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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/28185757/molecular-biomarkers-for-the-evaluation-of-colorectal-cancer-guideline-from-the-american-society-for-clinical-pathology-college-of-american-pathologists-association-for-molecular-pathology-and-american-society-of-clinical-oncology
#1
REVIEW
Antonia R Sepulveda, Stanley R Hamilton, Carmen J Allegra, Wayne Grody, Allison M Cushman-Vokoun, William K Funkhouser, Scott E Kopetz, Christopher Lieu, Noralane M Lindor, Bruce D Minsky, Federico A Monzon, Daniel J Sargent, Veena M Singh, Joseph Willis, Jennifer Clark, Carol Colasacco, R Bryan Rumble, Robyn Temple-Smolkin, Christina B Ventura, Jan A Nowak
OBJECTIVES: To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. METHODS: The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC...
February 2, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433081/correction
#2
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433080/correction
#3
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433079/utilization-of-whole-exome-next-generation-sequencing-variant-read-frequency-for-detection-of-lesion-specific-somatic-loss-of-heterozygosity-in-a-neurofibromatosis-type-1-cohort-with-tibial-pseudarthrosis
#4
Rebecca L Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A Stevenson, Rong Mao
A subset of neurofibromatosis type 1 patients develop tibial dysplasia, which can lead to pseudarthrosis. The tissue from the tibial pseudarthrosis region commonly has a somatic second hit in NF1: single-nucleotide variants, small deletions, or loss of heterozygosity (LOH). We used exome next-generation sequencing (NGS) variant frequency data (allelic imbalance analysis) to detect somatic LOH in pseudarthrosis tissue from three individuals with clinically and diagnostically confirmed neurofibromatosis type 1, and verified the results with microarray...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433078/haplotype-counting-for-sensitive-chimerism-testing-potential-for-early-leukemia-relapse-detection
#5
Marija Debeljak, Evelina Mocci, Max C Morrison, Aparna Pallavajjalla, Katie Beierl, Marie Amiel, Michaël Noë, Laura D Wood, Ming-Tseh Lin, Christopher D Gocke, Alison P Klein, Ephraim J Fuchs, Richard J Jones, James R Eshleman
Fields of forensics, transplantation, and paternity rely on human identity testing. Currently, this is accomplished through amplification of microsatellites followed by capillary electrophoresis. An alternative and theoretically better approach uses multiple single-nucleotide polymorphisms located within a small region of DNA, a method we initially developed using HLA-A and called haplotype counting. Herein, we validated seven additional polymorphic loci, sequenced a total of 45 individuals from three of the 1000 Genomes populations (15 from each), and determined the number of haplotypes, heterozygosity, and polymorphic information content for each locus...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433077/development-and-clinical-utility-of-a-blood-based-test-service-for-the-rapid-identification-of-actionable-mutations-in-non-small-cell-lung-carcinoma
#6
Hestia Mellert, Trudi Foreman, Leisa Jackson, Dianna Maar, Scott Thurston, Kristina Koch, Amanda Weaver, Samantha Cooper, Nicholas Dupuis, Ubaradka G Sathyanarayana, Jakkie Greer, Westen Hahn, Dawne Shelton, Paula Stonemetz, Gary A Pestano
Nearly 80% of cancer patients do not have genetic mutation results available at initial oncology consultation; up to 25% of patients begin treatment before receiving their results. These factors hinder the ability to pursue optimal treatment strategies. This study validates a blood-based genome-testing service that provides accurate results within 72 hours. We focused on targetable variants in advanced non-small cell lung carcinoma-epidermal growth factor receptor gene (EGFR) variant L858R, exon 19 deletion (ΔE746-A750), and T790M; GTPase Kirsten ras gene (KRAS) variants G12C/D/V; and echinoderm microtubule associated protein like and 4 anaplastic lymphoma receptor tyrosine kinase fusion (EML4-ALK) transcripts 1/2/3...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433076/identification-of-ntrk3-fusions-in-childhood-melanocytic-neoplasms
#7
Lu Wang, Klaus J Busam, Ryma Benayed, Robert Cimera, Jiajing Wang, Ryan Denley, Mamta Rao, Ruth Aryeequaye, Kerry Mullaney, Long Cao, Marc Ladanyi, Meera Hameed
Spitzoid neoplasms are a distinct group of melanocytic tumors. Genetically, they lack mutations in common melanoma-associated oncogenes. Recent studies have shown that spitzoid tumors may contain a variety of kinase fusions, including ROS1, NTRK1, ALK, BRAF, and RET fusions. We report herein the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms with spitzoid and/or atypical features, based on genome-wide copy number analysis by single-nucleotide polymorphism array, which showed intragenic copy number changes in NTRK3...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341590/guidelines-for-validation-of-next-generation-sequencing-based-oncology-panels-a-joint-consensus-recommendation-of-the-association-for-molecular-pathology-and-college-of-american-pathologists
#8
REVIEW
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341589/comprehensive-determination-of-prostate-tumor-ets-gene-status-in-clinical-samples-using-the-clia-decipher-assay
#9
Alba Torres, Mohammed Alshalalfa, Scott A Tomlins, Nicholas Erho, Ewan A Gibb, Jijumon Chelliserry, Lony Lim, Lucia L C Lam, Sheila F Faraj, Stephania M Bezerra, Elai Davicioni, Kasra Yousefi, Ashley E Ross, George J Netto, Edward M Schaeffer, Tamara L Lotan
ETS family gene fusions are common in prostate cancer and molecularly define a tumor subset. ERG is the most commonly rearranged, leading to its overexpression, followed by ETV1, ETV4, and ETV5, and these alterations are generally mutually exclusive. We validated the Decipher prostate cancer assay to detect ETS alterations in a Clinical Laboratory Improvement Amendments-accredited laboratory. Benchmarking against ERG immunohistochemistry and ETV1/4/5 RNA in situ hybridization, we examined the accuracy, precision, and reproducibility of gene expression ETS models using formalin-fixed, paraffin-embedded samples...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341588/targeted-next-generation-sequencing-of-51-genes-involved-in-primary-electrical-disease
#10
Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline M Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints, Jurgen Del Favero, Bart Loeys, Lut Van Laer
Primary electrical disease (PED) is characterized by cardiac arrhythmias, which can lead to sudden cardiac death in the absence of detectable structural heart disease. PED encompasses a diversity of inherited syndromes, predominantly Brugada syndrome, early repolarization syndrome, long QT syndrome, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and catecholaminergic polymorphic ventricular tachycardia. To overcome the diagnostic challenges imposed by the clinical and genetic heterogeneity of PED, we developed a targeted gene panel for next-generation sequencing of 51 PED genes...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341587/impact-of-rapid-molecular-respiratory-virus-testing-on-real-time-decision-making-in-a-pediatric-emergency-department
#11
Daniel T Rogan, Mohit S Kochar, Samuel Yang, James V Quinn
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory PCR testing is accurate albeit slow, whereas rapid antigen testing is inaccurate. We determined the impact of bedside PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28325688/current-and-emerging-molecular-tests-for-human-papillomavirus-related-neoplasia-in-the-genomic-era
#12
REVIEW
Sixto M Leal, Margaret L Gulley
Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28315673/chromosomal-microarray-detection-of-constitutional-copy-number-variation-using-saliva-dna
#13
Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A Scott
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28315672/principles-and-recommendations-for-standardizing-the-use-of-the-next-generation-sequencing-variant-file-in-clinical-settings
#14
Ira M Lubin, Nazneen Aziz, Lawrence J Babb, Dennis Ballinger, Himani Bisht, Deanna M Church, Shaun Cordes, Karen Eilbeck, Fiona Hyland, Lisa Kalman, Melissa Landrum, Edward R Lockhart, Donna Maglott, Gabor Marth, John D Pfeifer, Heidi L Rehm, Somak Roy, Zivana Tezak, Rebecca Truty, Mollie Ullman-Cullere, Karl V Voelkerding, Elizabeth A Worthey, Alexander W Zaranek, Justin M Zook
A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis for diagnosing human heritable conditions. The specifications for variant files were initially developed to be flexible with regard to content representation to support a variety of research applications. This flexibility permits variation with regard to how sequence findings are described and this depends, in part, on the conventions used...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28284778/detection-of-aberrant-tert-promoter-methylation-by-combined-bisulfite-restriction-enzyme-analysis-for-cancer-diagnosis
#15
Seungjae Lee, Sumit Borah, Armita Bahrami
Aberrant CpG dinucleotide methylation in a specific region of the telomerase reverse transcriptase (TERT) promoter is associated with increased TERT mRNA levels and malignancy in several cancer types. However, routine screening of this region to aid cancer diagnosis can be challenging because i) several established methylation assays may inaccurately report on hypermethylation of this particular region, ii) interpreting the results of methylation assays can sometimes be difficult for clinical laboratories, and iii) use of high-throughput methylation assays for a few patient samples can be cost prohibitive...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28268092/droplet-digital-pcr-is-a-reliable-tool-for-monitoring-minimal-residual-disease-in-acute-promyelocytic-leukemia
#16
Claudia Brunetti, Luisa Anelli, Antonella Zagaria, Angela Minervini, Crescenzio F Minervini, Paola Casieri, Nicoletta Coccaro, Cosimo Cumbo, Giuseppina Tota, Luciana Impera, Paola Orsini, Giorgina Specchia, Francesco Albano
Nested RT-PCR (nPCR) and real-time quantitative PCR (qPCR) are well-established methods for monitoring minimal residual disease (MRD) in acute promyelocytic leukemia (APL). Despite their remarkable sensitivity and specificity, both methods have inherent limitations, such as qualitative MRD evaluation and relative quantification. Herein, we used droplet digital PCR (ddPCR) to monitor MRD in 21 APL patients and compared its performance with nPCR and qPCR. After assessing the limit of detection (LOD) for each technique on serial dilutions of PML-RARA bcr1 and bcr3 transcripts, a total of 48 follow-up samples were analyzed and the results compared...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28222274/correction
#17
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28190462/correction
#18
(no author information available yet)
No abstract text is available yet for this article.
March 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28190461/detection-of-mycobacterium-chelonae-mycobacterium-abscessus-group-and-mycobacterium-fortuitum-complex-by-a-multiplex-real-time-pcr-directly-from-clinical-samples-using-the-bd-max-system
#19
Talita T Rocchetti, Suzane Silbert, Alicia Gostnell, Carly Kubasek, Antonio C Campos Pignatari, Raymond Widen
A new multiplex PCR test was designed to detect Mycobacterium chelonae, Mycobacterium abscessus group, and Mycobacterium fortuitum complex on the BD MAX System. A total of 197 clinical samples previously submitted for mycobacterial culture were tested using the new protocol. Samples were first treated with proteinase K, and then each sample was inoculated into the BD MAX Sample Buffer Tube. Extraction and multiplex PCR were performed by the BD MAX System, using the BD MAX ExK TNA-3 extraction kit and BD TNA Master Mix, along with specific in-house designed primers and probes for each target...
March 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28190460/guidelines-for-colorectal-cancer-testing-evidence-based-practice-recommendations
#20
EDITORIAL
Barbara Zehnbauer, Robyn Temple-Smolkin, Federico A Monzon
This Editorial provides readers additional insight on the colorectal guideline appearing in this issue.
March 2017: Journal of Molecular Diagnostics: JMD
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