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Molecular Diagnosis & Therapy

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https://www.readbyqxmd.com/read/28639239/significant-improvement-in-detecting-braf-kras-and-egfr-mutations-using-next-generation-sequencing-as-compared-with-fda-cleared-kits
#1
Wanlong Ma, Steven Brodie, Sally Agersborg, Vincent A Funari, Maher Albitar
INTRODUCTION: We compared mutations detected in EGFR, KRAS, and BRAF genes using next-generation sequencing (NGS) and confirmed by Sanger sequencing with mutations that could be detected by FDA-cleared testing kits. METHODS: Paraffin-embedded tissue from 822 patients was tested for mutations in EGFR, KRAS, and BRAF by NGS. Sanger sequencing of hot spots was used with locked nucleic acid to increase sensitivity for specific hot-spot mutations. This included 442 (54%) lung cancers, 168 (20%) colorectal cancers, 29 (4%) brain tumors, 33 (4%) melanomas, 14 (2%) thyroid cancers, and 16% others (pancreas, head and neck, and cancer of unknown origin)...
June 21, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28631163/evaluation-of-streck-bct-and-paxgene-stabilised-blood-collection-tubes-for-cell-free-circulating-dna-studies-in-plasma
#2
Kristina Warton, Nicole L Yuwono, Mark J Cowley, Mark J McCabe, Alwin So, Caroline E Ford
INTRODUCTION: Blood samples for studies of circulating DNA in disease are often collected in clinical settings where prompt processing of samples is not possible. In order to avoid problems associated with leukocyte lysis after prolonged blood storage, stabilised blood tubes have been developed containing preservatives that prevent cell lysis. We evaluated Streck BCT tubes and PAXgene ccfDNA tubes, as well as standard EDTA blood collection tubes, in terms of DNA yield and fragment size...
June 19, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28624903/early-diagnosis-of-sepsis-is-an-integrated-omics-approach-the-way-forward
#3
REVIEW
Raymond J Langley, Hector R Wong
Sepsis remains one of the leading causes of death in the USA and it is expected to get worse as the population ages. Moreover, the standard of care, which recommends aggressive treatment with appropriate antibiotics, has led to an increase in multiple drug-resistant organisms. There is a dire need for the development of new antibiotics, improved antibiotic stewardship, and therapies that treat the host response. Development of new sepsis therapeutics has been a disappointment as no drugs are currently approved to treat the various complications from sepsis...
June 17, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28620890/identification-and-characterization-of-a-new-brca2-rearrangement-in-an-italian-family-with-hereditary-breast-and-ovarian-cancer-syndrome
#4
Paola Concolino, Roberta Rizza, Karl Hackmann, Angelo Minucci, Giovanni Luca Scaglione, Maria De Bonis, Alessandra Costella, Cecilia Zuppi, Evelin Schrock, Ettore Capoluongo
INTRODUCTION: Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE: Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication...
June 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28620889/levels-of-microrna-heterogeneity-in-cancer-biology
#5
REVIEW
Nina Petrovic, Sercan Ergün, Esma R Isenovic
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression, involved in the silencing of messenger RNA (mRNA) translation. The importance of miRNA signatures in disease screening, prognosis, and progression of different tumor types and subtypes is increasing. miRNA expression levels change depending on numerous factors. In this review, we are describing the circumstances under which miRNA levels can change, these are named 'levels' of heterogeneity of miRNAs. miRNAs can have oncogenic, tumor suppressive, or both roles depending on tumor type and target mRNA whose translation they silence...
June 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28589341/highly-sensitive-and-reliable-detection-of-egfr-exon-19-deletions-by-droplet-digital-polymerase-chain-reaction
#6
Natalya Oskina, Igor Oscorbin, Evgeniy Khrapov, Ulyana Boyarskikh, Dmitriy Subbotin, Irina Demidova, Evgeny Imyanitov, Maxim Filipenko
BACKGROUND: Analysis of EGFR mutations is becoming a routine clinical practice but the optimal EGFR mutation testing method is still to be determined. METHODS: We determined the nucleotide sequence of deletions located in exon 19 of the EGFR gene in lung tumor samples of patients residing in different regions of Russia (153 tumor DNA specimens), using Sanger sequencing. We developed a droplet digital polymerase chain reaction assay capable of detecting all common EGFR deletions in exon 19...
June 6, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28567595/do-alpha-thalassemia-fetal-hemoglobin-and-the-ugt1a1-polymorphism-have-an-influence-on-serum-bilirubin-levels-and-cholelithiasis-in-patients-with-sickle-cell-disease
#7
Laura Alencastro de Azevedo, Joyce Bonazzoni, Sandrine Comparsi Wagner, Mariela Granero Farias, Christina M Bittar, Liane Daudt, Simone Martins de Castro
BACKGROUND: Increased destruction of erythrocytes in patients with sickle cell disease results in chronic hyperbilirubinemia and leads to the formation of gallstones. OBJECTIVES: The objective of this study was to determine the combined influence of alpha thalassemia, fetal hemoglobin, and the UGT1A1 polymorphism on serum bilirubin levels and cholelithiasis in patients with sickle cell disease. METHODS: We analyzed 72 patients treated in the outpatient hematology unit of the Clinical Hospital of Porto Alegre...
May 31, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28536827/genetic-counselling-for-maternally-inherited-mitochondrial-disorders
#8
REVIEW
Joanna Poulton, Josef Finsterer, Patrick Yu-Wai-Man
The aim of this review was to provide an evidence-based approach to frequently asked questions relating to the risk of transmitting a maternally inherited mitochondrial disorder (MID). We do not address disorders linked with disturbed mitochondrial DNA (mtDNA) maintenance, causing mtDNA depletion or multiple mtDNA deletions, as these are autosomally inherited. The review addresses questions regarding prognosis, recurrence risks and the strategies available to prevent disease transmission. The clinical and genetic complexity of maternally inherited MIDs represent a major challenge for patients, their relatives and health professionals...
May 23, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28527151/association-of-the-mir-196a2-mir-146a-and-mir-499-polymorphisms-with-asthma-phenotypes-in-a-korean-population
#9
Hoang Kim Tu Trinh, Duy Le Pham, Su-Chin Kim, Ri-Yeon Kim, Hae-Sim Park, Seung-Hyun Kim
BACKGROUND: MicroRNAs (miRNAs) modulate expressions of inflammatory genes, thereby regulating inflammatory responses. Single nucleotide polymorphisms (SNPs) in miRNAs could affect their efficiency in binding to messenger RNAs (mRNAs). OBJECTIVE: We investigated the associations of miRNA SNPs with asthma phenotypes. miR-196a2 (rs11614913 T>C), miR-146a (rs2910164 C>G), and miR-499 (rs3746444 A>G) were genotyped in 347 asthma patients and 172 normal healthy controls (NCs)...
May 19, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28477149/current-and-emerging-applications-of-droplet-digital-pcr-in-oncology
#10
REVIEW
Susana Olmedillas-López, Mariano García-Arranz, Damián García-Olmo
The clinical management of cancer has evolved in recent years towards more personalized strategies that require a comprehensive knowledge of the complex molecular features involved in tumor growth and evolution, and the development of drug resistance mechanisms leading to disease progression. Droplet digital PCR (ddPCR) has become one of the most accurate and reliable tools for the examination of genetic alterations in a wide variety of cancers because of its high sensitivity and specificity. ddPCR is currently being applied for absolute allele quantification, rare mutation detection, analysis of copy number variations, DNA methylation, and gene rearrangements in different kinds of clinical samples...
May 5, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28452038/is-next-generation-sequencing-the-way-to-go-for-residual-disease-monitoring-in-acute-lymphoblastic-leukemia
#11
REVIEW
Michaela Kotrova, Jan Trka, Michael Kneba, Monika Brüggemann
Minimal residual disease (MRD) is the most important independent prognostic factor in acute lymphoblastic leukemia (ALL). Since it has been implemented into in treatment stratification strategies, cure rates have improved significantly for all age groups. Real time quantitative (RQ)-PCR of clonal immunoglobulin and T-cell receptor gene rearrangements using allele-specific primers is currently regarded as the gold standard for MRD analysis in ALL, as it is not only highly sensitive and specific but also provides accurate MRD quantification...
April 27, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28405803/mir-15a-5p-a-novel-prognostic-biomarker-predicting-recurrent-colorectal-adenocarcinoma
#12
Christos K Kontos, Panagiotis Tsiakanikas, Margaritis Avgeris, Iordanis N Papadopoulos, Andreas Scorilas
INTRODUCTION: Colorectal cancer is one of the most common gastrointestinal diseases and the second leading cause of cancer-associated deaths among adults. miR-15a-5p is a post-transcriptional regulator of the proto-oncogene MYB, a transcription factor essential for prolonged cancer cell proliferation and survival. In the current study, we assessed the potential diagnostic and prognostic utility of miR-15a-5p expression in colorectal adenocarcinoma. METHODS: To accomplish this goal, total RNA was extracted from 182 colorectal adenocarcinoma specimens and 86 non-cancerous colorectal mucosae...
April 12, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28374122/the-role-of-pharmacogenetics-in-chronic-plaque-psoriasis-update-of-the-literature
#13
REVIEW
Marina Talamonti, Simone D'Adamio, Luca Bianchi, Marco Galluzzo
Psoriasis is a chronic inflammatory disease triggered by both genetic and environmental factors. Systemic and biologic therapies used to treat moderate-to-severe psoriasis show significant variability in efficacy, are associated with various degrees of toxicity, and, for biologic therapies, are expensive. There is a great need for non-invasive biomarkers to predict treatment outcomes of these therapies and to individualize care for patients with psoriasis. This article reviews currently recognized pharmacogenetic targets related to the treatment of chronic plaque psoriasis, in particular to biologic therapies...
April 3, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#14
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28247182/impact-of-availability-of-companion-diagnostics-on-the-clinical-development-of-anticancer-drugs
#15
Ariadna Tibau, Laura Díez-González, Beatriz Navarro, Eva M Galán-Moya, Arnoud J Templeton, Bostjan Seruga, Atanasio Pandiella, Eitan Amir, Alberto Ocana
BACKGROUND: Companion diagnostics permit the selection of patients likely to respond to targeted anticancer drugs; however, it is unclear if the drug development process differs between drugs developed with or without companion diagnostics. Identification of differences in study design could help future clinical development. PATIENTS AND METHODS: Anticancer drugs approved for use in solid tumors between 28 September 2000 and 4 January 2014 were identified using a search of the US FDA website...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#16
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...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28213806/clinical-ugt1a1-genetic-analysis-in-pediatric-patients-experience-of-a-reference-laboratory
#17
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...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28164252/snap-tag-technology-a-promising-tool-for-ex-vivo-immunophenotyping
#18
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...
June 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
#19
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...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28130757/microrna-29-a-crucial-player-in-fibrotic-disease
#20
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...
June 2017: Molecular Diagnosis & Therapy
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