, 60637, USA.
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave, MC 2007, Chicago, IL, 60637, USA.
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49
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Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, Cohn RD, Scherer SW, Ungar WJ. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur J Hum Genet 2017; 25:1303-1312. [PMID: 29158552 PMCID: PMC5865210 DOI: 10.1038/s41431-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Accepted: 09/09/2017] [Indexed: 01/14/2023] Open
Abstract
The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.
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Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Jasmin Bhawra
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Canada
| | - Kate Tsiplova
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Nasim Monfared
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Sarah Bowdin
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - D James Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Christian R Marshall
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Raveen Basran
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Cheryl Shuman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Shinya Ito
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Courtney Hum
- Prenatal Diagnosis and Medical Genetics Program, Sinai Health System, Toronto, Canada
| | - Marta Girdea
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
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Raskin L, Guo Y, Du L, Clendenning M, Rosty C, Lindor NM, Gruber SB, Buchanan DD. Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort. Oncotarget 2017; 8:93450-93463. [PMID: 29212164 PMCID: PMC5706810 DOI: 10.18632/oncotarget.18596] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/19/2017] [Indexed: 01/07/2023] Open
Abstract
The underlying genetic cause of colorectal cancer (CRC) can be identified for 5-10% of all cases, while at least 20% of CRC cases are thought to be due to inherited genetic factors. Screening for highly penetrant mutations in genes associated with Mendelian cancer syndromes using next-generation sequencing (NGS) can be prohibitively expensive for studies requiring large samples sizes. The aim of the study was to identify rare single nucleotide variants and small indels in 40 established or candidate CRC susceptibility genes in 1,046 familial CRC cases (including both MSS and MSI-H tumor subtypes) and 1,006 unrelated controls from the Colon Cancer Family Registry Cohort using a robust and cost-effective DNA pooling NGS strategy. We identified 264 variants in 38 genes that were observed only in cases, comprising either very rare (minor allele frequency <0.001) or not previously reported (n=90, 34%) in reference databases, including six stop-gain, three frameshift, and 255 non-synonymous variants predicted to be damaging. We found novel germline mutations in established CRC genes MLH1, APC, and POLE, and likely pathogenic variants in cancer susceptibility genes BAP1, CDH1, CHEK2, ENG, and MSH3. For the candidate CRC genes, we identified likely pathogenic variants in the helicase domain of POLQ and in the LRIG1, SH2B3, and NOS1 genes and present their clinicopathological characteristics. Using a DNA pooling NGS strategy, we identified novel germline mutations in established CRC susceptibility genes in familial CRC cases. Further studies are required to support the role of POLQ, LRIG1, SH2B3 and NOS1 as CRC susceptibility genes.
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Affiliation(s)
- Leon Raskin
- Division of Epidemiology, School of Medicine, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA
| | - Yan Guo
- Center for Quantitative Sciences, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA
| | - Liping Du
- Center for Quantitative Sciences, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
- Envoi Specialist Pathologists, Herston, Queensland, Australia
- University of Queensland, School of Medicine, Herston, Queensland, Australia
| | - Colon Cancer Family Registry (CCFR)
- Division of Epidemiology, School of Medicine, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center and Vanderbilt Ingram Comprehensive Cancer Center, Nashville, TN, USA
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
- Envoi Specialist Pathologists, Herston, Queensland, Australia
- University of Queensland, School of Medicine, Herston, Queensland, Australia
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Stephen B. Gruber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
- University of Queensland, School of Medicine, Herston, Queensland, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Victoria, Australia
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