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Journal of Personalized Medicine

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https://read.qxmd.com/read/30987214/aligning-the-aligners-comparison-of-rna-sequencing-data-alignment-and-gene-expression-quantification-tools-for-clinical-breast-cancer-research
#1
Isaac D Raplee, Alexei V Evsikov, Caralina Marín de Evsikova
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...
April 3, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30934600/metformin-pharmacogenetics-effects-of-slc22a1-slc22a2-and-slc22a3-polymorphisms-on-glycemic-control-and-hba1c-levels
#2
Laith N Al-Eitan, Basima A Almomani, Ahmad M Nassar, Barakat Z Elsaqa, Nesreen A Saadeh
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...
March 25, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30836656/mutation-based-therapeutic-strategies-for-duchenne-muscular-dystrophy-from-genetic-diagnosis-to-therapy
#3
REVIEW
Akinori Nakamura
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...
March 4, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30832243/genetic-testing-to-guide-risk-stratified-screens-for-breast-cancer
#4
REVIEW
Ava Willoughby, Paul R Andreassen, Amanda Ewart Toland
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...
March 1, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30781705/autonomy-challenges-in-epigenetic-risk-stratified-cancer-screening-how-can-patient-decision-aids-support-informed-consent
#5
REVIEW
Maaike Alblas, Maartje Schermer, Yvonne Vergouwe, Ineke Bolt
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...
February 18, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30781516/the-association-between-plasma-omega-6-omega-3-ratio-and-anthropometric-traits-differs-by-racial-ethnic-groups-and-nfkb1-genotypes-in-healthy-young-adults
#6
Jeremy Bauman-Fortin, David W L Ma, David M Mutch, Salma A Abdelmagid, Alaa Badawi, Ahmed El-Sohemy, Bénédicte Fontaine-Bisson
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...
February 16, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30736475/the-developing-story-of-predictive-biomarkers-in-colorectal-cancer
#7
REVIEW
Stergios Boussios, Mehmet Akif Ozturk, Michele Moschetta, Afroditi Karathanasi, Nikolaos Zakynthinakis-Kyriakou, Konstantinos H Katsanos, Dimitrios K Christodoulou, Nicholas Pavlidis
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...
February 7, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30764585/the-interaction-between-genetic-polymorphisms-in-fto-and-tcf7l2-genes-and-dietary-intake-with-regard-to-body-mass-and-composition-an-exploratory-study
#8
Lara Nasreddine, Reem Akika, Aurelie Mailhac, Hani Tamim, Nathalie Khoueiry Zgheib
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...
February 5, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30717290/varifi-web-based-automatic-variant-identification-filtering-and-annotation-of-amplicon-sequencing-data
#9
Milica Krunic, Peter Venhuizen, Leonhard Müllauer, Bettina Kaserer, Arndt von Haeseler
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)...
February 1, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30717118/understanding-implementation-challenges-to-genetic-testing-for-familial-hypercholesterolemia-in-the-united-states
#10
Rachele M Hendricks-Sturrup, Christine Y Lu
Cardiovascular disease (CVD) is the leading cause of death in the United States (US), with familial hypercholesterolemia (FH) being a major inherited and genetic risk factor for premature CVD and atherosclerosis. Genetic testing has helped patients and providers confirm the presence of known pathogenic and likely pathogenic variations in FH-associated genes. Key organizations, such as the Centers for Disease Control and Prevention (CDC), American Heart Association (AHA), FH Foundation, and National Lipid Association (NLA), have recognized the clinical utility of FH genetic testing...
February 1, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30682871/personalized-assessment-of-the-coronary-atherosclerotic-arteries-by-intravascular-ultrasound-imaging-hunting-the-vulnerable-plaque
#11
REVIEW
Theodore G Papaioannou, Charalampos Kalantzis, Efstratios Katsianos, Despina Sanoudou, Manolis Vavuranakis, Dimitrios Tousoulis
The term "vulnerable plaque" is commonly used to refer to an atherosclerotic plaque that is prone to rupture and the formation of thrombosis, which can lead to several cardiovascular and cerebrovascular events. Coronary artery atherosclerosis has a wide variety of different phenotypes among patients who may have a substantially variable risk for plaque rupture and cardiovascular events. Mounting evidence has proposed three distinctive histopathological mechanisms: plaque rupture, plaque erosion and calcified nodules...
January 24, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30658513/pharmacogenomics-of-novel-direct-oral-anticoagulants-newly-identified-genes-and-genetic-variants
#12
REVIEW
Sri H Kanuri, Rolf P Kreutz
Direct oral anticoagulants (DOAC) have shown an upward prescribing trend in recent years due to favorable pharmacokinetics and pharmacodynamics without requirement for routine coagulation monitoring. However, recent studies have documented inter-individual variability in plasma drug levels of DOACs. Pharmacogenomics of DOACs is a relatively new area of research. There is a need to understand the role of pharmacogenomics in the interpatient variability of the four most commonly prescribed DOACs, namely dabigatran, rivaroxaban, apixaban, and edoxaban...
January 17, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30654522/the-emerging-role-of-checkpoint-inhibition-in-microsatellite-stable-colorectal-cancer
#13
REVIEW
David J Hermel, Darren Sigal
Checkpoint inhibitor therapy has introduced a revolution in contemporary anticancer therapy. It has led to dramatic improvements in patient outcomes and has spawned tremendous research into novel immunomodulatory agents and combination therapy that has changed the trajectory of cancer care. However, clinical benefit in patients with colorectal cancer has been generally limited to tumors with loss of mismatch repair function and those with specific germline mutations in the DNA polymerase gene. Unfortunately, tumors with these specific mutator phenotypes are in the minority...
January 16, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30650548/re-examining-genetic-screening-and-oral-contraceptives-a-patient-centered-review
#14
REVIEW
Bridget Hiedemann, Erin Vernon, Bonnie H Bowie
The World Health Organization classifies combined hormonal contraception as an unacceptable health risk in the presence of a known thrombogenic mutation but advises against routine thrombophilia screening before initiating combined oral contraceptives (COCs) on the grounds of high screening costs and low prevalence. From the perspective of patient-centered care, we examine cost, prevalence, and other published arguments for and against thrombophilia screening before initiating COCs. Our patient-centered review draws on relevant empirical evidence concerning the advantages and disadvantages of thrombophilia screening, while placing the discussion in the broader context of evolving attitudes toward genetic testing and a shifting policy landscape that provides many women direct access to COCs and/or thrombophilia screening...
January 15, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30646508/colorectal-cancer-biomarkers-in-the-era-of-personalized-medicine
#15
REVIEW
Jai N Patel, Mei Ka Fong, Megan Jagosky
The 5-year survival probability for patients with metastatic colorectal cancer has not drastically changed over the last several years, nor has the backbone chemotherapy in first-line disease. Nevertheless, newer targeted therapies and immunotherapies have been approved primarily in the refractory setting, which appears to benefit a small proportion of patients. Until recently, rat sarcoma ( RAS ) mutations remained the only genomic biomarker to assist with therapy selection in metastatic colorectal cancer...
January 14, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30641993/association-of-tlr4-polymorphisms-expression-and-vitamin-d-with-helicobacter-pylori-infection
#16
Shafika Assaad, Christy Costanian, Lama Jaffal, Fida Tannous, Maria G Stathopoulou, Said El Shamieh
Helicobacter pylori ( H. pylori ) infection is the strongest recognized risk factor for gastric adenocarcinoma. Since previous observations have shown that polymorphisms in innate immune system genes, as well as vitamin D (VitD) levels, could modify the risk of infection with Helicobacter pylori ( H. pylori ), we analyzed the relation between single nucleotide polymorphisms (SNPs) in TLRs ( TLR1 , TLR2 , TLR4 ) CD14 , RUNX3 and VitD levels with H. pylori infection. A case-control study on four hundred sixty Lebanese individuals was conducted...
January 11, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30621068/restoring-dystrophin-expression-in-duchenne-muscular-dystrophy-current-status-of-therapeutic-approaches
#17
REVIEW
Yuko Shimizu-Motohashi, Hirofumi Komaki, Norio Motohashi, Shin'ichi Takeda, Toshifumi Yokota, Yoshitsugu Aoki
Duchenne muscular dystrophy (DMD), a rare genetic disorder characterized by progressive muscle weakness, is caused by the absence or a decreased amount of the muscle cytoskeletal protein dystrophin. Currently, several therapeutic approaches to cure DMD are being investigated, which can be categorized into two groups: therapies that aim to restore dystrophin expression, and those that aim to compensate for the lack of dystrophin. Therapies that restore dystrophin expression include read-through therapy, exon skipping, vector-mediated gene therapy, and cell therapy...
January 7, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30551678/dpyd-tyms-and-mthfr-genes-polymorphism-frequencies-in-a-series-of-turkish-colorectal-cancer-patients
#18
Arsalan Amirfallah, Gizem Calibasi Kocal, Olcun Umit Unal, Hulya Ellidokuz, Ilhan Oztop, Yasemin Basbinar
Fluoropyrimidine-based chemotherapy is extensively used for the treatment of solid cancers, including colorectal cancer. However, fluoropyrimidine-driven toxicities are a major problem in the management of the disease. The grade and type of the toxicities depend on demographic factors, but substantial inter-individual variation in fluoropyrimidine-related toxicity is partly explained by genetic factors. The aim of this study was to investigate the effect of dihydropyrimidine dehydrogenase (DPYD), thymidylate synthase (TYMS), and methylenetetrahydrofolate reductase (MTHFR) polymorphisms in colorectal cancer patients...
December 13, 2018: Journal of Personalized Medicine
https://read.qxmd.com/read/30551677/personalized-medicine-and-molecular-interaction-networks-in-amyotrophic-lateral-sclerosis-als-current-knowledge
#19
REVIEW
Stephen Morgan, Stephanie Duguez, William Duddy
Multiple genes and mechanisms of pathophysiology have been implicated in amyotrophic lateral sclerosis (ALS), suggesting it is a complex systemic disease. With this in mind, applying personalized medicine (PM) approaches to tailor treatment pipelines for ALS patients may be necessary. The modelling and analysis of molecular interaction networks could represent valuable resources in defining ALS-associated pathways and discovering novel therapeutic targets. Here we review existing omics datasets and analytical approaches, in order to consider how molecular interaction networks could improve our understanding of the molecular pathophysiology of this fatal neuromuscular disorder...
December 13, 2018: Journal of Personalized Medicine
https://read.qxmd.com/read/30545130/the-9th-santorini-conference-systems-medicine-personalised-health-and-therapy-the-odyssey-from-hope-to-practice-santorini-greece-30-september%C3%A2-3-october-2018
#20
Sophie Visvikis-Siest, Vesna Gorenjak, Maria G Stathopoulou, Alexandros M Petrelis, Georges Weryha, Christine Masson, Brigitte Hiegel, Satish Kumar, Robert Barouki, Eric Boerwinkle, Georges Dagher, Panagiotis Deloukas, Federico Innocenti, John Lamont, Michael Marschler, Heiko Meyer, Urs A Meyer, Charity Nofziger, Markus Paulmichl, Cora Vacher, Lynn Webster
The 9th traditional biannual conference on Systems Medicine, Personalised Health & Therapy-"The Odyssey from Hope to Practice", inspired by the Greek mythology, was a call to search for practical solutions in cardio-metabolic diseases and cancer, to resolve and overcome the obstacles in modern medicine by creating more interactions among disciplines, as well as between academic and industrial research, directed towards an effective 'roadmap' for personalised health and therapy. The 9th Santorini Conference, under the Presidency of Sofia Siest, the director of the INSERM U1122; IGE-PCV (www...
December 12, 2018: Journal of Personalized Medicine
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