463 results on '"Genomics economics"'
Search Results
2. Exploring the benefits, harms and costs of genomic newborn screening for rare diseases.
- Author
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Baple EL, Scott RH, Banka S, Buchanan J, Fish L, Wynn S, Wilkinson D, Ellard S, MacArthur DG, and Stark Z
- Subjects
- Humans, Infant, Newborn, Genetic Testing economics, Cost-Benefit Analysis, Neonatal Screening economics, Rare Diseases genetics, Rare Diseases diagnosis, Genomics economics
- Published
- 2024
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3. Real-world clinical and economic outcomes for patients with advanced non-small cell lung cancer enrolled in a clinical trial following comprehensive genomic profiling via liquid biopsy.
- Author
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Wiedower JA, Forbes SP, Tsai LJ, Liao J, and Raez LE
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- Humans, Liquid Biopsy economics, Female, Male, Middle Aged, Aged, Clinical Trials as Topic economics, Biomarkers, Tumor genetics, Genomics economics, United States, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung economics, Lung Neoplasms drug therapy, Lung Neoplasms economics, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Background: Oncology clinical trial enrollment is strongly recommended for patients with cancer who are not eligible for established and approved therapies. Many trials are specific to biomarker-targeted therapies, which are typically managed as specialty pharmacy services. Comprehensive genomic profiling (CGP) of advanced cancers has been shown to detect biomarkers, guide targeted treatment, improve outcomes, and result in the clinical trial enrollment of patients, which is modeled to offset pharmacy costs experienced by US payers, yet payer policy coverage remains inconsistent. A common concern limiting coverage of CGP by payers is the potential of identifying biomarkers beyond guideline-recommended treatments, which creates a perception that insurance companies are being positioned to "pay for research." However, these biomarkers can increase clinical trial eligibility, and specialty pharmacy management may have an interest in maximizing the clinical trial enrollment of members., Objective: To investigate if clinical trial enrollment following liquid biopsy CGP for non-small cell lung cancer (NSCLC) is clinically and/or economically impactful from a payer claims perspective., Methods: Clinical and economic outcomes were studied using a real-world clinical genomic database (including payer claims data) from patients with NSCLC who enrolled in clinical trials immediately following liquid biopsy CGP (using Guardant360) and matched NSCLC patient controls also tested with liquid biopsy CGP., Results: Real-world overall survival was significantly (log-rank P < 0.0001) better for patients enrolled in clinical trials with similar costs of care, albeit with more outpatient encounters among those enrolled compared with matched controls., Conclusions: The results, together with previous analyses, suggest that, in addition to the clinical benefits associated with targeted therapies directed by CGP and other testing approaches, payers and specialty pharmacy managers may consider clinical trial direction and enrollment as a clinical and economic benefit of liquid biopsy CGP and adopt this into coverage decision frameworks and formularies.
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- 2024
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4. Cost-effective genomic prediction of critical economic traits in sturgeons through low-coverage sequencing.
- Author
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Song H, Dong T, Wang W, Jiang B, Yan X, Geng C, Bai S, Xu S, and Hu H
- Subjects
- Animals, Whole Genome Sequencing economics, Whole Genome Sequencing methods, Genomics methods, Genomics economics, Cost-Benefit Analysis, Linkage Disequilibrium, Fishes genetics, Polymorphism, Single Nucleotide
- Abstract
Low-coverage whole-genome sequencing (LCS) offers a cost-effective alternative for sturgeon breeding, especially given the lack of SNP chips and the high costs associated with whole-genome sequencing. In this study, the efficiency of LCS for genotype imputation and genomic prediction was assessed in 643 sequenced Russian sturgeons (∼13.68×). The results showed that using BaseVar+STITCH at a sequencing depth of 2× with a sample size larger than 300 resulted in the highest genotyping accuracy. In addition, when the sequencing depth reached 0.5× and SNP density was reduced to 50 K through linkage disequilibrium pruning, the prediction accuracy was comparable to that of whole sequencing depth. Furthermore, an incremental feature selection method has the potential to improve prediction accuracy. This study suggests that the combination of LCS and imputation can be a cost-effective strategy, contributing to the genetic improvement of economic traits and promoting genetic gains in aquaculture species., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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5. Investing in Africa's scientific future.
- Author
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de Oliveira T and Baxter C
- Subjects
- Humans, Africa epidemiology, Workforce, Prevalence, Incidence, Brain Drain, Communicable Diseases economics, Communicable Diseases epidemiology, Communicable Diseases mortality, Global Burden of Disease, Genomics economics, Genomics trends
- Abstract
Africa bears a disproportionate burden of infectious diseases, accounting for a substantial percentage of global cases. Malaria, HIV/AIDS, tuberculosis, cholera, Ebola, Lassa fever, and other tropical diseases, such as dengue and chikungunya, have had a profound impact on morbidity and mortality. Various factors contribute to the higher prevalence and incidence of infectious diseases in Africa, including socioeconomic challenges, limited access to health care, inadequate sanitation and hygiene infrastructure, climate-related factors, and endemicity of certain diseases in specific regions. A skilled workforce is crucial to addressing these challenges. Unfortunately, many countries in Africa often lack the required resources, and aspiring scientists frequently seek educational and career opportunities abroad, leading to a substantial loss of talent and expertise from the continent. This talent migration, referred to as "brain drain," exacerbates the existing training gaps and hampers the sustainability of research within Africa.
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- 2024
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6. Terra takes the pain out of 'omics' computing in the cloud.
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Perkel JM
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- Aging genetics, Animals, Biomedical Research, Datasets as Topic, Dogs, Genome genetics, Genomics economics, Humans, Internet, National Human Genome Research Institute (U.S.), Pets genetics, United States, Workflow, Cloud Computing economics, Genomics methods, Information Dissemination methods, Multicenter Studies as Topic methods, Software economics
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- 2022
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7. Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs.
- Author
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Hamazaki K and Iwata H
- Subjects
- Bayes Theorem, Computer Simulation, Costs and Cost Analysis, Datasets as Topic, Phenotype, Genomics economics, Models, Genetic, Oryza genetics
- Abstract
Key Message: We propose a novel approach to the Bayesian optimization of multivariate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation. Multivariate genomic prediction based on secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle-based remote sensing), has attracted much attention because it offers improved accuracy gains compared with genomic prediction based only on marker genotypes. Although there is a trade-off between accuracy gains and phenotyping costs of secondary traits, no attempt has been made to optimize these trade-offs. In this study, we propose a novel approach to optimize multivariate genomic prediction models for secondary traits measurable at early growth stages for improved accuracy gains and phenotyping costs. The proposed approach employs Bayesian optimization for efficient Pareto frontier estimation, representing the maximum accuracy at a given cost. The proposed approach successfully estimated the optimal secondary trait combinations across a range of costs while providing genomic predictions for only about [Formula: see text] of all possible combinations. The simulation results reflecting the characteristics of each scenario of the simulated target traits showed that the obtained optimal combinations were reasonable. Analysis of real-time target trait data showed that the proposed multivariate genomic prediction model had significantly superior accuracy compared to the univariate genomic prediction model., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2022
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8. SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs.
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Belman S, Saha S, and Beale MA
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- Africa epidemiology, Bangladesh epidemiology, COVID-19 diagnosis, COVID-19 economics, COVID-19 transmission, Developing Countries economics, Epidemiological Monitoring, Genomics instrumentation, Genomics methods, Humans, Nanopore Sequencing instrumentation, Nanopore Sequencing methods, Phylogeny, SARS-CoV-2 classification, SARS-CoV-2 isolation & purification, SARS-CoV-2 pathogenicity, COVID-19 epidemiology, Genome, Viral, Genomics economics, Nanopore Sequencing economics, SARS-CoV-2 genetics
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- 2022
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9. Returning actionable genomic results in a research biobank: Analytic validity, clinical implementation, and resource utilization.
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Blout Zawatsky CL, Shah N, Machini K, Perez E, Christensen KD, Zouk H, Steeves M, Koch C, Uveges M, Shea J, Gold N, Krier J, Boutin N, Mahanta L, Rehm HL, Weiss ST, Karlson EW, Smoller JW, Lebo MS, and Green RC
- Subjects
- Adult, Cohort Studies, DNA, Disclosure, Duty to Recontact, Female, Genetic Research, Genetic Testing, Humans, Informed Consent, Male, Middle Aged, Reproducibility of Results, Biological Specimen Banks, Disease genetics, Genetic Variation, Genome, Human, Genomics economics, Genomics standards, Genomics trends
- Abstract
Over 100 million research participants around the world have had research array-based genotyping (GT) or genome sequencing (GS), but only a small fraction of these have been offered return of actionable genomic findings (gRoR). Between 2017 and 2021, we analyzed genomic results from 36,417 participants in the Mass General Brigham Biobank and offered to confirm and return pathogenic and likely pathogenic variants (PLPVs) in 59 genes. Variant verification prior to participant recontact revealed that GT falsely identified PLPVs in 44.9% of samples, and GT failed to identify 72.0% of PLPVs detected in a subset of samples that were also sequenced. GT and GS detected verified PLPVs in 1% and 2.5% of the cohort, respectively. Of 256 participants who were alerted that they carried actionable PLPVs, 37.5% actively or passively declined further disclosure. 76.3% of those carrying PLPVs were unaware that they were carrying the variant, and over half of those met published professional criteria for genetic testing but had never been tested. This gRoR protocol cost approximately $129,000 USD per year in laboratory testing and research staff support, representing $14 per participant whose DNA was analyzed or $3,224 per participant in whom a PLPV was confirmed and disclosed. These data provide logistical details around gRoR that could help other investigators planning to return genomic results., Competing Interests: Declaration of interests S.T.W. has received compensation from UpToDate. J.W.S. is a member of the Leon Levy Foundation Neuroscience Advisory Board and received an honorarium for an internal seminar at Biogen. He is PI of a collaborative study of the genetics of depression and bipolar disorder sponsored by 23andMe for which 23andMe provides analysis time as in-kind support but no payments. R.C.G. has received compensation for advising the following companies: AIA, Genomic Life, Grail, Humanity, Kneed Media, Plumcare, OptumLabs, Verily, and Vibrent Health. He is co-founder of Genome Medical., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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10. Using Online Mendelian Inheritance in Man in low- and middle-income countries.
- Author
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de Macena Sobreira NL, Repetto GM, Temtamy SA, and Alvarez Perez AB
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- Chromosome Mapping, Developing Countries economics, Genetic Diseases, Inborn economics, Genetic Diseases, Inborn epidemiology, Genomics economics, High-Throughput Nucleotide Sequencing economics, Humans, Mass Screening economics, Phenotype, Databases, Genetic economics, Genetic Diseases, Inborn genetics, Genetics, Medical economics
- Abstract
Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders, has been used in the low- and middle-income countries largely as a tool for improving clinical care, teaching genetics and genomics, and for clinical and research analysis of next-generation sequencing. By facilitating free access to curated, updated, and comprehensive information in genetics and genomics, OMIM has led to better clinical care and research advancement in countries where clinicians and researchers in private or public hospitals and universities cannot afford to pay for other resources including journal subscriptions., (© 2021 Wiley Periodicals LLC.)
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- 2021
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11. Molecular Genomic Assessment Using a Blood-based mRNA Signature (NETest) is Cost-effective and Predicts Neuroendocrine Tumor Recurrence With 94% Accuracy.
- Author
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Modlin IM, Kidd M, Frilling A, Falconi M, Filosso PL, Malczewska A, and Kitz A
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- Adult, Aged, Aged, 80 and over, Biomarkers, Tumor genetics, Cost-Benefit Analysis, Disease Progression, Female, Genomics economics, Genomics methods, Humans, Liquid Biopsy economics, Male, Middle Aged, Neoplasm Recurrence, Local genetics, Neoplasm, Residual diagnosis, Neoplasm, Residual genetics, Neuroendocrine Tumors genetics, Predictive Value of Tests, Prognosis, Prospective Studies, RNA, Messenger blood, Reagent Kits, Diagnostic economics, Sensitivity and Specificity, Biomarkers, Tumor blood, Liquid Biopsy instrumentation, Neoplasm Recurrence, Local diagnosis, Neuroendocrine Tumors surgery
- Abstract
Introduction: Identification of residual disease after neuroendocrine tumor (NET) resection is critical for management. Post-surgery imaging is insensitive, expensive, and current biomarkers ineffective. We evaluated whether the NETest, a multigene liquid biopsy blood biomarker, correlated with surgical resection and could predict recurrence., Methods: Multicenter evaluation of NET resections over 24 months (n = 103): 47 pancreas, 26 small bowel, 26 lung, 2 appendix, 1 duodenum, 1 stomach. Surgery: R0 (83), R1/R2 (20). One millilitre of blood was collected at D0 and posroperative day (POD) 30. Transcript quantification by polymerase chain reaction (normal: ≤20), CgA by NEOLISA (normal ≤108 ng/mL). Standard-of-care (SoC) follow-up costs were calculated and compared to POD30 NETest-stratification approach. Analyses: Wilcoxon-paired test, Chi-square test., D Biomarkers: NETest: 103 of 103 (100%)-positive, whereas 23 of 103 (22%) were CgA-positive (Chi-square = 78, P < 0.0001).In the R0 group, the NETest decreased 59 ± 28 to 26 ± 23 (P < 0.0001); 36% (30/83) remained elevated. No significant decrease was evident for CgA. In the R1/R2 group the NETest decreased but 100% remained elevated. CgA levels did not decrease.An elevated POD30 NETest was present in R0 and 25 (83%) developed radiological recurrences. Normal score R0 s (n = 53) did not develop recurrence (Chi-square = 56, P < 0.0001). Recurrence prediction was 94% accurate with the NETest., Cost Evaluation: Using the NETest to stratify postoperative imaging resulted in a cost-savings of 42%., Conclusion: NETest diagnosis is more accurate than CgA (100% vs 22%). Surgery significantly decreased NETest. An elevated POD30 NETest predicted recurrence with 94% accuracy and post-surgical POD30 NETest follow-up stratification decreased costs by 42%. CgA had no surgical utility. Further studies would define the accuracy and cost-effectiveness of the NETest in the detection of postoperative recurrent disease., Competing Interests: Conflict of Interest Statement: M.F.: research grants and advisory role for J&J, Novartis, Ipsen, AAA, Mylan, and Celgene; A.F.: advisory roles for Novartis, Ipsen, and SIRTEXl; I.M.M.: consultant for Wren Laboratories; M.K. and A.K. are employees of Wren Laboratories; E.L.K., P.L.F., and A.M. have no disclosures. The authors report no conflicts of interest., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)
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- 2021
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12. Clinical and cost outcomes following genomics-informed treatment for advanced cancers.
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Weymann D, Pollard S, Chan B, Titmuss E, Bohm A, Laskin J, Jones SJM, Pleasance E, Nelson J, Fok A, Lim H, Karsan A, Renouf DJ, Schrader KA, Sun S, Yip S, Schaeffer DF, Marra MA, and Regier DA
- Subjects
- Breast Neoplasms, Costs and Cost Analysis, Female, Gastrointestinal Neoplasms genetics, Gastrointestinal Neoplasms mortality, Gastrointestinal Neoplasms pathology, Gastrointestinal Neoplasms therapy, Genome-Wide Association Study, Genomics economics, Genomics methods, Humans, Logistic Models, Male, Middle Aged, Neoplasms mortality, Neoplasms pathology, Precision Medicine methods, Retrospective Studies, Treatment Outcome, Withholding Treatment, Neoplasms genetics, Neoplasms therapy, Precision Medicine economics, Sequence Analysis, DNA
- Abstract
Background: Single-arm trials are common in precision oncology. Owing to the lack of randomized counterfactual, resultant data are not amenable to comparative outcomes analyses. Difference-in-difference (DID) methods present an opportunity to generate causal estimates of time-varying treatment outcomes. Using DID, our study estimates within-cohort effects of genomics-informed treatment versus standard care on clinical and cost outcomes., Methods: We focus on adults with advanced cancers enrolled in the single-arm BC Cancer Personalized OncoGenomics program between 2012 and 2017. All individuals had a minimum of 1-year follow up. Logistic regression explored baseline differences across patients who received a genomics-informed treatment versus a standard care treatment after genomic sequencing. DID estimated the incremental effects of genomics-informed treatment on time to treatment discontinuation (TTD), time to next treatment (TTNT), and costs. TTD and TTNT correlate with improved response and survival., Results: Our study cohort included 346 patients, of whom 140 (40%) received genomics-informed treatment after sequencing and 206 (60%) received standard care treatment. No significant differences in baseline characteristics were detected across treatment groups. DID estimated that the incremental effect of genomics-informed versus standard care treatment was 102 days (95% CI: 35, 167) on TTD, 91 days (95% CI: -9, 175) on TTNT, and CAD$91,098 (95% CI: $46,848, $176,598) on costs. Effects were most pronounced in gastrointestinal cancer patients., Conclusions: Genomics-informed treatment had a statistically significant effect on TTD compared to standard care treatment, but at increased treatment costs. Within-cohort evidence generated through this single-arm study informs the early-stage comparative effectiveness of precision oncology., (© 2021 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.)
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- 2021
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13. Clinically Responsive Genomic Analysis Pipelines: Elements to Improve Detection Rate and Efficiency.
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Sundercombe SL, Berbic M, Evans CA, Cliffe C, Elakis G, Temple SEL, Selvanathan A, Ewans L, Quayum N, Nixon CY, Dias KR, Lang S, Richards A, Goh S, Wilson M, Mowat D, Sachdev R, Sandaradura S, Walsh M, Farrar MA, Walsh R, Fletcher J, Kirk EP, Teunisse GM, Schofield D, Buckley MF, Zhu Y, and Roscioli T
- Subjects
- Cost-Benefit Analysis, Exome, Genetic Testing economics, Genome, Human, Genomics economics, High-Throughput Nucleotide Sequencing economics, Humans, INDEL Mutation, Phenotype, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Exome Sequencing economics, Genetic Diseases, Inborn genetics, Genetic Testing methods, Genomics methods, Germ-Line Mutation, High-Throughput Nucleotide Sequencing methods, Exome Sequencing methods
- Abstract
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness., (Crown Copyright © 2021. Published by Elsevier Inc. All rights reserved.)
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- 2021
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14. How scientists are embracing NFTs.
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Jones N
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- Art, Banking, Personal economics, Genome, Human, Genomics economics, Humans, Male, Blockchain, Commerce ethics, Research Personnel economics, Science economics
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- 2021
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15. Pandemic whistle-blower: we need a non-political way to track viruses.
- Author
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Maxmen A
- Subjects
- Centers for Disease Control and Prevention, U.S. organization & administration, Communicable Diseases, Emerging prevention & control, Communicable Diseases, Emerging virology, Data Analysis, Disaster Planning economics, Financing, Organized economics, Genome, Viral genetics, Genomics economics, Genomics trends, Humans, Leadership, Pandemics, SARS-CoV-2 isolation & purification, Sequence Analysis, United States epidemiology, COVID-19 epidemiology, COVID-19 virology, Disaster Planning methods, Epidemiological Monitoring, Politics, SARS-CoV-2 genetics, Whistleblowing
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- 2021
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16. National differences in cost analysis of Afirma Genomic sequencing classifier.
- Author
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Ronen O and Oichman M
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- Australia, Biopsy, Fine-Needle, Cost-Benefit Analysis, Genomics economics, Genomics methods, Humans, Israel, Retrospective Studies, Thyroid Neoplasms diagnosis, Thyroid Neoplasms genetics, Thyroid Neoplasms surgery, Thyroid Nodule diagnosis, Thyroid Nodule genetics, Thyroid Nodule surgery
- Abstract
Context: Thyroid nodules of indeterminate cytology can be subjected to molecular testing such as the Afirma Genomic Sequencing Classifier (GSC), thereby minimizing the number of unnecessary diagnostic surgeries., Objective: This work aimed to evaluate and compare the cost of routine GSC testing of indeterminate thyroid nodules in different countries., Design, Patients and Main Outcome Measures: The cost of diagnostic hemithyroidectomy of indeterminate thyroid nodules was calculated by performing a Monte Carlo simulation cost analysis on a Markov decision-analytic model and then compared to that of GSC testing in the UK, Australia, USA, and Israel., Results: Assuming that patients are treated by surgical resection and routine GSC testing is performed for all nodules of indeterminate significance, we found the GSC test to be more cost effective compared with diagnostic hemithyroidectomy when malignancy rates of thyroid nodules are less than 22.6%-37.1%, depending on the country where the test is performed. Given the cost of a thyroidectomy in the UK, Australia and Israel, performing routine GSC tests on all Bethesda IV nodules is more expensive than routine diagnostic hemithyroidectomy and becomes cost effective for Bethesda III when the GSC cost is below 3,031-3,087 USD. In comparison, in the USA, higher cost of thyroidectomy makes the GSC test cost effective for Bethesda III nodules at its current cost, but not for Bethesda IV nodules where it becomes cost effective under the price of 3,031 USD., Conclusions: Different molecular testing and surgical costs in different countries should be considered when performing cost analysis. In addition, since different medical centres have different malignancy rates, personalized in-house assessment of cost-effectiveness is warranted., (© 2021 John Wiley & Sons Ltd.)
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- 2021
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17. Establishment and implementation of Cancer Genomic Medicine in Japan.
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Mukai Y and Ueno H
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- Clinical Trials as Topic organization & administration, Genetic Counseling economics, Genetic Counseling organization & administration, Genetic Testing economics, Genomics economics, Genomics methods, Humans, Japan, Medical Oncology economics, Medical Oncology methods, National Health Programs economics, Neoplasms diagnosis, Neoplasms economics, Neoplasms genetics, Precision Medicine economics, Precision Medicine methods, Reimbursement Mechanisms, Therapies, Investigational economics, Genomics organization & administration, Health Plan Implementation, Medical Oncology organization & administration, National Health Programs organization & administration, Neoplasms therapy
- Abstract
Approximately 1 in 2 Japanese people are estimated to be diagnosed with cancer during their lifetime. Cancer still remains the leading cause of death in Japan, therefore the government of Japan has decided to develop a better cancer control policy and launched the Cancer Genomic Medicine (CGM) program. The Ministry of Health, Labour, and Welfare (MHLW) held a consortium at their headquarters with leading academic authorities and the representatives of related organizations to discuss ways to advance CGM in Japan. Based on the report of the consortium, the CGM system under the national health insurance system has gradually been realized. Eleven hospitals were designated in February 2018 as core hospitals for CGM; subsequently, the MHLW built the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) as an institution to aggregate and manage genomic and clinical information on cancer patients, and support appropriate secondary use of the aggregated information to develop research aimed at medical innovation. As the first step in Japan's CGM in routine practice, in June 2019 the MHLW started reimbursement of 2 types of tumor profiling tests for advanced solid cancer patients using the national insurance system. Japan's CGM has swiftly been spreading nationwide with the collaboration of 167 hospitals and patients. The health and research authorities are expected to embody personalized cancer medicine and promote CGM utilizing state-of-the-art technologies., (© 2020 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)
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- 2021
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18. The role of genomics in global cancer prevention.
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Ginsburg O, Ashton-Prolla P, Cantor A, Mariosa D, and Brennan P
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- Brazil, Cost-Benefit Analysis, Founder Effect, Genetic Predisposition to Disease, Genomics economics, Germ-Line Mutation, Humans, Mendelian Randomization Analysis, Mutation, Neoplasms epidemiology, United States, Genomics methods, Neoplasms genetics, Neoplasms prevention & control
- Abstract
Despite improvements in the understanding of cancer causation, much remains unknown regarding the mechanisms by which genomic and non-genomic factors initiate carcinogenesis, drive cell invasion and metastasis, and enable cancer to develop. Technological advances have enabled the analysis of whole genomes, comprising thousands of tumours across populations worldwide, with the aim of identifying mutation signatures associated with particular tumour types. Large collaborative efforts have resulted in the identification and improved understanding of causal factors, and have shed light on new opportunities to prevent cancer. In this new era in cancer genomics, discoveries from studies conducted on an international scale can inform evidence-based strategies in cancer control along the cancer care continuum, from prevention to treatment. In this Review, we present the relevant history and emerging frontiers of cancer genetics and genomics from the perspective of global cancer prevention. We highlight the importance of local context in the adoption of new technologies and emergent evidence, with illustrative examples from worldwide. We emphasize the challenges in implementing important genomic findings in clinical settings with disparate resource availability and present a conceptual framework for the translation of such findings into clinical practice, and evidence-based policies in order to maximize the utility for a population.
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- 2021
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19. Sequence three million genomes across Africa.
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Wonkam A
- Subjects
- Africa ethnology, Anemia, Sickle Cell genetics, Goals, Hearing Loss genetics, Human Genome Project economics, Humans, Black People genetics, Genome, Human genetics, Genomics economics, Genomics organization & administration, Sequence Analysis, DNA economics
- Published
- 2021
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20. Alarming COVID variants show vital role of genomic surveillance.
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Cyranoski D
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- COVID-19 transmission, Databases, Genetic, Evolution, Molecular, Genomics economics, Humans, Internationality, Pandemics statistics & numerical data, South Africa epidemiology, United Kingdom epidemiology, COVID-19 epidemiology, COVID-19 virology, Epidemiological Monitoring, Genome, Viral genetics, Molecular Epidemiology economics, Molecular Epidemiology organization & administration, Mutation, SARS-CoV-2 genetics, SARS-CoV-2 isolation & purification
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- 2021
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21. Economic impact of medical genetic testing on clinical applications in Thailand.
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Jittikoon J, Sangroongruangsri S, Thavorncharoensap M, Chitpim N, and Chaikledkaew U
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- Genomics economics, HIV genetics, HIV pathogenicity, HIV Infections epidemiology, HIV Infections genetics, HIV Infections virology, Health Care Costs standards, High-Throughput Nucleotide Sequencing economics, Humans, Thailand epidemiology, Cost of Illness, Cost-Benefit Analysis economics, Genetic Testing economics, HIV Infections economics
- Abstract
Background: Although the clinical benefits of medical genetic testing have been proven, there has been limited evidence on its economic impact in Thai setting. Thus, this study aimed to evaluate the economic impact of genetic testing services provided by the Center for Medical Genomics (CMG) in Thailand., Methods: Cost-benefit analysis was conducted from provider and societal perspectives. Cost and output data of genetic testing services provided by the CMG during 2014 to 2018 and published literature reviews were applied to estimate the costs and benefits. Monetary benefits related to genetic testing services were derived through human capital approach., Results: The total operation cost was 126 million baht over five years with an average annual cost of 21 million baht per year. The net benefit, benefit-to-cost ratio, and return on investment were 5,477 million baht, 43 times, and 42 times, respectively. Productivity gain was the highest proportion (50.57%) of the total benefit., Conclusions: The provision of genetic testing services at the CMG gained much more benefits than the cost. This study highlighted a good value for money in the establishment of medical genomics settings in Thailand and other developing countries., Competing Interests: The authors have declared that no competing interests exist.
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- 2020
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22. Strategic vision for improving human health at The Forefront of Genomics.
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Green ED, Gunter C, Biesecker LG, Di Francesco V, Easter CL, Feingold EA, Felsenfeld AL, Kaufman DJ, Ostrander EA, Pavan WJ, Phillippy AM, Wise AL, Dayal JG, Kish BJ, Mandich A, Wellington CR, Wetterstrand KA, Bates SA, Leja D, Vasquez S, Gahl WA, Graham BJ, Kastner DL, Liu P, Rodriguez LL, Solomon BD, Bonham VL, Brody LC, Hutter CM, and Manolio TA
- Subjects
- Biomedical Research economics, COVID-19 genetics, Genomics economics, Humans, National Human Genome Research Institute (U.S.) economics, Social Change, Translational Research, Biomedical economics, United States, Biomedical Research trends, Genome, Human genetics, Genomics trends, Public Health standards, Translational Research, Biomedical trends
- Abstract
Starting with the launch of the Human Genome Project three decades ago, and continuing after its completion in 2003, genomics has progressively come to have a central and catalytic role in basic and translational research. In addition, studies increasingly demonstrate how genomic information can be effectively used in clinical care. In the future, the anticipated advances in technology development, biological insights, and clinical applications (among others) will lead to more widespread integration of genomics into almost all areas of biomedical research, the adoption of genomics into mainstream medical and public-health practices, and an increasing relevance of genomics for everyday life. On behalf of the research community, the National Human Genome Research Institute recently completed a multi-year process of strategic engagement to identify future research priorities and opportunities in human genomics, with an emphasis on health applications. Here we describe the highest-priority elements envisioned for the cutting-edge of human genomics going forward-that is, at 'The Forefront of Genomics'.
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- 2020
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23. Recent advances and future perspectives in vector-omics.
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Compton A, Sharakhov IV, and Tu Z
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- Animals, Genomics economics, Genomics statistics & numerical data, Genome, Insect, Genomics methods, Insect Vectors genetics, Insecta genetics
- Abstract
We have reviewed recent progress and the remaining challenges in vector-omics. We have highlighted several technologies and applications that facilitate novel biological insights beyond achieving a reference-quality genome assembly. Among other topics, we have discussed the applications of chromatin conformation capture, chromatin accessibility assays, optical mapping, full-length RNA sequencing, single cell RNA analysis, proteomics, and population genomics. We anticipate that we will witness a great expansion in vector-omics research not only in its application in a broad range of species, but also its ability to uncover novel genetic elements and tackle previously inaccessible regions of the genome. It is our hope that the continued innovation in device portability, cost reduction, and informatics support will in the foreseeable future bring vector-omics to every vector laboratory and field station in the world, which will have an unparalleled impact on basic research and the control of vector-borne infectious diseases., (Copyright © 2020. Published by Elsevier Inc.)
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- 2020
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24. Impacts of genomics on the health and social costs of intellectual disability.
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Doble B, Schofield D, Evans CA, Groza T, Mattick JS, Field M, and Roscioli T
- Subjects
- Health Care Costs statistics & numerical data, Humans, Intellectual Disability diagnosis, Intellectual Disability epidemiology, Genomics economics, Intellectual Disability economics, Intellectual Disability genetics, Exome Sequencing economics
- Abstract
Background: This study provides an integrated assessment of the economic and social impacts of genomic sequencing for the detection of monogenic disorders resulting in intellectual disability (ID)., Methods: Multiple knowledge bases were cross-referenced and analysed to compile a reference list of monogenic disorders associated with ID. Multiple literature searches were used to quantify the health and social costs for the care of people with ID. Health and social expenditures and the current cost of whole-exome sequencing and whole-genome sequencing were quantified in relation to the more common causes of ID and their impact on lifespan., Results: On average, individuals with ID incur annual costs in terms of health costs, disability support, lost income and other social costs of US$172 000, accumulating to many millions of dollars over a lifetime., Conclusion: The diagnosis of monogenic disorders through genomic testing provides the opportunity to improve the diagnosis and management, and to reduce the costs of ID through informed reproductive decisions, reductions in unproductive diagnostic tests and increasingly targeted therapies., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2020
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25. The Melanoma Genomics Managing Your Risk Study randomised controlled trial: statistical analysis plan.
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Lo SN, Smit AK, Espinoza D, and Cust AE
- Subjects
- Australia, Cost-Benefit Analysis, Environmental Exposure prevention & control, Health Behavior, Humans, Melanoma economics, Melanoma genetics, Melanoma psychology, Randomized Controlled Trials as Topic, Risk Assessment, Skin Neoplasms economics, Skin Neoplasms genetics, Skin Neoplasms psychology, Ultraviolet Rays adverse effects, Data Interpretation, Statistical, Genetic Predisposition to Disease, Genetic Testing economics, Genomics economics, Melanoma prevention & control, Skin Neoplasms prevention & control
- Abstract
Background: The Melanoma Genomics Managing Your Risk Study is a randomised controlled trial that aims to evaluate the efficacy of providing information on personal genomic risk of melanoma in reducing ultraviolet radiation (UV) exposure, stratified by traditional risk group (low or high phenotypic risk) in the general population. The primary outcome is objectively measured total daily Standard Erythemal Doses at 12 months. Secondary outcomes include UV exposure at specific time periods, self-reported sun protection and skin-examination behaviours, psychosocial outcomes, and ethical considerations surrounding offering genomic testing at a population level. A within-trial and modelled economic evaluation will be undertaken from an Australian health system perspective to assess the cost-effectiveness of the intervention., Objective: To publish the pre-determined statistical analysis plan (SAP) before database lock and the start of analysis., Methods: This SAP describes the data synthesis, analysis principles and statistical procedures for analysing the outcomes from this trial. The SAP was approved after closure of recruitment and before completion of patient follow-up. It outlines the planned primary analyses and a range of subgroup and sensitivity analyses. Health economic outcomes are not included in this plan but will be analysed separately. The SAP will be adhered to for the final data analysis of this trial to avoid potential analysis bias that may arise from knowledge of the outcome data., Results: This SAP is consistent with best practice and should enable transparent reporting., Conclusion: This SAP has been developed for the Melanoma Genomics Managing Your Risk Study and will be followed to ensure high-quality standards of internal validity and to minimise analysis bias., Trial Registration: Prospectively registered with the Australian New Zealand Clinical Trials Registry, ID: ACTR N12617000691347 . Registered on 15 May 2017.
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- 2020
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26. Estimating the costs of genomic sequencing in cancer control.
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Gordon LG, White NM, Elliott TM, Nones K, Beckhouse AG, Rodriguez-Acevedo AJ, Webb PM, Lee XJ, Graves N, and Schofield DJ
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- Australia, Humans, Neoplasms genetics, Costs and Cost Analysis, Genomics economics, Neoplasms prevention & control
- Abstract
Background: Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings., Methods: We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories., Results: The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person., Conclusions: Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.
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- 2020
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27. Factors Associated With Oncologist Discussions of the Costs of Genomic Testing and Related Treatments.
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Yabroff KR, Zhao J, de Moor JS, Sineshaw HM, Freedman AN, Zheng Z, Han X, Rai A, and Klabunde CN
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- Adult, Female, Genetic Testing economics, Humans, Male, Medical Oncology methods, Middle Aged, Neoplasms economics, Neoplasms genetics, Oncologists psychology, Oncologists statistics & numerical data, Surveys and Questionnaires, United States, Communication, Genomics economics, Medical Oncology economics, Physician-Patient Relations
- Abstract
Background: Use of genomic testing is increasing in the United States. Testing can be expensive, and not all tests and related treatments are covered by health insurance. Little is known about how often oncologists discuss costs of testing and treatment or about the factors associated with those discussions., Methods: We identified 1220 oncologists who reported discussing genomic testing with their cancer patients from the 2017 National Survey of Precision Medicine in Cancer Treatment. Multivariable polytomous logistic regression analyses were used to assess associations between oncologist and practice characteristics and the frequency of cost discussions. All statistical tests were two-sided., Results: Among oncologists who discussed genomic testing with patients, 50.0% reported often discussing the likely costs of testing and related treatments, 26.3% reported sometimes discussing costs, and 23.7% reported never or rarely discussing costs. In adjusted analyses, oncologists with training in genomic testing or working in practices with electronic medical record alerts for genomic tests were more likely to have cost discussions sometimes (odds ratio [OR] = 2.09, 95% confidence interval [CI] = 1.19 to 3.69) or often (OR = 2.22, 95% CI = 1.30 to 3.79), respectively, compared to rarely or never. Other factors statistically significantly associated with more frequent cost discussions included treating solid tumors (rather than only hematological cancers), using next-generation sequencing gene panel tests, having higher patient volume, and working in practices with higher percentages of patients insured by Medicaid, or self-paid or uninsured., Conclusions: Interventions targeting modifiable oncologist and practice factors, such as training in genomic testing and use of electronic medical record alerts, may help improve cost discussions about genomic testing and related treatments., (Published by Oxford University Press 2019. This work is written by US Government employees and is in the public domain in the US.)
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- 2020
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28. The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis.
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Hong P, Jiang H, Xu W, Lin D, Xu Q, Cao G, and Li G
- Subjects
- Chromatin Assembly and Disassembly, Chromosomes chemistry, Costs and Cost Analysis, Genomics economics, Genomics standards, Humans, Whole Genome Sequencing economics, Whole Genome Sequencing standards, Chromosomes genetics, Genomics methods, Whole Genome Sequencing methods
- Abstract
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.
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- 2020
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29. The Future of DTC Genomics and the Law.
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Greely HT
- Subjects
- Genetic Testing economics, Genetic Testing methods, Genetic Testing trends, Humans, United States, Direct-To-Consumer Screening and Testing economics, Direct-To-Consumer Screening and Testing legislation & jurisprudence, Direct-To-Consumer Screening and Testing trends, Genomics economics, Genomics legislation & jurisprudence, Genomics trends
- Abstract
Direct-to-Consumer ("DTC") genomics has been a controversial topic for over a decade. Much work has been done on the legal issues it raises. This article asks a different question: What will DTC genomics and its legal issues look like in ten to twenty years? After discussing the five current uses of DTC genomics, it describes three current legal issues: medical uses, privacy of genomic information, and privacy in collection and analysis of human DNA. It then suggests that changes in human genomics and how it is used will make the first of those DTC genomics legal issues less important in the future, but that the third will be increasingly significant.
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- 2020
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30. Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish.
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Pochardt M, Allen JM, Hart T, Miller SDL, Yu DW, and Levi T
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- Animals, Female, Genomics economics, Male, Osmeriformes classification, Population Density, Rivers chemistry, DNA, Environmental genetics, Genomics methods, Osmeriformes genetics
- Abstract
Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and "eDNA rates" which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance, respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible., (© 2019 John Wiley & Sons Ltd.)
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- 2020
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31. Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon.
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Tsairidou S, Hamilton A, Robledo D, Bron JE, and Houston RD
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- Algorithms, Animals, Genetic Testing, Genome-Wide Association Study, Models, Genetic, Phenotype, Polymorphism, Single Nucleotide, Reproducibility of Results, Genetic Markers, Genomics economics, Genomics methods, Genotype, Genotyping Techniques economics, Salmo salar classification, Salmo salar genetics, Selection, Genetic
- Abstract
Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can be prohibitively expensive. Genotype imputation is a cost-effective method for obtaining high-density genotypes, but its value in aquaculture breeding programs which are characterized by large full-sibling families has yet to be fully assessed. The aim of this study was to optimize the use of low-density genotypes and evaluate genotype imputation strategies for cost-effective genomic prediction. Phenotypes and genotypes (78,362 SNPs) were obtained for 610 individuals from a Scottish Atlantic salmon breeding program population (Landcatch, UK) challenged with sea lice, Lepeophtheirus salmonis The genomic prediction accuracy of genomic selection was calculated using GBLUP approaches and compared across SNP panels of varying densities and composition, with and without imputation. Imputation was tested when parents were genotyped for the optimal SNP panel, and offspring were genotyped for a range of lower density imputation panels. Reducing SNP density had little impact on prediction accuracy until 5,000 SNPs, below which the accuracy dropped. Imputation accuracy increased with increasing imputation panel density. Genomic prediction accuracy when offspring were genotyped for just 200 SNPs, and parents for 5,000 SNPs, was 0.53. This accuracy was similar to the full high density and optimal density dataset, and markedly higher than using 200 SNPs without imputation. These results suggest that imputation from very low to medium density can be a cost-effective tool for genomic selection in Atlantic salmon breeding programs., (Copyright © 2020 Tsairidou et al.)
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- 2020
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32. The next chapter for African genomics.
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Maxmen A
- Subjects
- Biological Specimen Banks, Facility Design and Construction, Genetic Variation, Genomics economics, Human Genetics economics, Humans, Nigeria epidemiology, Precision Medicine economics, Research Personnel standards, Research Support as Topic, Stroke epidemiology, Stroke genetics, Yellow Fever diagnosis, Yellow Fever epidemiology, Black People genetics, Genome, Human genetics, Genomics trends, Human Genetics trends, Precision Medicine trends, Research Personnel supply & distribution
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- 2020
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33. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries.
- Author
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Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, and Gavrilov AA
- Subjects
- Animals, Biotinylation, Cell Line, Chromatin chemistry, Chromatin genetics, Chromatin isolation & purification, Chromatin metabolism, Chromosome Mapping economics, Chromosomes, Artificial, Bacterial genetics, DNA genetics, DNA isolation & purification, DNA metabolism, Gene Library, Genomics economics, High-Throughput Nucleotide Sequencing economics, Humans, Nucleic Acid Conformation, Nucleic Acid Hybridization methods, Chromosome Mapping methods, Genomics methods, High-Throughput Nucleotide Sequencing methods
- Abstract
Studies performed using Hi-C and other high-throughput whole-genome C-methods have demonstrated that 3D organization of eukaryotic genomes is functionally relevant. Unfortunately, ultra-deep sequencing of Hi-C libraries necessary to detect loop structures in large vertebrate genomes remains rather expensive. However, many studies are in fact aimed at determining the fine-scale 3D structure of comparatively small genomic regions up to several Mb in length. Such studies typically focus on the spatial structure of domains of coregulated genes, molecular mechanisms of loop formation, and interrogation of functional significance of GWAS-revealed polymorphisms. Therefore, a handful of molecular techniques based on Hi-C have been developed to address such issues. These techniques commonly rely on in-solution hybridization of Hi-C/3C-seq libraries with pools of biotinylated baits covering the region of interest, followed by deep sequencing of the enriched library. Here, we describe a new protocol of this kind, C-TALE (Chromatin TArget Ligation Enrichment). Preparation of hybridization probes from bacterial artificial chromosomes and an additional round of enrichment make C-TALE a cost-effective alternative to existing many-versus-all C-methods., (Copyright © 2019 Elsevier Inc. All rights reserved.)
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- 2020
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34. BAT Hi-C maps global chromatin interactions in an efficient and economical way.
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Huang J, Jiang Y, Zheng H, and Ji X
- Subjects
- Animals, Cell Line, Cell Nucleus genetics, Chromatin isolation & purification, Chromatin metabolism, Chromosome Mapping economics, Deoxyribonucleases, Type II Site-Specific metabolism, Embryonic Stem Cells, Gene Library, Genomics economics, Mice, Transposases metabolism, Chromatin genetics, Chromosome Mapping methods, Genomics methods
- Abstract
Chromosome Conformation Capture (3C)-based technologies, such as Hi-C, have represented a significant breakthrough in investigating the structure and function of higher-order genome architecture. However, the mapping of global chromatin interactions remains challenging across many biological conditions due to high background noise and financial constraints, especially for small laboratories. Here, we describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops. This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs. The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time. Importantly, with only one-third sequencing depth, our method revealed the same spectrum of chromatin contacts as in situ Hi-C. BAT Hi-C is an economical (i.e., approximately $40 for library preparation) and straightforward (total hands-on time of 3 days) tool that is ideal for the in-depth analysis of long-range chromatin looping events in a genome-wide fashion., (Copyright © 2019 Elsevier Inc. All rights reserved.)
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- 2020
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35. A Low-Cost High-Throughput Method for Plant Genomic DNA Isolation.
- Author
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Gupta P, Salava H, Sreelakshmi Y, and Sharma R
- Subjects
- Plants genetics, DNA, Plant isolation & purification, Genomics economics, Genomics methods, High-Throughput Screening Assays economics, High-Throughput Screening Assays methods
- Abstract
Many of the functional genomics methods require isolation of genomic DNA from large population of plants. The selection of DNA isolation protocols depends on several factors such as choice of starting material, ease of handling, time and labor required for isolation, the final quantity as well as the quality of genomic DNA. We outline here a high-throughput method of DNA extraction from different plant species including cereal crops. The protocol can be used for extraction of DNA in single tubes as well as for large formats in 96-well plates. The protocol includes steps for eliminating interfering secondary products such as phenolics. This protocol can be applied for high-throughput isolation of DNA for varied applications such as TILLING, mapping, fingerprinting, etc. as a cost-effective protocol compared to commercial kits.
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- 2020
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36. Crowdfunding science.
- Author
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Wilson MA
- Subjects
- Animals, Crowdsourcing economics, Humans, Lizards genetics, Crowdsourcing methods, Fund Raising methods, Genomics economics
- Published
- 2019
- Full Text
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37. Opportunities and Challenges for Implementing Genomics into Clinical Care.
- Subjects
- Clinical Decision-Making, Disease Management, Humans, Precision Medicine, Genetic Testing economics, Genetic Testing methods, Genomics economics, Genomics methods, Patient Care economics, Patient Care methods, Patient Care standards
- Published
- 2019
- Full Text
- View/download PDF
38. Harnessing the Genomic Landscape of the Small Renal Mass to Guide Clinical Management.
- Author
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Silagy AW, Sanchez A, Manley BJ, Bensalah K, Bex A, Karam JA, Ljungberg B, Shuch B, and Hakimi AA
- Subjects
- Biopsy, Carcinoma, Renal Cell epidemiology, Carcinoma, Renal Cell surgery, Cost-Benefit Analysis, Disease Management, Female, Genomics economics, Humans, Male, Neoplasm Staging, Nephrectomy methods, Precision Medicine methods, Prognosis, Reproducibility of Results, Risk Assessment, Carcinoma, Renal Cell genetics, Genomics methods, Kidney Neoplasms pathology
- Abstract
Context: Small renal masses (SRMs; tumors <4 cm) encompass a diagnostic and therapeutic challenge. Genomic profiling has the potential to improve risk stratification and personalize treatment selection., Objective: Herein, we review the evidence regarding the utility, challenges, and potential implications of genomic profiling in the management of SRMs., Evidence Acquisition: Pertinent publications available on PubMed database pertaining to kidney cancer, tumor size, genomics, and clinical management were reviewed., Evidence Synthesis: Compared with larger tumors, SRMs range from benign to lethal, necessitating strategies for improved treatment selection. Recent advances in the molecular characterization of renal cell carcinoma have improved our understanding of the disease; however, utility of these tools for the management of SRMs is less clear. While intratumoral heterogeneity (ITH) reduces the accuracy and reliability of sequencing, relative genomic uniformity of SRMs somewhat lessens the impact of ITH. Therefore, renal mass biopsy of SRMs represents an appealing opportunity to evaluate how incorporation of molecular profiles may improve management strategies., Conclusions: Ongoing research into the genomic landscape of SRMs has advanced our understanding of the spectrum of disease aggressiveness and may hold promise in matching disease biology to treatment intensity., Patient Summary: Small renal masses are a clinical challenge, as they range from benign to lethal. Genomic profiling may eventually improve treatment selection, but more research is needed., (Copyright © 2019 European Association of Urology. Published by Elsevier B.V. All rights reserved.)
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- 2019
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39. Evaluation of the cost and effectiveness of diverse recruitment methods for a genetic screening study.
- Author
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Milo Rasouly H, Wynn J, Marasa M, Reingold R, Chatterjee D, Kapoor S, Piva S, Kil BH, Mu X, Alvarez M, Nestor J, Mehl K, Revah-Politi A, Lippa N, Ernst ME, Bier L, Espinal A, Haser B, Sinha A, Halim I, Fasel D, Cuneo N, Thompson JJ, Verbitsky M, Cohn EG, Goldman J, Marder K, Klitzman RL, Orjuela MA, So YS, Fedotov A, Crew KD, Kiryluk K, Appelbaum PS, Weng C, Siegel K, Gharavi AG, and Chung WK
- Subjects
- Adult, Clinical Trials as Topic methods, Costs and Cost Analysis, Ethnicity, Female, Genomics economics, Genomics methods, Humans, Male, Mass Screening economics, Middle Aged, Research Design, Retrospective Studies, Clinical Trials as Topic economics, Genetic Testing economics, Patient Selection ethics
- Abstract
Purpose: Recruitment of participants from diverse backgrounds is crucial to the generalizability of genetic research, but has proven challenging. We retrospectively evaluated recruitment methods used for a study on return of genetic results., Methods: The costs of study design, development, and participant enrollment were calculated, and the characteristics of the participants enrolled through the seven recruitment methods were examined., Results: A total of 1118 participants provided consent, a blood sample, and questionnaire data. The estimated cost across recruitment methods ranged from $579 to $1666 per participant and required a large recruitment team. Recruitment methods using flyers and staff networks were the most cost-efficient and resulted in the highest completion rate. Targeted sampling that emphasized the importance of Latino/a participation, utilization of translated materials, and in-person recruitments contributed to enrolling a demographically diverse sample., Conclusions: Although all methods were deployed in the same hospital or neighborhood and shared the same staff, each recruitment method was different in terms of cost and characteristics of the enrolled participants, suggesting the importance of carefully choosing the recruitment methods based on the desired composition of the final study sample. This analysis provides information about the effectiveness and cost of different methods to recruit adults for genetic research.
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- 2019
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40. The Daunting Economics of Therapeutic Genome Editing.
- Author
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Wilson RC and Carroll D
- Subjects
- CRISPR-Cas Systems, Gene Editing ethics, Genetic Engineering ethics, Genetic Therapy economics, Genome, Genome, Human genetics, Genomics economics, Genomics ethics, Germ Cells metabolism, Germ Cells physiology, Humans, Gene Editing economics, Genetic Engineering economics
- Abstract
There is no shortage of enthusiasm for the clinical potential of CRISPR-based genome editing: many life-changing cures appear to be just around the corner. However, as mature genetic therapies reach the market, it seems that million-dollar price tags are the new normal. Several factors contribute to the extreme pricing of next-generation medicines, including the need to recoup development costs, the undeniable value of these powerful therapies, and the inherent technical challenges of manufacture and delivery. CRISPR technology has been hailed as a great leveler and a democratizing force in biomedicine. But for this principle to hold true in clinical contexts, therapeutic genome editing must avoid several pitfalls that could substantially limit access to its transformative potential, especially in the developing world.
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- 2019
- Full Text
- View/download PDF
41. BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.
- Author
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Uzbas F, Opperer F, Sönmezer C, Shaposhnikov D, Sass S, Krendl C, Angerer P, Theis FJ, Mueller NS, and Drukker M
- Subjects
- Breast Neoplasms genetics, Cost-Benefit Analysis, Embryonic Stem Cells metabolism, Female, Gene Expression Profiling economics, Genomics economics, High-Throughput Nucleotide Sequencing economics, Humans, Pluripotent Stem Cells metabolism, Sequence Analysis, RNA economics, Single-Cell Analysis economics, Single-Cell Analysis methods, Wnt Signaling Pathway, Workflow, Gene Expression Profiling methods, Genomics methods, High-Throughput Nucleotide Sequencing methods, Sequence Analysis, RNA methods
- Abstract
We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico. By applying the matrices in a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq), we analyze developmental states of thousands of single human pluripotent stem cells, either in different maintenance media or upon Wnt/β-catenin pathway activation, which identifies the mechanisms of differentiation induction. Moreover, we apply BART-Seq to the genetic screening of breast cancer patients and identify BRCA mutations with very high precision. The processing of thousands of samples and dynamic range measurements that outperform global transcriptomics techniques makes BART-Seq first targeted sequencing technique suitable for numerous research applications.
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- 2019
- Full Text
- View/download PDF
42. Challenges in funding and developing genomic software: roots and remedies.
- Author
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Siepel A
- Subjects
- Genetic Research, Genomics economics, Software economics
- Abstract
The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences. However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the research community. I examine the roots of the incongruity between the importance of and the degree of investment in genomic software, and I suggest several potential remedies for current problems. As genomics continues to grow, new strategies for funding and developing the software that powers the field will become increasingly essential.
- Published
- 2019
- Full Text
- View/download PDF
43. Medical genetics and genomic medicine in Japan.
- Author
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Suzuki H, Watanabe T, Uehara T, and Kosaki K
- Subjects
- Genetics, Medical trends, Genomics economics, Humans, Japan, Genetics, Medical methods, Genomics methods, National Health Programs organization & administration
- Abstract
Since 1961, all Japanese citizens have belonged to one of the available medical care insurance systems. This "universal care" system has contributed to the maintenance of health: the life expectancy at birth was 84 years in 2016, and the infant mortality rate (the number of infants dying before reaching 1 year of age) was 2.0 per 1,000 live births, which is one of the lowest rates in the world. The Japanese government initiated the National Program on Rare and Intractable Diseases in 1972. This program has promoted research and expanded support for patients with rare and intractable diseases. Registered patients are eligible for a subsidy scheme that helps to cover medical care costs. Among the 331 diseases that are currently included in this program, more than half of the diseases are Mendelian disorders. The National Program on Rare and Intractable Diseases has fostered research in medical genetics in Japan and many causative genes for Mendelian diseases have been identified by Japanese geneticists. Recently, the Japanese government has determined to support several genomic medicine initiatives including the undiagnosed disease program (Initiative on Rare and Undiagnosed Diseases) and pathogenic variant databases., (© 2019 Wiley Periodicals, Inc.)
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- 2019
- Full Text
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44. The ethics of sequencing infectious disease pathogens for clinical and public health.
- Author
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Johnson SB and Parker M
- Subjects
- Blood-Borne Pathogens isolation & purification, Civil Defense methods, Communicable Diseases diagnosis, Communicable Diseases economics, Communicable Diseases therapy, Genomics economics, Global Health economics, High-Throughput Nucleotide Sequencing economics, Humans, Information Dissemination ethics, Poverty economics, Public Health economics, Public Health Surveillance, Communicable Disease Control organization & administration, Genomics ethics, Global Health ethics, High-Throughput Nucleotide Sequencing ethics, Public Health ethics
- Published
- 2019
- Full Text
- View/download PDF
45. Stakeholders' views on the value of outcomes from clinical genetic and genomic interventions.
- Author
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Scheuner MT, Russell MM, Chanfreau-Coffinier C, Peredo J, Yano EM, Hamilton AB, Lerner B, Provenzale D, Knight SJ, and Voils CI
- Subjects
- Attitude of Health Personnel, Delphi Technique, Genetic Testing trends, Genomics economics, Genomics ethics, Genomics trends, Humans, Surveys and Questionnaires, Genetic Testing economics, Genetic Testing ethics, Stakeholder Participation psychology
- Abstract
Purpose: Robust evidence about the value of clinical genomic interventions (CGIs), such as genetic/genomic testing or clinical genetic evaluation, is limited. We obtained stakeholders' perspectives on outcomes from CGIs to help inform their value., Methods: We used an adapted Delphi expert panel process. Two anonymous survey rounds assessed the value of 44 CGI outcomes and whether a third party should pay for them, with discussion in between rounds., Results: Sixty-six panelists responded to the first-round survey and 60 to the second. Policy-makers/payers gave the lowest ratings for value and researchers gave the highest. Patients/consumers had the most uncertainty about value and payment by a third party. Uncertainty about value was observed when evidence of proven health benefit was lacking, potential harms outweighed benefits for reproductive outcomes, and outcomes had only personal utility for individuals or family members. Agreement about outcomes for which a third party should not pay included prevention through surgery with unproven health benefits, establishing ancestry, parental consanguinity, and paternity., Conclusion: Research is needed to understand factors contributing to uncertainty and stakeholder differences about the value of CGI outcomes. Reaching consensus will accelerate the creation of metrics to generate the evidence needed to inform value and guide policies that promote availability, uptake, and coverage of CGIs.
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- 2019
- Full Text
- View/download PDF
46. What does Australia's investment in genomics mean for public health?
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Belcher A, Mangelsdorf M, McDonald F, Curtis C, Waddell N, and Hussey K
- Subjects
- Australia, Humans, Biomedical Research economics, Genomics economics, Health Services Research economics, Public Health
- Published
- 2019
- Full Text
- View/download PDF
47. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans.
- Author
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Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, and Bracken-Grissom HD
- Subjects
- Animals, Genomics economics, Genomics methods, Phylogeny, Biological Evolution, Decapoda genetics, Genome, Transcriptome
- Abstract
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
- Published
- 2019
- Full Text
- View/download PDF
48. Cost Effectiveness of the Oncotype DX Genomic Prostate Score for Guiding Treatment Decisions in Patients With Early Stage Prostate Cancer.
- Author
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Chang EM, Punglia RS, Steinberg ML, and Raldow AC
- Subjects
- Aged, Humans, Male, Markov Chains, Neoplasm Staging, Prostatic Neoplasms classification, Prostatic Neoplasms pathology, Clinical Decision-Making, Cost-Benefit Analysis, Gene Expression Regulation, Neoplastic, Genomics economics, Prostatic Neoplasms genetics, Prostatic Neoplasms therapy
- Abstract
Objective: To determine the cost-effectiveness of using the Oncotype DX Genomic Prostate Score (GPS), a 17-gene expression assay that can be used to inform decisions regarding active surveillance (AS) vs immediate treatment., Methods: We developed a Markov model simulating 20-year outcomes for 65-year-old men with very low-, low-, or favorable intermediate-risk prostate cancer undergoing AS vs immediate treatment using GPS vs no testing. Utilities, costs, and probabilities were extracted from the literature and National Medicare Fee Schedules to determine incremental cost-effectiveness ratios (ICER) from a payer perspective., Results: In the overall cohort, the ICER of GPS-guided therapy was $31,394 per quality-adjusted life-year (QALY). When stratified by risk group, the ICER was $25,343 per QALY in very low-risk, $28,911 per QALY in low-risk, and $39,695 per QALY in favorable intermediate-risk patients. On sensitivity analysis, findings were robust against a willingness-to-pay of $100,000 per QALY to variations in key model parameters, including the cost of annual management of AS, probability of exiting AS to treatment, cost of treatment, and probability of biochemical failure post-treatment. However, the cost-effectiveness was sensitive to small differences in the utility of AS and the utility of no evidence of disease post-treatment states., Conclusion: The use of the GPS was cost-effective in guiding treatment decisions regarding AS vs immediate treatment. The cost-effectiveness was sensitive to small differences in the utilities of the AS and no evidence of disease post-treatment states, highlighting the importance of assessing patient preferences., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
49. Precision medicine/personalized medicine: a critical analysis of movements in the transformation of biomedicine in the early 21st century.
- Author
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Iriart JAB
- Subjects
- Biomedical Technology economics, Genomics economics, Genomics methods, Health Equity, Humans, Neoplasms economics, Neoplasms therapy, Pharmaceutical Preparations economics, Precision Medicine economics, Biomedical Technology trends, Precision Medicine trends
- Abstract
The enormous development of genomics research in recent decades has raised great expectations concerning its impact on biomedicine. There has been growing investment in research in personalized or precision medicine, which aims to customize medical practice with a focus on the individual, based on the use of genetic tests, identification of biomarkers, and development of targeted drugs. However, the personalized or precision medicine movement is controversial and has sparked an important debate between its defenders and critics. This essay aims to discuss the assumptions, promises, limits, and possibilities of personalized or precision medicine based on a review of the recent literature situating the debate on the theme. The review indicates that many of the promises of personalized or precision medicine remain unfulfilled. While there has been huge progress in knowledge on the molecular mechanisms of diseases and the development of drugs that have significantly impacted the treatment of some types of cancer, thus far there is no evidence that this same pattern will be reproduced in other complex diseases. Personalized or precision medicine is expected to generate incremental developments in specific areas of medicine, but there are obstacles to its generalization. The high cost of new biotechnologies can exacerbate health inequalities and become a problem for health services' sustainability, especially in low and middle-income countries. The emphasis on personalized or precision medicine may shift funds away from less costly interventions that have greater public health impact.
- Published
- 2019
- Full Text
- View/download PDF
50. A low cost and input tailing method of quality control on multiple annealing, and looping-based amplification cycles-based whole-genome amplification products.
- Author
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Chen C, Li J, Wan J, Lu Y, Zhang Z, and Xu Z
- Subjects
- Genome, Human genetics, Humans, Quality Control, Genomics economics, Genomics methods, Genomics standards, Nucleic Acid Amplification Techniques economics, Nucleic Acid Amplification Techniques methods, Nucleic Acid Amplification Techniques standards
- Abstract
Background: Single-cell whole-genome sequencing provides novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, amplification of formalin-fixed tissues with low cell numbers is still problematic and multiple annealing, and looping-based amplification cycles (MALBAC) is a commonly used whole-genome amplification (WGA) method with low cell numbers., Methods: We developed a low-input tailing method to evaluate the MALBAC-based WGA from sub-nanogram or less quantities of input DNA. The tailing method uses 2100 BioAnalyzer to evaluate the size distribution of MALBAC products, and comparing the tailing with 10380 bp., Results: Compared with a 22 loci qPCR panel, the tailing method provided a similar WGA evaluation efficiency in 13 samples on one set of study, with lower input, cheaper cost, shorter manual time, and a clear filtering cut off. Later, we demonstrated a strong correlation between tailing size and coverage breadth in another 29 samples on two sets of assays. As a result, the tailing method showed that it could predict whether a sequence breadth achieved 70% or not with 100% accuracy on these three sets of assays. Although further studies are needed, this tailing method is expected to be used as an excellent tool to select high-quality WGA products before library construction., Conclusions: Our tailing method can provide a new WGA quality test to evaluate the WGA efficiency with 100% accuracy (42/42). Compared with qPCR panel, our tailing method needs lower input, cheaper cost, shorter manual time, a clear filtering cut off, and extendable high throughput as well as the same sensitivity., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2019
- Full Text
- View/download PDF
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