Journal of Personalized Medicine — Open Access Journal

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

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

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

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

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

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

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

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

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

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

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

Type 2 diabetes mellitus (T2DM) constitutes a major portion of Jordan’s disease burden, and incidence rates are rising at a rapid rate. Due to variability in the drug’s response between ethnic groups, it is imperative that the pharmacogenetics of metformin be investigated in the Jordanian population. The objective of this study was to investigate the relationship between twenty-one single nucleotide polymorphisms (SNPs) in the SLC22A1, SLC22A2, and SLC22A3 genes and their effects on metformin pharmacogenetics in Jordanian patients diagnosed with type 2 diabetes mellitus. Blood samples were collected from 212 Jordanian diabetics who fulfilled the inclusion criteria, which were then used in SNP genotyping and determination of HbA1c levels. The rs12194182 SNP in the SLC22A3 gene was found to have a significant association (p < 0.05) with lower mean HbA1c levels, and this association more pronounced in patients with the CC genotype (i.e., p-value was significant before correcting for multiple testing). Moreover, the multinomial logistic regression analysis showed that SNP genotypes within the SLC22A1, SLC22A2, and SLC22A3 genes, body mass index (BMI) and age of diagnosis were significantly associated with glycemic control (p < 0.05). The results of this study can be used to predict response to metformin and other classes of T2DM drugs, making treatment more individualized and resulting in better clinical outcomes. Full article

Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked muscle disorders caused by mutations of the DMD gene, which encodes the subsarcolemmal protein dystrophin. In DMD, dystrophin is not expressed due to a disruption in the reading frame of the DMD gene, resulting in a severe phenotype. Becker muscular dystrophy exhibits a milder phenotype, having mutations that maintain the reading frame and allow for the production of truncated dystrophin. To date, various therapeutic approaches for DMD have been extensively developed. However, the pathomechanism is quite complex despite it being a single gene disorder, and dystrophin is expressed not only in a large amount of skeletal muscle but also in cardiac, vascular, intestinal smooth muscle, and nervous system tissue. Thus, the most appropriate therapy would be complementation or restoration of dystrophin expression, such as gene therapy using viral vectors, readthrough therapy, or exon skipping therapy. Among them, exon skipping therapy with antisense oligonucleotides can restore the reading frame and yield the conversion of a severe phenotype to one that is mild. In this paper, I present the significance of molecular diagnosis and the development of mutation-based therapeutic strategies to complement or restore dystrophin expression. Full article

Breast cancer screening modalities and guidelines continue to evolve and are increasingly based on risk factors, including genetic risk and a personal or family history of cancer. Here, we review genetic testing of high-penetrance hereditary breast and ovarian cancer genes, including BRCA1 and BRCA2, for the purpose of identifying high-risk individuals who would benefit from earlier screening and more sensitive methods such as magnetic resonance imaging. We also consider risk-based screening in the general population, including whether every woman should be genetically tested for high-risk genes and the potential use of polygenic risk scores. In addition to enabling early detection, the results of genetic screens of breast cancer susceptibility genes can be utilized to guide decision-making about when to elect prophylactic surgeries that reduce cancer risk and the choice of therapeutic options. Variants of uncertain significance, especially missense variants, are being identified during panel testing for hereditary breast and ovarian cancer. A finding of a variant of uncertain significance does not provide a basis for increased cancer surveillance or prophylactic procedures. Given that variant classification is often challenging, we also consider the role of multifactorial statistical analyses by large consortia and functional tests for this purpose. Full article

Information of an individual’s epigenome can be useful in cancer screening to enable personalised decision making on participation, treatment options and further screening strategies. However, adding this information might result in complex risk predictions on multiple diseases, unsolicited findings and information on (past) environmental exposure and behaviour. This complicates informed consent procedures and may impede autonomous decision-making. In this article we investigate and identify the specific features of epigenetic risk-stratified cancer screening that challenge the current informed consent doctrine. Subsequently we describe current and new informed consent models and the principle of respect for autonomy and argue for a specific informed consent model for epigenetic risk-stratified screening programmes. Next, we propose a framework that guides the development of Patient Decision Aids (PDAs) to support informed consent and promote autonomous choices in the specific context of epigenetic cancer screening programmes. Full article

Evidence for a relationship between omega-6/omega-3 (n-6/n-3) polyunsaturated fatty acid (PUFA) ratio and obesity in humans is inconsistent, perhaps due to differences in dietary intake or metabolism of PUFAs between different subsets of the population. Since chronic inflammation is central to obesity and inflammatory pathways are regulated by PUFAs, the objective of this study was to examine whether variants in the NFKB1 gene, an upstream regulator of the inflammatory response, modify the association between the n-6/n-3 ratio (from diet and plasma) and anthropometric traits in a multiethnic/multiracial population of young adults. Participants’ (n = 898) dietary PUFA intake was assessed using a food frequency questionnaire and plasma PUFA concentrations by gas chromatography. Nine tag single nucleotide polymorphisms (SNP) in NFKB1 were genotyped. Significant interactions were found between racial/ethnic groups and plasma n-6/n-3 ratio for body mass index (BMI) (p = 0.02) and waist circumference (WC) (p = 0.007). Significant interactions were also observed between racial/ethnic groups and three NFKB1 genotypes (rs11722146, rs1609798, and rs230511) for BMI and WC (all p ≤ 0.04). Significant interactions were found between two NFKB1 genotypes and plasma n-6/n-3 ratio for BMI and WC (rs4648090 p = 0.02 and 0.03; rs4648022 p = 0.06 and 0.04, respectively). Our findings suggest that anthropometric traits may be influenced by a unique combination of n-6/n-3 ratio, racial/ethnic background, and NFKB1 genotypes. Full article

Colorectal cancer (CRC) is the third most common malignancy worldwide. Surgery remains the most important treatment for non-metastatic CRC, and the administration of adjuvant chemotherapy depends mainly on the disease stage, which is still the strongest prognostic factor. A refined understanding of the genomics of CRC has recently been achieved thanks to the widespread use of next generation sequencing with potential future therapeutic implications. Microsatellite instability (MSI) has been suggested as a predictive marker for response to anti-programmed-cell-death protein 1 (PD-1) therapy in solid tumors, including CRC. It should be noted that not all cancers with MSI phenotype respond to anti-PD-1 immunotherapy, highlighting the urgent need for even better predictive biomarkers. Mitogen-Activated Protein Kinase (MAPK) pathway genes KRAS, NRAS, and BRAF represent important molecular targets and could serve as independent prognostic biomarkers in CRC, and identify those who potentially benefit from anti-epidermal growth factor receptor (EGFR) treatment. Emerging evidence has attributed a significant role to inflammatory markers including blood cell ratios in the prognosis and survival of CRC patients; these biomarkers can be easily assessed in routine blood exams and be used to identify high-risk patients or those more likely to benefit from chemotherapy, targeted therapies and potentially immunotherapy. Analysis of cell-free DNA (cfDNA), circulating tumor cells (CTC) and/or micro RNAs (miRNAs) could provide useful information for the early diagnosis of CRC, the identification of minimal residual disease and, the evaluation of the risk of recurrence in early CRC patients. Even the selection of patients suitable for the new targeted therapy is becoming possible with the use of predictive miRNA biomarkers. Finally, the development of treatment resistance with the emergence of chemo-resistance clones after treatment remains the most important challenge in the clinical practice. In this context it is crucial to identify potential biomarkers and therapeutic targets which could lead to development of new and more effective treatments. Full article

In contrast to the large number of genetic studies on obesity, there has been significantly less nutrigenetics investigation of the interaction between diet and single nucleotide polymorphisms (SNPs) in obesity, especially within Eastern Mediterranean populations. The aim of this study was to evaluate the potential interactions between three candidate SNPs, namely, rs1558902 and rs9939609 in the fat mass and obesity (FTO) gene and the rs7903146 variant of the Transcription factor 7 like 2 (TCF7L2) gene, and macronutrient intake with regard to obesity, body fat, and muscle composition. Three hundred and eight healthy Lebanese adults were included in this study. Data collection included a questionnaire for demographics and lifestyle in addition to a detailed dietary assessment using a culture-specific 80-item semi-quantitative food frequency questionnaire. This was coupled with anthropometric measurements and peripheral blood withdrawal for DNA and genotyping using Taqman allele discrimination assays. The two FTO candidate SNPs were not associated with risk of obesity in this population sample, yet there was a trend, though not a significant one, towards lower muscle mass among carriers of the risk allele of either FTO SNPs. To our knowledge, these results have not been previously reported. As for the TCF7L2rs7903146 variant, results were congruent with the literature, given that individuals who were homozygous for the risk allele had significantly higher body mass index (BMI) and body fat despite lower intakes of saturated fat. Similar interactions, though not significant, were shown with muscle mass, whereby individuals who were homozygous for the risk allele had lower muscle mass with higher intakes of saturated fat, a result that, to our knowledge, has not been previously reported. Full article

Fast and affordable benchtop sequencers are becoming more important in improving personalized medical treatment. Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge. Here we present VARIFI, a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)). We optimized parameters in VARIFI by analyzing more than 170 amplicon-sequenced cancer samples produced on the Personal Genome Machine (PGM). In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to each identified variant. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g., incorrectly identified homopolymer-associated indels with Ion Torrent). VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction. VARIFI requires little computational experience and no in-house compute power since the analyses are conducted on our server. VARIFI is a web-based tool available at varifi.cibiv.univie.ac.at. Full article