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Molecular Diagnosis & Therapy

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https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#1
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28213806/clinical-ugt1a1-genetic-analysis-in-pediatric-patients-experience-of-a-reference-laboratory
#2
Ann M Moyer, Jennifer M Skierka, Katrina E Kotzer, Michelle L Kluge, John L Black, Linnea M Baudhuin
BACKGROUND: Neonatal hyperbilirubinemia can be severe or prolonged and warrant exploration into the underlying etiology, which may include genetic assessment of UGT1A1 for inherited disorders (i.e. Crigler-Najjar syndrome or Gilbert syndrome). METHODS: In our reference laboratory, we performed UGT1A1 gene sequencing analysis on 346 pediatric patients referred for a clinical indication of hyperbilirubinemia. RESULTS: Males (n = 241) had significantly higher mean total bilirubin concentration compared to females (n = 105) (9...
February 17, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28197949/the-impact-of-next-generation-sequencing-on-the-diagnosis-and-treatment-of-epilepsy-in-paediatric-patients
#3
REVIEW
Davide Mei, Elena Parrini, Carla Marini, Renzo Guerrini
Next-generation sequencing (NGS) has contributed to the identification of many monogenic epilepsy syndromes and is favouring earlier and more accurate diagnosis in a subset of paediatric patients with epilepsy. The cumulative information emerging from NGS studies is rapidly changing our comprehension of the relations between early-onset severe epilepsy and the associated neurological impairment, progressively delineating specific entities previously gathered under the umbrella definition of epileptic encephalopathies, thereby influencing treatment choices and limiting the most aggressive drug regimens only to those conditions that are likely to actually benefit from them...
February 14, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28164252/snap-tag-technology-a-promising-tool-for-ex-vivo-immunophenotyping
#4
Swati Choudhary, Stefan Barth, Rama S Verma
BACKGROUND: SNAP-tag, a self-labeling protein tag, is commonly used for in vitro and in vivo analysis of bound target proteins. We report the first evidence that SNAP-tag could be used for ex vivo detection of enriched biological markers. METHODS: Proof of concept was established for target c-kit receptor, a pathological and diagnostic marker for a variety of cancers. SNAP-tag conjugates with stem-cell factor (SCF) fusion proteins were designed and their binding and specificity was validated in vitro using flow cytometry and immunostaining...
February 6, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28161869/high-resolution-melting-analysis-is-very-useful-to-identify-breast-cancer-type-1-susceptibility-protein-brca1-c-4964_4982del19-rs80359876-founder-calabrian-pathogenic-variant-on-peripheral-blood-and-buccal-swab-dna
#5
Angelo Minucci, Maria De Bonis, Elisa De Paolis, Leonarda Gentile, Concetta Santonocito, Paola Concolino, Flavio Mignone, Ettore Capoluongo
INTRODUCTION: Detection of pathogenic variants in hereditary breast and ovarian cancer-related breast cancer type 1 and type 2 susceptibility proteins (BRCA1/2) genes is an effective strategy in cancer prevention and treatment. Some ethnic and geographical regions show different BRCA1/2 mutation spectrum and prevalence. In Italy, elucidation of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a healthcare system level, making genetic testing more affordable and cost effective in certain regions...
February 4, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28160193/correlation-between-tumor-mesothelin-expression-and-serum-mesothelin-in-patients-with-epithelial-ovarian-carcinoma-a-potential-noninvasive-biomarker-for-mesothelin-targeted-therapy
#6
Tatsuya Hanaoka, Kosei Hasegawa, Tomomi Kato, Sho Sato, Akira Kurosaki, Akiko Miyara, Shoji Nagao, Hiroyuki Seki, Masanori Yasuda, Keiichi Fujiwara
BACKGROUND: The cell surface glycoprotein mesothelin is highly expressed in several malignant diseases. Normal mesothelin expression is limited to mesothelial cells lining the pleura, peritoneum, and pericardium, making it a biomarker and an attractive target for cancer therapy. METHODS: We investigated tumor mesothelin expression and serum mesothelin levels in patients with epithelial ovarian cancer or borderline tumors. In total, 161 patients selected from a previous prospective study were analyzed for tumor mesothelin expression using immunohistochemistry and serum mesothelin expression using enzyme-linked immunosorbent assay...
February 3, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28155091/epi-procolon-%C3%A2-2-0-ce-a-blood-based-screening-test-for-colorectal-cancer
#7
Yvette N Lamb, Sohita Dhillon
Epi proColon(®) 2.0 CE is a blood-based test designed to aid in the early detection of colorectal cancer. The test comprises a qualitative assay for the polymerase chain reaction (PCR) detection of methylated Septin9 DNA, the presence of which is associated with colorectal cancer: however, positive results should be verified by colonoscopy or sigmoidoscopy. Epi proColon(®) 2.0 CE discriminated between patients with colorectal cancer and healthy controls with high clinical sensitivity and specificity in pivotal case-control studies...
February 2, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28130758/hla-c-06-02-does-not-predispose-to-clinical-response-following-long-term-adalimumab-treatment-in-psoriatic-patients-a-retrospective-cohort-study
#8
Marina Talamonti, Marco Galluzzo, Arianna Zangrilli, Marina Papoutsaki, Colin Gerard Egan, Mauro Bavetta, Sara Tambone, Maria Concetta Fargnoli, Luca Bianchi
BACKGROUND: The genetic basis of predisposition to psoriasis is recognised; however, the response to psoriasis treatment in patients with different genetic predisposition is poorly understood. OBJECTIVE: To analyse the presence of the HLA-C*06:02 polymorphism in psoriatic patients treated with adalimumab. METHODS: Genomic DNA was extracted from whole blood of 122 patients with moderate-to-severe psoriasis treated with adalimumab for 3 years...
January 28, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28130757/microrna-29-a-crucial-player-in-fibrotic-disease
#9
REVIEW
Zhenjun Deng, Yongjing He, Xujuan Yang, Hang Shi, Ao Shi, Lechun Lu, Li He
Fibrosis is a common pathological state characterized by the excessive accumulation of extracellular matrix components, but the pathogenesis of the disease is still not clear. Previous studies have shown that microRNA-29 (miR-29) can play pivotal roles in the regulation of a variety of organ fibrosis, including cardiac fibrosis, hepatic fibrosis, lung fibrosis, systemic sclerosis, and keloid. In this review, we outline the structure, expression, and regulation of miR-29 as well as its role in fibrotic diseases...
January 28, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28130756/comparison-of-five-different-assays-for-the-detection-of-braf-mutations-in-formalin-fixed-paraffin-embedded-tissues-of-patients-with-metastatic-melanoma
#10
Claire Franczak, Julia Salleron, Cindy Dubois, Pierre Filhine-Trésarrieu, Agnès Leroux, Jean-Louis Merlin, Alexandre Harlé
BACKGROUND: Metastatic or unresectable melanoma is a serious and deadly disease. Anti-BRAF and immunotherapy improved overall survival in patients with metastatic disease. Thus, BRAF genotyping is important to choose the right therapy. METHODS: In our study, we assessed and compared BRAF mutations in 59 formalin-fixed and paraffin-embedded tumor samples of patients with metastatic melanoma with next-generation sequencing (NGS), Cobas(®) 4800 BRAF V600 mutation test CE-IVD commercial kit, high-resolution melting PCR (HRM), multiplex real-time allele specific amplification (multiplexed RT-ASA) and immunohistochemistry (IHC)...
January 27, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28120299/analysis-of-rs8067378-polymorphism-in-the-risk-of-uterine-cervical-cancer-from-a-polish-population-and-its-impact-on-gasdermin-b-expression
#11
Anna Lutkowska, Andrzej Roszak, Margarita Lianeri, Anna Sowińska, Emianka Sotiri, Pawel P Jagodziński
OBJECTIVE: We studied the role of the NC_000017.10:g.38051348A>G (rs8067378) single nucleotide polymorphism (SNP) located 9.5 kb downstream of gasdermin B (GSDMB), in the development and progression of cervical squamous cell carcinomas (SCC). METHODS: Using high-resolution melting curve analysis, we genotyped this SNP in patients with cervical SCC (n = 486) and controls (n = 511) from the Polish Caucasian population. Logistic regression analysis was used to adjust for the effect of confounders such as age, parity, oral contraceptive use, tobacco smoking, and menopausal status...
January 25, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28101802/cold-pcr-technologies-in-the-area-of-personalized-medicine-methodology-and-applications
#12
REVIEW
Florence Mauger, Alexandre How-Kit, Jörg Tost
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation...
January 18, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28044257/targeted-therapy-for-severe-asthma-identifying-the-right-patients
#13
Kathy Low, Philip G Bardin
Asthma affects over 300 million people worldwide. Most asthmatics are well controlled with inhaled corticosteroids and long-acting beta-agonists; however, a proportion of patients are unresponsive and attain limited disease control. This group represents a considerable healthcare and financial burden, particularly patients who experience frequent exacerbations and require hospital admission. Development of new biological agents and disease biomarkers has provided novel avenues for treatment. These treatments have been highly successful, reducing exacerbations and yielding modest improvements in quality of life and lung function...
January 2, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28039579/discordance-of-somatic-mutations-between-asian-and-caucasian-patient-populations-with-gastric-cancer
#14
Feifei Jia, Jamie K Teer, Todd C Knepper, Jae K Lee, Hong-Hao Zhou, Yi-Jing He, Howard L McLeod
BACKGROUND: Differences in response to cancer treatments have been observed among racially and ethnically diverse gastric cancer (GC) patient populations. In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. Mapping driver gene mutations for the GC patient population as a whole has significant potential to advance precision therapy. METHODS: GC patients with sequencing data (N = 473) were obtained from The Cancer Genome Atlas (TCGA; n = 295), Moffitt Cancer Center Total Cancer Care™ (TCC; n = 33), and three published studies (n = 145)...
December 30, 2016: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28039578/the-importance-of-standardization-on-analyzing-circulating-rna
#15
REVIEW
Inyoul Lee, David Baxter, Min Young Lee, Kelsey Scherler, Kai Wang
Circulating RNAs, especially microRNAs (miRNAs), have recently emerged as non-invasive disease biomarkers. Despite enthusiasm and numerous reports on disease-associated circulating miRNAs, currently there is no circulating miRNA-based diagnostic in use. In addition, there are many contradictory reports on the concentration changes of specific miRNA in circulation. Here we review the impact of various technical and non-technical factors related to circulating miRNA measurement and elucidate the importance of having a general guideline for sample preparation and concentration measurement in studying circulating RNA...
December 30, 2016: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28000172/implementation-of-a-precision-pathology-program-focused-on-oncology-based-prognostic-and-predictive-outcomes
#16
Michael J Donovan, Carlos Cordon-Cardo
Personalized or precision medicine as a diagnostic and therapeutic paradigm was introduced some 10-15 years ago, with the advent of biomarker discovery as a mechanism for identifying prognostic and predictive attributes associated with treatment indication and outcome. While the concept is not new, the successful development and implementation of novel 'companion diagnostics', especially in oncology, continues to represent a significant challenge and is currently at the forefront of smart trial design and therapeutic choice...
December 20, 2016: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/27995550/somatic-mutations-in-prostate-cancer-closer-to-personalized-medicine
#17
REVIEW
M J Alvarez-Cubero, L J Martinez-Gonzalez, I Robles-Fernandez, J Martinez-Herrera, G Garcia-Rodriguez, M Pascual-Geler, J M Cozar, J A Lorente
The molecular cause of prostate cancer (PCa) is still unclear; however, its progression involves androgen, PI3K/Akt, and PTEN signaling, as cycle and apoptotic pathways. Alterations in oncogenes and tumor suppressor genes as PIK3CA, BRAF, KRAS and TP53 are not very common. Recently, somatic mutations have been discovered in relation to cancer progression mainly in genes such as PIK3CA; however, little data has been described in PCa. Nowadays genetic tools allow us to investigate multiple details about the biological heterogeneity of PCa, to better understand the mechanisms of disease progression and treatment resistance...
December 19, 2016: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/27878474/quantitative-assessment-of-cyp2c9-genetic-polymorphisms-effect-on-the-oral-clearance-of-s-warfarin-in-healthy-subjects
#18
Chanan Shaul, Simcha Blotnick, Mordechai Muszkat, Meir Bialer, Yoseph Caraco
BACKGROUND: Genetic polymorphisms in CYP2C9 account for 10-20% of the variability in warfarin dose requirement. As such CYP2C9 genetic polymorphisms are commonly included in algorithms aimed to optimize warfarin therapy as a way to account for variability in warfarin responsiveness that is due to altered pharmacokinetics. However, most of the currently available pharmacokinetic data were derived from studies among patients on chronic warfarin therapy and therefore suffer from the confounding effects of disease states and drug interactions...
February 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/27798813/economic-evaluation-of-a-pharmacogenomics-test-for-statin-induced-myopathy-in-cardiovascular-high-risk-patients-initiating-a-statin
#19
Dominic Mitchell, Jason R Guertin, Ange Christelle Iliza, Fiorella Fanton-Aita, Jacques LeLorier
BACKGROUND: Statins are the mainstay hypercholesterolemia treatment and reduce the risk of cardiovascular events in patients. However, statin therapy is often interrupted in patients experiencing musculoskeletal pain or myopathy, which are common in this patient group. Currently, the standard tests for diagnosing statin myopathies are difficult to interpret. A pharmacogenomics (PGx) test to diagnose statin-induced myopathy would be highly desirable. METHODS: We developed a Markov state model to assess the cost-effectiveness of a hypothetical PGx test, which aims to identify statin-induced myopathy in high-risk, secondary prevention cardiovascular patients...
February 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/27667773/an-analytical-comparison-of-dako-28-8-pharmdx-assay-and-an-e1l3n-laboratory-developed-test-in-the-immunohistochemical-detection-of-programmed-death-ligand-1
#20
John Cogswell, H David Inzunza, Qiuyan Wu, John N Feder, Gabe Mintier, James Novotny, Diana M Cardona
AIM: Nivolumab, a fully human immunoglobulin G4 programmed death-1 (PD-1) immune checkpoint inhibitor antibody, has activity in melanoma, non-small-cell lung cancer (NSCLC), renal cell carcinoma (RCC), and Hodgkin lymphoma. Nivolumab is approved in the USA and EU for advanced melanoma, NSCLC, and RCC, and relapsed Hodgkin lymphoma in the USA. Programmed death-ligand 1 (PD-L1), a PD-1 ligand, is expressed on mononuclear leukocytes, myeloid cells, and tumor cells. PD-L1 is being investigated as a potential biomarker to predict the association of tumor PD-L1 expression with nivolumab efficacy...
February 2017: Molecular Diagnosis & Therapy
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