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J. Pers. Med., Volume 9, Issue 2 (June 2019)

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Cover Story (view full-size image) Personalized medicine is based on an individual’s genome to select therapeutics for disease or its [...] Read more.
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Open AccessFeature PaperViewpoint
A Scientific Overview of Smartphone Applications and Electronic Devices for Weight Management in Adults
J. Pers. Med. 2019, 9(2), 31; https://doi.org/10.3390/jpm9020031
Received: 31 March 2019 / Revised: 14 May 2019 / Accepted: 4 June 2019 / Published: 7 June 2019
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Abstract
Worldwide, there are rising trends in overweight and obesity. Therefore, novel digital tools are discussed to improve health-related behaviors. The use of smartphone applications (apps) and wearables (e.g., activity trackers) for self-monitoring of diet and physical activity might have an impact on body [...] Read more.
Worldwide, there are rising trends in overweight and obesity. Therefore, novel digital tools are discussed to improve health-related behaviors. The use of smartphone applications (apps) and wearables (e.g., activity trackers) for self-monitoring of diet and physical activity might have an impact on body weight. By now, the scientific evaluation of apps and wearables for weight management is limited. Although some intervention studies have already investigated the efficacy of aforementioned digital tools on weight management, there are no clear recommendations for its clinical and therapeutic use. Besides the lack in long-term randomized controlled trials, there are also concerns regarding the scientific quality of apps and wearables (e.g., no standards for development and evaluation). Therefore, the objective of present work is: (1) To address challenges and concerns regarding the current digital health market and (2) to provide a selective overview about intervention studies using apps and activity trackers for weight-related outcomes. Based on cited literature, the efficacy of apps and wearables on weight management is assessed. Finally, it is intended to derive potential recommendations for practical guidance. Full article
(This article belongs to the Special Issue Wearable (or Electronic) Devices to Enhance Personalized Medicine)
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Open AccessArticle
Evaluation of the Association of Omentin 1 rs2274907 A>T and rs2274908 G>A Gene Polymorphisms with Coronary Artery Disease in Indian Population: A Case Control Study
J. Pers. Med. 2019, 9(2), 30; https://doi.org/10.3390/jpm9020030
Received: 15 May 2019 / Revised: 31 May 2019 / Accepted: 4 June 2019 / Published: 6 June 2019
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Abstract
Coronary artery disease (CAD) is a major cause of death all over the world. CAD is caused by atherosclerosis which is induced by the interaction of genetic factors and environmental factors. Traditional environmental risk factors include hyperlipidemia, diabetes mellitus, lack of exercise, obesity, [...] Read more.
Coronary artery disease (CAD) is a major cause of death all over the world. CAD is caused by atherosclerosis which is induced by the interaction of genetic factors and environmental factors. Traditional environmental risk factors include hyperlipidemia, diabetes mellitus, lack of exercise, obesity, poor diet and others. Genome-wide association studies have revealed the association of certain gene polymorphisms with susceptibility to CAD. Omentin 1 is an adipokine secreted by the visceral adipose tissues and has been reported to have anti-inflammatory, cardioprotective, and enhances insulin sensitivity. In this study, we examined the role of omentin-1 common single nucleotide polymorphisms (SNPs) (rs2274907 A>T and rs2274908 G>A) in CAD. We genotyped 100 CAD patients and 100 matched healthy controls from the south Indian population using an amplification refractory mutation system (ARMS-PCR) and allele-specific PCR (AS-PCR). Our result indicated the rs2274908 G>A is not associated with CAD. Results showed that there was a significant difference in rs2274907 A>T genotype distribution between controls and CAD cases (P-value < 0.05). Results indicated that the AT genotype of the rs2274907 is associated with CAD with OR = 3.0 (95% confidence interval (CI), 1.64 to 5.49), 1.65 (1.27 to 2.163), P = 0.002. The T allele of the rs2274907 was also associated with CAD with OR = 1.82 (95% CI, 1.193 to 2.80), 1.37 (1.08 to 1.74), P = 0.005. Rs2274907 genotype distribution was also correlated with serum total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), hypertension and diabetes. We conclude that the AT genotype and the T allele of the rs2274907 A>T is associated with Cad in the south Indian population. Further studies on the effect of the rs2274907 A>T on omentin-1 function are recommended, and future well-designed studies with larger sample sizes and in different populations are required to validate our findings. Full article
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Open AccessArticle
Primary Care Physicians’ Knowledge, Attitudes, and Experience with Personal Genetic Testing
J. Pers. Med. 2019, 9(2), 29; https://doi.org/10.3390/jpm9020029
Received: 19 April 2019 / Revised: 21 May 2019 / Accepted: 22 May 2019 / Published: 24 May 2019
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Abstract
Primary care providers (PCPs) will play an important role in precision medicine. However, their lack of training and knowledge about genetics and genomics may limit their ability to advise patients or interpret or utilize test results. We evaluated PCPs’ awareness of the role [...] Read more.
Primary care providers (PCPs) will play an important role in precision medicine. However, their lack of training and knowledge about genetics and genomics may limit their ability to advise patients or interpret or utilize test results. We evaluated PCPs’ awareness of the role of genetics/genomics in health, knowledge about key concepts in genomic medicine, perception/attitudes towards direct-to-consumer (DTC) genetic testing, and their level of confidence/comfort in discussing testing with patients prior to and after undergoing DTC testing through the 23andMe Health + Ancestry Service. A total of 130 PCPs completed the study. Sixty-three percent were board-certified in family practice, 32% graduated between 1991 and 2000, and 88% had heard of 23andMe prior to the study. Seventy-two percent decided to participate in the study to gain a better understanding about testing. At baseline, 23% of respondents indicated comfort discussing genetics as a risk factor for common diseases, increasing to 59% after undergoing personal genetic testing (PGT) (p < 0.01). In summary, we find that undergoing PGT augments physicians’ confidence, comfort, and interest in DTC testing. Full article
(This article belongs to the Special Issue Genomic Medicine and Policy)
Open AccessCommunication
Assessing the Joint Value of Genomic-Based Diagnostic Tests and Gene Therapies
J. Pers. Med. 2019, 9(2), 28; https://doi.org/10.3390/jpm9020028
Received: 1 April 2019 / Revised: 10 May 2019 / Accepted: 16 May 2019 / Published: 21 May 2019
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Abstract
Gene therapy is an emerging type of treatment that may aim to provide a cure to individuals with a genetic mutation known to be causative of a specific disease. A diagnosis of the causative mutation must precede treatment with a in vivo gene [...] Read more.
Gene therapy is an emerging type of treatment that may aim to provide a cure to individuals with a genetic mutation known to be causative of a specific disease. A diagnosis of the causative mutation must precede treatment with a in vivo gene therapy. Both achieving a genomic-based diagnosis and treatment with a gene therapy may result in substantial expenditures for health care systems. Uncertainties around the health care costs, risks, and benefits derived from diagnosis and treatment with a subsequent gene therapy suggests a need for developing an evidence base, underpinned by opportunity cost, to inform if, and how, these health technologies should be introduced into health care systems funded by finite budgets. This article discusses why current methods to evaluate health technologies (decision-analytic model-based cost-effectiveness analysis from the perspective of a health care system over a lifetime time horizon) are appropriate to quantify the costs and consequences of using genomic-based diagnostic tests and gene therapies in combination, rather than as separate interventions, within clinical practice. Evaluating the economic impact of test-and-treatment strategies will ensure that the opportunity cost of these health technologies is quantified fully for decision-makers who are responsible for allocating limited resources in health care systems. Full article
(This article belongs to the Special Issue Genomic Medicine and Policy)
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Open AccessArticle
A Theoretical Framework and Conceptual Design for Engaging Children in Therapy at Home—The Design of a Wearable Breathing Trainer
J. Pers. Med. 2019, 9(2), 27; https://doi.org/10.3390/jpm9020027
Received: 31 March 2019 / Revised: 9 May 2019 / Accepted: 16 May 2019 / Published: 20 May 2019
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Abstract
Wearable technologies are being implemented in the health and medical context with increasing frequency. Such technologies offer valuable opportunities to stimulate self-management in these domains. In this context, engagement plays a crucial role. An engaged patient is a patient who is emotionally involved [...] Read more.
Wearable technologies are being implemented in the health and medical context with increasing frequency. Such technologies offer valuable opportunities to stimulate self-management in these domains. In this context, engagement plays a crucial role. An engaged patient is a patient who is emotionally involved and committed to the therapy or care process. Particularly for children who have to follow some sort of therapy, engagement is important to ensure a successful outcome of the therapy. To design for engagement, a framework based on theories of motivation in child therapy was developed. This framework was applied to the design of a wearable breathing trainer for children with asthma and dysfunctional breathing. As such, the present paper provides knowledge about the implementation of theory on engagement and motivation in design. Expert and first user evaluations found that the resulting prototype is appealing, perceived as useful, and may engage children in breathing training and stimulate self-management. Full article
(This article belongs to the Special Issue Wearable (or Electronic) Devices to Enhance Personalized Medicine)
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Open AccessArticle
Exploring Predictors of Genetic Counseling and Testing for Hereditary Breast and Ovarian Cancer: Findings from the 2015 U.S. National Health Interview Survey
J. Pers. Med. 2019, 9(2), 26; https://doi.org/10.3390/jpm9020026
Received: 4 April 2019 / Revised: 26 April 2019 / Accepted: 29 April 2019 / Published: 10 May 2019
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Abstract
Despite efforts to increase the availability of clinical genetic testing and counseling for Hereditary Breast and Ovarian (HBOC)-related cancers, these services remain underutilized in clinical settings. There have been few efforts to understand the public’s use of cancer genetic services, particularly for HBOC-related [...] Read more.
Despite efforts to increase the availability of clinical genetic testing and counseling for Hereditary Breast and Ovarian (HBOC)-related cancers, these services remain underutilized in clinical settings. There have been few efforts to understand the public’s use of cancer genetic services, particularly for HBOC-related cancers. This analysis is based on data from the 2015 National Health Interview Survey (NHIS), a U.S.-based nationwide probability sample, to better understand the public’s use of HBOC-related clinical cancer genetic services. Bivariate analyses were used to compute percentages and examine the associations of familial cancer risk for three genetic services outcomes (ever had genetic counseling for cancer risk, ever discussed genetic testing for cancer risk with a provider, and ever had genetic testing for cancer risk). Multivariable logistic regression models were used to estimate the association of familial cancer risk and other demographic and health variables with genetic services. Most women (87.67%) in this study were at low risk based on self-reported family history of breast and ovarian cancer, 10.65% were at medium risk, and 1.68% were at high risk. Overall, very small numbers of individuals had ever had genetic counseling (2.78%), discussed genetic testing with their physician (4.55%) or had genetic testing (1.64%). Across all genetic services outcomes, individuals who were at higher familial risk were more likely to have had genetic counseling than those at lower risk (high risk: aOR = 5.869, 95% CI = 2.911–11.835; medium risk: aOR = 4.121, 95% CI = 2.934–5.789), discussed genetic testing (high risk: aOR = 5.133, 95% CI = 2.699–9.764; medium risk: aOR = 3.649, 95% CI = 2.696–4.938), and completed genetic testing (high risk: aOR = 8.531, 95% CI = 3.666–19.851; medium risk aOR = 3.057, 95% CI = 1.835–5.094). Those who perceived themselves as being more likely to develop cancer than the average woman were more likely to engage in genetic counseling (aOR = 1.916, 95% CI = 1.334–2.752), discuss genetic testing (aOR = 3.314, 95% CI = 2.463–4.459) or have had genetic testing (aOR = 1.947, 95% CI = 1.13–3.54). Personal cancer history was also a significant predictor of likelihood to have engaged in genetic services. Our findings highlight: (1) potential under-utilization of cancer genetic services among high risk populations in the U.S. and (2) differences in genetic services use based on individual’s characteristics such as self-reported familial risk, personal history, and beliefs about risk of cancer. These results align with other studies which have noted that awareness and use of genetic services are low in the general population and likely not reaching individuals who could benefit most from screening for inherited cancers. Efforts to promote public awareness of familial cancer risk may lead to better uptake of cancer genetic services. Full article
(This article belongs to the Special Issue Genomic Medicine and Policy)
Open AccessCommentary
Direct-to-Consumer Genetic Testing Data Privacy: Key Concerns and Recommendations Based on Consumer Perspectives
J. Pers. Med. 2019, 9(2), 25; https://doi.org/10.3390/jpm9020025
Received: 27 March 2019 / Revised: 29 April 2019 / Accepted: 6 May 2019 / Published: 9 May 2019
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Abstract
Direct-to-consumer genetic testing (DTC-GT) companies are engaging health consumers in unprecedented ways and leveraging the genetic information they collect to further engage health companies. This has produced controversy about DTC-GT consumer expectations, standards, and perceptions of privacy. In this commentary, we highlight recent [...] Read more.
Direct-to-consumer genetic testing (DTC-GT) companies are engaging health consumers in unprecedented ways and leveraging the genetic information they collect to further engage health companies. This has produced controversy about DTC-GT consumer expectations, standards, and perceptions of privacy. In this commentary, we highlight recent events involving DTC-GT companies and controversy about privacy that followed those events and discuss recent studies that have explored DTC-GT consumer concerns about privacy. We discuss DTC-GT company standards of upholding consumer privacy and the general accessibility of DTC-GT company terms of use agreements and privacy policies that are written at reading levels above that of many consumers. We conclude that broader discussions and more research are needed to identify DTC-GT consumer concerns about and expectations of privacy. We anticipate that our recommendations will advance discussions on consumer privacy expectations and protections in an era of increasing engagement in DTC-GT. Full article
(This article belongs to the Special Issue Genomic Medicine and Policy)
Open AccessArticle
Clinical and Prognostic Significance of Cell Sensitivity to Chemotherapy Detected In Vitro on Treatment Response and Survival of Leukemia Patients
J. Pers. Med. 2019, 9(2), 24; https://doi.org/10.3390/jpm9020024
Received: 6 March 2019 / Revised: 23 April 2019 / Accepted: 6 May 2019 / Published: 7 May 2019
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Abstract
Multidrug resistance (MDR) is a major challenge in leukemia treatment. The objective of this study was to identity predictors of MDR to allow for rapid and economical assessment of the efficacy of planned antitumor therapy for leukemia patients. The study included 113 patients [...] Read more.
Multidrug resistance (MDR) is a major challenge in leukemia treatment. The objective of this study was to identity predictors of MDR to allow for rapid and economical assessment of the efficacy of planned antitumor therapy for leukemia patients. The study included 113 patients with acute and chronic leukemias. Prior to antitumor therapy, we measured the sensitivity of tumor cells of patients to the panel of chemotherapeutic drugs, together with MDR1 mRNA and P-glycoprotein (P-gp) expression as one of the mechanisms of MDR, and compared these data with the response to therapy. The scales for leukemia patients according to therapy response, drug sensitivity of tumor cells, MDR1 mRNA and P-gp levels, and the presence of unfavorable immunological and cytogenetic markers were introduced for subsequent correlation analysis. We show that the drug resistance of tumor cells of leukemia patients estimated in vitro at diagnosis correlates with a poor response to chemotherapy and is usually combined with aberrant and immature immunological markers, cytogenetic abnormalities, and a high expression of MDR1 mRNA and P-gp. All together, these factors indicate unfavorable prognosis and low survival of leukemia patients. Thus, the sensitivity of tumor cells to chemotherapeutic drugs measured in vitro at diagnosis may have prognostic value for individual types of leukemia. Full article
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Open AccessArticle
Feasibility of a Comprehensive Home Monitoring Program for Sarcoidosis
J. Pers. Med. 2019, 9(2), 23; https://doi.org/10.3390/jpm9020023
Received: 27 March 2019 / Revised: 28 April 2019 / Accepted: 4 May 2019 / Published: 5 May 2019
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Abstract
Sarcoidosis is a chronic, heterogeneous disease which most commonly affects the lungs. Currently, evidence-based and individually tailored treatment options in sarcoidosis are lacking. We aimed to evaluate patient experiences with a home monitoring program for sarcoidosis and assess whether home monitoring is a [...] Read more.
Sarcoidosis is a chronic, heterogeneous disease which most commonly affects the lungs. Currently, evidence-based and individually tailored treatment options in sarcoidosis are lacking. We aimed to evaluate patient experiences with a home monitoring program for sarcoidosis and assess whether home monitoring is a feasible tool to enhance personalized treatment. Outpatients with pulmonary sarcoidosis tested the home monitoring program “Sarconline” for one month. This is a secured personal platform which consists of online patient-reported outcomes, real-time wireless home spirometry, an activity tracker, an information library, and an eContact option. Patients wore an activity tracker, performed daily home spirometry, and completed patient-reported outcomes at baseline and after one month. Patient experiences were evaluated during a phone interview. Ten patients were included in the study. Experiences with the home monitoring program were positive; 90% of patients considered the application easy to use, none of the patients found daily measurements burdensome, and all patients wished to continue the home monitoring program after the study. Mean adherence to daily spirometry and activity tracking was, respectively, 94.6% and 91.3%. In conclusion, a comprehensive home monitoring program for sarcoidosis is feasible and can be used in future research and clinical practice. Full article
(This article belongs to the Special Issue Wearable (or Electronic) Devices to Enhance Personalized Medicine)
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Open AccessArticle
Pharmacogenetic Tests in Reducing Accesses to Emergency Services and Days of Hospitalization in Bipolar Disorder: A 2-Year Mirror Analysis
J. Pers. Med. 2019, 9(2), 22; https://doi.org/10.3390/jpm9020022
Received: 11 March 2019 / Revised: 25 April 2019 / Accepted: 26 April 2019 / Published: 30 April 2019
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Abstract
Despite the enormous costs associated to mood disorders’, few studies evaluate potential cost saving from the use of pharmacogenetic tests (PGT). This study compares 12 months before the execution of the PGT versus 12 months after, in terms of number and days of [...] Read more.
Despite the enormous costs associated to mood disorders’, few studies evaluate potential cost saving from the use of pharmacogenetic tests (PGT). This study compares 12 months before the execution of the PGT versus 12 months after, in terms of number and days of hospitalization and accesses to emergency services, in a sample of 30 patients affected by bipolar disorder. Secondarily, the study gives an economic value to the data based on the diagnosis-related group (DRG). Patients included in the study were required to be aged ≥18 years, sign an informed consent, have a score of Clinical Global Impression item Severity (CGIs) ≥3, and have a discordant therapy compared to the PGT in the 12 months preceding it and a therapy consistent with it for the following 12 months. Cost saving has been evaluated by paired t-tests in a mirror analysis. Statistically significant differences in all the comparisons (p < 0.0001) emerged. Important cost saving emerged after the use of PGT (€148,920 the first year versus €39,048 the following year). Despite the small sample size and lack of a control group in this study, the potential role of PGT in cost saving for the treatment of bipolar disorder treatment emerged. To confirm this result, larger and clinical trials are needed. Full article
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Open AccessArticle
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
J. Pers. Med. 2019, 9(2), 21; https://doi.org/10.3390/jpm9020021
Received: 30 March 2019 / Revised: 20 April 2019 / Accepted: 25 April 2019 / Published: 29 April 2019
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Abstract
As one of the most widespread metabolic diseases, atherosclerosis affects nearly everyone as they age; arteries gradually narrow from plaque accumulation over time reducing oxygenated blood flow to central and periphery causing heart disease, stroke, kidney problems, and even pulmonary disease. Personalized medicine [...] Read more.
As one of the most widespread metabolic diseases, atherosclerosis affects nearly everyone as they age; arteries gradually narrow from plaque accumulation over time reducing oxygenated blood flow to central and periphery causing heart disease, stroke, kidney problems, and even pulmonary disease. Personalized medicine promises to bring treatments based on individual genome sequencing that precisely target the molecular pathways underlying atherosclerosis and its symptoms, but to date only a few genotypes have been identified. A promising alternative to this genetic approach is the identification of pathways altered in atherosclerosis by transcriptome analysis of atherosclerotic tissues to target specific aspects of disease. Transcriptomics is a potentially useful tool for both diagnostics and discovery science, exposing novel cellular and molecular mechanisms in clinical and translational models, and depending on experimental design to identify and test novel therapeutics. The cost and time required for transcriptome analysis has been greatly reduced by the development of next generation sequencing. The goal of this resource article is to provide background and a guide to appropriate technologies and downstream analyses in transcriptomics experiments generating ever-increasing amounts of gene expression data. Full article
(This article belongs to the Special Issue Personalized and Targeted Atherosclerosis Treatments)
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Open AccessCommentary
Inflammation, Biomarkers and Immuno-Oncology Pathways in Pancreatic Cancer
J. Pers. Med. 2019, 9(2), 20; https://doi.org/10.3390/jpm9020020
Received: 11 March 2019 / Revised: 16 April 2019 / Accepted: 23 April 2019 / Published: 26 April 2019
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Abstract
It is estimated that pancreatic cancer will be the second leading cause of cancer-related deaths globally by 2030, highlighting the ongoing lack of effective treatment options for this devastating condition. There is a lack of reliable prognostic or predictive markers in pancreatic cancer [...] Read more.
It is estimated that pancreatic cancer will be the second leading cause of cancer-related deaths globally by 2030, highlighting the ongoing lack of effective treatment options for this devastating condition. There is a lack of reliable prognostic or predictive markers in pancreatic cancer to guide management decisions, whether for systemic chemotherapy, molecularly targeted therapies, or immunotherapies. To date, the results for targeted agents and immunotherapies in unselected populations of chemo-refractory pancreatic cancer have not met expectations. The reasons for this lack of efficacy of immunotherapy in pancreatic cancer are not completely understood. The challenges in pancreatic cancer include the physical barrier created by the dense desmoplastic stroma surrounding the tumor, chemokine-mediated exclusion of T cells, relatively poorer antigenicity compared to other solid tumors, paucity of infiltrating T cells within the tumor, ultimately leading to an immunosuppressive microenvironment. A better understanding of the role of inflammation in pancreatic cancer, its tumor microenvironment and individualized patient-related features, be they molecular, clinical or histopathological, would enable a more effective tailored approach to the management of pancreatic cancer. In this review, the role of inflammation, the immune tumor microenvironment and potential immune biomarkers in pancreatic cancer are explored. Full article
(This article belongs to the Special Issue Biomarkers and Personalized Therapies in Pancreatic Cancer)
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Open AccessArticle
A Tool for Shared Decision Making on Referral for Prostate Biopsy in the Primary Care Setting: Integrating Risks of Cancer with Life Expectancy
J. Pers. Med. 2019, 9(2), 19; https://doi.org/10.3390/jpm9020019
Received: 30 January 2019 / Revised: 27 March 2019 / Accepted: 18 April 2019 / Published: 22 April 2019
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Abstract
Prostate cancer (PCa) testing involves a complex individually based decision making process. It should consider competing risks from other comorbidities when estimating a survival benefit from the early detection of clinically significant (cs)PCa. We aimed to develop a prediction tool that provides concrete [...] Read more.
Prostate cancer (PCa) testing involves a complex individually based decision making process. It should consider competing risks from other comorbidities when estimating a survival benefit from the early detection of clinically significant (cs)PCa. We aimed to develop a prediction tool that provides concrete advice for the general practitioner (GP) on whether to refer a man for further assessment. We hereto combined the probability of detecting csPCa and the potential overall survival benefit from early detection and treatment. The PCa detection probabilities were derived from 3616 men enrolled in the Dutch arm of the European Randomized Study of Screening for Prostate Cancer (ERSPC). Survival estimates were derived from 19,834 men from the Surveillance, Epidemiology, and End Results (SEER) registry, ERSPC, and Dutch life tables. Treatment benefit was estimated from the Prostate Cancer Intervention versus Observation Trial (PIVOT, n = 731). The prediction of csPCa detection was based on prostate-specific antigen (PSA), age, %freePSA, and digital rectal examination (DRE). The life expectancy (LE) for patients with PCa receiving no treatment was adjusted for age and Charlson comorbidity index. A negative impact on LE and treatment benefit was found with higher age and more comorbidity. The proposed integrated approach may support triage at GP practices, as PCa is a heterogeneous disease in predominantly elderly men. Full article
(This article belongs to the Special Issue Risk-stratified Cancer Screening)
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Open AccessArticle
Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
J. Pers. Med. 2019, 9(2), 18; https://doi.org/10.3390/jpm9020018
Received: 27 February 2019 / Revised: 25 March 2019 / Accepted: 28 March 2019 / Published: 3 April 2019
Cited by 1 | Viewed by 1943 | PDF Full-text (4869 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The rapid expansion of transcriptomics and affordability of next-generation sequencing (NGS) technologies generate rocketing amounts of gene expression data across biology and medicine, including cancer research. Concomitantly, many bioinformatics tools were developed to streamline gene expression and quantification. We tested the concordance of [...] Read more.
The rapid expansion of transcriptomics and affordability of next-generation sequencing (NGS) technologies generate rocketing amounts of gene expression data across biology and medicine, including cancer research. Concomitantly, many bioinformatics tools were developed to streamline gene expression and quantification. We tested the concordance of NGS RNA sequencing (RNA-seq) analysis outcomes between two predominant programs for read alignment, HISAT2, and STAR, and two most popular programs for quantifying gene expression in NGS experiments, edgeR and DESeq2, using RNA-seq data from breast cancer progression series, which include histologically confirmed normal, early neoplasia, ductal carcinoma in situ and infiltrating ductal carcinoma samples microdissected from formalin fixed, paraffin embedded (FFPE) breast tissue blocks. We identified significant differences in aligners’ performance: HISAT2 was prone to misalign reads to retrogene genomic loci, STAR generated more precise alignments, especially for early neoplasia samples. edgeR and DESeq2 produced similar lists of differentially expressed genes, with edgeR producing more conservative, though shorter, lists of genes. Gene Ontology (GO) enrichment analysis revealed no skewness in significant GO terms identified among differentially expressed genes by edgeR versus DESeq2. As transcriptomics of FFPE samples becomes a vanguard of precision medicine, choice of bioinformatics tools becomes critical for clinical research. Our results indicate that STAR and edgeR are well-suited tools for differential gene expression analysis from FFPE samples. Full article
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J. Pers. Med. EISSN 2075-4426 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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