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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/27916435/analytical-validation-of-androgen-receptor-splice-variant-7-detection-in-a-clinical-laboratory-improvement-amendments-clia-laboratory-setting
#1
Parvez M Lokhandwala, Stacy L Riel, Lisa Haley, Changxue Lu, Yan Chen, John Silberstein, Yezi Zhu, Gang Zheng, Ming-Tseh Lin, Christopher D Gocke, Alan W Partin, Emmanuel S Antonarakis, Jun Luo, James R Eshleman
Patients with castration-resistant prostate cancer (CRPC) often are treated with drugs that target the androgen receptor (AR) ligand-binding domain. Constitutively active AR splice variant 7 (AR-V7) lacks the ligand-binding domain and, if detected in circulating tumor cells, may be associated with resistance to these agents. We validated an AR-V7 assay in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. Circulating tumor cells were isolated, and mRNA was reverse-transcribed into cDNA...
December 1, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27870944/application-of-single-molecule-amplification-and-resequencing-technology-for-broad-surveillance-of-plasma-mutations-in-patients-with-advanced-lung-adenocarcinoma
#2
Zheng Wang, Gang Cheng, Xiaohong Han, Xinlin Mu, Yuhui Zhang, Di Cui, Chang Liu, Li Zhang, Zaiwen Fan, Lingyun Ma, Li Yang, Jing Di, David S Cram, Yuankai Shi, Dongge Liu
Liquid biopsy to access the circulating tumor DNA is a promising surrogate for invasive tumor genotyping. We designed a multiplex assay based on circulating single-molecule amplification and resequencing technology (cSMART) to simultaneously detect and quantitate hot spot EGFR, KRAS, BRAF, ERBB2, and ALK plasma DNA variants in 103 patients with advanced lung adenocarcinoma. In validation studies using an analytical mutation standard, the sensitivity of the assay for EGFR mutation detection was at least 0.1% and specificity was 100%...
November 18, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27865784/a-comparison-of-cell-free-dna-isolation-kits-isolation-and-quantification-of-cell-free-dna-in-plasma
#3
Laure Sorber, Karen Zwaenepoel, Vanessa Deschoolmeester, Geert Roeyen, Filip Lardon, Christian Rolfo, Patrick Pauwels
The analysis of cell-free DNA (cfDNA) as a sensitive biomarker for cancer diagnosis and monitoring has resulted in a need for efficient and standardized cfDNA isolation. In this study, we compared the isolation efficiency of the QIAamp circulating nucleic acid kit (QIA) with four other cfDNA isolation kits: the PME free-circulating DNA Extraction Kit (PME), the Maxwell RSC ccfDNA Plasma Kit (RSC), the EpiQuick Circulating Cell-Free DNA Isolation Kit (EQ), and two consecutive versions of the NEXTprep-Mag cfDNA Isolation Kit (NpMV1/2)...
November 17, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863262/in-silico-proficiency-testing-for-clinical-next-generation-sequencing
#4
REVIEW
Eric J Duncavage, Haley J Abel, John D Pfeifer
Quality assurance for clinical next-generation sequencing (NGS)-based assays is difficult given the complex methods and the range of sequence variants such assays can detect. As the number and range of mutations detected by clinical NGS assays has increased, it is difficult to apply standard analyte-specific proficiency testing (PT). Most current proficiency testing challenges for NGS are methods-based PT surveys that use DNA from reference samples engineered to harbor specific mutations that test both sequence generation and bioinformatics analysis...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863261/a-next-generation-sequencing-strategy-for-evaluating-the-most-common-genetic-abnormalities-in-multiple-myeloma
#5
Cristina Jiménez, María Jara-Acevedo, Luis A Corchete, David Castillo, Gonzalo R Ordóñez, M Eugenia Sarasquete, Noemí Puig, Joaquín Martínez-López, M Isabel Prieto-Conde, María García-Álvarez, M Carmen Chillón, Ana Balanzategui, Miguel Alcoceba, Albert Oriol, Laura Rosiñol, Luis Palomera, Ana I Teruel, Juan J Lahuerta, Joan Bladé, María V Mateos, Alberto Orfão, Jesús F San Miguel, Marcos González, Norma C Gutiérrez, Ramón García-Sanz
Identification and characterization of genetic alterations are essential for diagnosis of multiple myeloma and may guide therapeutic decisions. Currently, genomic analysis of myeloma to cover the diverse range of alterations with prognostic impact requires fluorescence in situ hybridization (FISH), single nucleotide polymorphism arrays, and sequencing techniques, which are costly and labor intensive and require large numbers of plasma cells. To overcome these limitations, we designed a targeted-capture next-generation sequencing approach for one-step identification of IGH translocations, V(D)J clonal rearrangements, the IgH isotype, and somatic mutations to rapidly identify risk groups and specific targetable molecular lesions...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863260/applications-of-dna-based-liquid-biopsy-for-central-nervous-system-neoplasms
#6
REVIEW
Joanna Wang, Chetan Bettegowda
The management of central nervous system malignancies remains reliant on histopathological analysis and neuroimaging, despite their complex genetic profile. The intratumoral heterogeneity displayed by these tumors necessitates a more sophisticated method of tumor analysis and monitoring, with the ability to assess tumors over space and time. Circulating biomarkers, including circulating tumor cells, circulating tumor DNA, and extracellular vesicles, hold promise as a type of real-time liquid biopsy able to provide dynamic information not only regarding tumor burden to monitor disease progression and treatment response, but also regarding genetic profile to enable changes in management to match a constantly evolving tumor...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863259/validation-of-a-gene-expression-test-for-mesothelioma-prognosis-in-formalin-fixed-paraffin-embedded-tissues
#7
Assunta De Rienzo, Robert W Cook, Jeff Wilkinson, Corinne E Gustafson, Waqas Amin, Clare E Johnson, Kristen M Oelschlager, Derek J Maetzold, John F Stone, Michael D Feldman, Michael J Becich, Beow Y Yeap, William G Richards, Raphael Bueno
A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments-approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863258/detection-of-mismatch-repair-deficiency-and-microsatellite-instability-in-colorectal-adenocarcinoma-by-targeted-next-generation-sequencing
#8
Jonathan A Nowak, Matthew B Yurgelun, Jacqueline L Bruce, Vanesa Rojas-Rudilla, Dimity L Hall, Priyanka Shivdasani, Elizabeth P Garcia, Agoston T Agoston, Amitabh Srivastava, Shuji Ogino, Frank C Kuo, Neal I Lindeman, Fei Dong
Mismatch repair protein deficiency (MMR-D) and high microsatellite instability (MSI-H) are features of Lynch syndrome-associated colorectal carcinomas and have implications in clinical management. We evaluate the ability of a targeted next-generation sequencing panel to detect MMR-D and MSI-H based on mutational phenotype. Using a criterion of >40 total mutations per megabase or >5 single-base insertion or deletion mutations in repeats per megabase, sequencing achieves 92% sensitivity and 100% specificity for MMR-D by immunohistochemistry in a training cohort of 149 colorectal carcinomas and 91% sensitivity and 98% specificity for MMR-D in a validation cohort of 94 additional colorectal carcinomas...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27855276/detection-of-calr-and-mpl-mutations-in-low-allelic-burden-jak2-v617f-essential-thrombocythemia
#9
Fabrice Usseglio, Nathalie Beaufils, Anne Calleja, Sophie Raynaud, Jean Gabert
Myeloproliferative neoplasms are clonal hematopoietic stem cell disorders characterized by aberrant proliferation and an increased tendency toward leukemic transformation. The genes JAK2, MPL, and CALR are frequently altered in these syndromes, and their mutations are often a strong argument for diagnosis. We analyzed the mutational profiles of these three genes in a cohort of 164 suspected myeloproliferative neoplasms. JAK2 V617F mutation was detected by real-time PCR, whereas high-resolution melting analysis followed by Sanger sequencing were used for searching for mutations in JAK2 exon 12, CALR, and MPL...
November 14, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27840062/deamination-effects-in-formalin-fixed-paraffin-embedded-tissue-samples-in-the-era-of-precision-medicine
#10
Seokhwi Kim, Charny Park, Yongick Ji, Deok G Kim, Hyunsik Bae, Michael van Vrancken, Duk-Hwan Kim, Kyoung-Mee Kim
Deamination of nucleotides causes C:G>T:A changes in formalin-fixed, paraffin-embedded (FFPE) tissue samples and produces false positives during next-generation sequencing (NGS). Uracil DNA glycosylase (UDG) helps eliminate this issue, but the effect of UDG in different tissue preparation conditions has not been rigorously studied. To investigate whether UDG can reduce false-positive single-nucleotide variant (SNV) calls, we used tumor and normal tissues from gastric adenocarcinoma patients prepared using different fixation times and pH conditions...
November 10, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27836695/clinical-validation-of-a-next-generation-sequencing-genomic-oncology-panel-via-cross-platform-benchmarking-against-established-amplicon-sequencing-assays
#11
Sabah Kadri, Bradley C Long, Ibro Mujacic, Chao J Zhen, Michelle N Wurst, Shruti Sharma, Nadia McDonald, Nifang Niu, Sonia Benhamed, Jigyasa Tuteja, Tanguy Seiwert, Kevin White, Megan E McNerney, Carrie Fitzpatrick, Y Lynn Wang, Larissa V Furtado, Jeremy P Segal
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations...
November 8, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27815002/methodologic-considerations-in-the-application-of-next-generation-sequencing-of-human-trb-repertoires-for-clinical-use
#12
Liwen Xu, Xiaoqing You, PingPing Zheng, Bing M Zhang, Puja K Gupta, Philip Lavori, Everett Meyer, James L Zehnder
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant...
November 1, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27810331/differences-in-microsatellite-instability-profiles-between-endometrioid-and-colorectal-cancers-a-potential-cause-for-false-negative-results
#13
Yang Wang, Chanjuan Shi, Rosana Eisenberg, Cindy L Vnencak-Jones
Colorectal (CRCs) and endometrioid (EMCs) cancers in patients with Lynch syndrome exhibit microsatellite instability (MSI) detected by PCR or IHC. While both assays are equally sensitive for CRCs, some suggest that MSI has a higher false-negative rate than does IHC in EMCs. We assessed the MSI profiles of 91 EMC and 311 CRC specimens using five mononucleotide repeat markers: BAT25, BAT26, NR21, NR24, and MONO27. EMCs with high MSI (MSI-H) showed a mean left shift of 3 nucleotides (nt), which was significantly different from 6 nt in CRCs...
October 31, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27810330/foxl2-402c-g-mutation-can-be-identified-in-the-circulating-tumor-dna-of-patients-with-adult-granulosa-cell-tumors
#14
Anniina Färkkilä, Melissa K McConechy, Winnie Yang, Aline Talhouk, Ying Ng, Amy Lum, Ryan D Morin, Kevin Bushell, Annika Riska, Jessica N McAlpine, C Blake Gilks, Leila Unkila-Kallio, Mikko Anttonen, David G Huntsman
Adult granulosa cell tumors (AGCTs) of the ovary are molecularly characterized by the pathognomonic FOXL2 402C>G (C134W) mutation. To improve diagnostics and follow-up, we developed a specific digital droplet PCR (ddPCR) assay to detect the FOXL2 mutation in the circulating tumor DNA (ctDNA) of AGCT patients. Optimization of the ddPCR assay was performed using a TaqMan primer/probe with the RainDance RainDrop digital PCR system. The ddPCR assay was performed on circulating cell-free DNA extracted from 120 serial plasma samples collected prospectively from 35 AGCT patients...
October 31, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27771190/emerging-and-future-applications-of-matrix-assisted-laser-desorption-ionization-time-of-flight-maldi-tof-mass-spectrometry-in-the-clinical-microbiology-laboratory-a-report-of-the-association-for-molecular-pathology
#15
Christopher D Doern, Susan M Butler-Wu
The performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) for routine bacterial and yeast identification as well as direct-from-blood culture bottle identification has been thoroughly evaluated in the peer-reviewed literature. Microbiologists are now moving beyond these methods to apply MS to other areas of the diagnostic process. This review discusses the emergence of advanced matrix-assisted laser desorption ionization time-of-flight MS applications, including the identification of filamentous fungi and mycobacteria and the current and future state of antimicrobial resistance testing...
October 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27727019/validation-of-a-clinical-grade-assay-to-measure-donor-derived-cell-free-dna-in-solid-organ-transplant-recipients
#16
Marica Grskovic, David J Hiller, Lane A Eubank, John J Sninsky, Cindy Christopherson, John P Collins, Kathryn Thompson, Mindy Song, Yue S Wang, David Ross, Mitchell J Nelles, James P Yee, Judith C Wilber, Maria G Crespo-Leiro, Susan L Scott, Robert N Woodward
The use of circulating cell-free DNA (cfDNA) as a biomarker in transplant recipients offers advantages over invasive tissue biopsy as a quantitative measure for detection of transplant rejection and immunosuppression optimization. However, the fraction of donor-derived cfDNA (dd-cfDNA) in transplant recipient plasma is low and challenging to quantify. Previously reported methods to measure dd-cfDNA require donor and recipient genotyping, which is impractical in clinical settings and adds cost. We developed a targeted next-generation sequencing assay that uses 266 single-nucleotide polymorphisms to accurately quantify dd-cfDNA in transplant recipients without separate genotyping...
October 7, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27720647/sanger-confirmation-is-required-to-achieve-optimal-sensitivity-and-specificity-in-next-generation-sequencing-panel-testing
#17
Wenbo Mu, Hsiao-Mei Lu, Jefferey Chen, Shuwei Li, Aaron M Elliott
Next-generation sequencing (NGS) has rapidly replaced Sanger sequencing as the method of choice for diagnostic gene-panel testing. For hereditary-cancer testing, the technical sensitivity and specificity of the assay are paramount as clinicians use results to make important clinical management and treatment decisions. There is significant debate within the diagnostics community regarding the necessity of confirming NGS variant calls by Sanger sequencing, considering that numerous laboratories report having 100% specificity from the NGS data alone...
October 4, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27664753/next-generation-sequencing-in-cancer-diagnostics
#18
Christopher L Corless
This commentary highlights the article by Misyura et al that underscores the use of next-generation sequencing platforms for detection and verification of somatic variants.
September 21, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27657456/corrections
#19
(no author information available yet)
No abstract text is available yet for this article.
September 19, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27657455/corrections
#20
(no author information available yet)
No abstract text is available yet for this article.
September 19, 2016: Journal of Molecular Diagnostics: JMD
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