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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/28087349/combination-of-multiple-ligation-dependent-probe-amplification-and-illumina-miseq-amplicon-sequencing-for-tsc1-tsc2-gene-analyses-in-patients-with-tuberous-sclerosis-complex
#1
Nur Farrah Dila Ismail, Abdul Qawee Rani, Nik Mohd Ariff Nik Abdul Malik, Chia Boon Hock, Siti Nabilahuda Mohd Azlan, Salmi Abdul Razak, Wee Teik Keng, Lock Hock Ngu, Abdul Rashid Silawati, Nor AzniYahya, Narazah Mohd Yusoff, Teguh Haryo Sasongko, Zabidi Azhar Mohd Hussin
Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous disorder characterized by tumor growth in multiple organs and caused by mutations in either TSC1 or TSC2 genes. Because of their relatively large genomic sizes, absence of hotspots, and common type of mutations, mutation detection in TSC1 and TSC2 genes has been challenging. We devised a combination of multiple ligation-dependent probe amplification (MLPA) and amplicon sequencing (AS) to simplify the detection strategy, yet we come up with reasonably high detection rate...
January 10, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28081922/application-of-nuclear-magnetic-resonance-to-detect-toxigenic-clostridium-difficile-from-stool-specimens-a-proof-of-concept
#2
Paul Yang, Sara Hash, Katherine Park, Charlene Wong, Loganathan Doraisamy, Jonas Petterson, Cathy A Petti, Pamela M Ward, Seung H Lee, Suresh Menon, Rosemary C She
We evaluated the performance of an early prototype core molecular mirroring nuclear magnetic resonance detection platform (Mentor-100) to detect toxigenic Clostridium difficile from stool. This technology uses customized nanoparticles bound to target specific oligonucleotide probes that form binaries in the presence of nucleic acid from the target microorganism. Liquid patient stool specimens were seeded with C. difficile or other Clostridium species to determine the analytical sensitivity and specificity. Samples underwent nucleic acid extraction and target amplification with probes conjugated with iron nanoparticles...
January 9, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28042970/targeted-next-generation-sequencing-in-molecular-subtyping-of-lower-grade-diffuse-gliomas-application-of-the-world-health-organization-s-2016-revised-criteria-for-cns-tumors
#3
Jamal H Carter, Samantha N McNulty, Patrick J Cimino, Catherine E Cottrell, Jonathan W Heusel, Katinka A Vigh-Conrad, Eric J Duncavage
The 2007 World Health Organization Classification of Tumours of the Central Nervous System classifies lower-grade gliomas [LGGs (grades II to III diffuse gliomas)] morphologically as astrocytomas or oligodendrogliomas, and tumors with unclear ambiguous morphology as oligoastrocytomas. The World Health Organization's newly released (2016) classification incorporates molecular data. A single, targeted next-generation sequencing (NGS) panel was used for detecting single-nucleotide variation and copy number variation in 50 LGG cases originally classified using the 2007 criteria, including 36 oligoastrocytomas, 11 oligodendrogliomas, 2 astrocytomas, and 1 LGG not otherwise specified...
December 30, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28041871/development-and-validation-of-a-preanalytic-procedure-for-performing-the-cobas-hpv-test-in-surepath-preservative-fluid
#4
Mark D Krevolin, David Hardy, Jim Pane, Shagufta Aslam, Catherine M Behrens
The formation of chemical cross-links between nucleic acids and proteins in formalin-containing media presents challenges for human papillomavirus (HPV) testing of cervical samples collected in SurePath Preservative Fluid. A preanalytic process involving addition of a nucleophilic buffer and heating the sample to 120°C was developed to reverse the effects of cross-linking and improve nucleic acid accessibility for the cobas HPV Test in SurePath. Cycle threshold (CT) values for cobas HPV detection were evaluated over time and various temperatures, and mean CT differences between pretreated and both untreated SurePath samples and those collected in PreservCyt were assessed...
December 29, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28041870/the-effect-of-nucleic-acid-extraction-platforms-and-sample-storage-on-the-integrity-of-viral-rna-for-use-in-whole-genome-sequencing
#5
Kuiama Lewandowski, Andrew Bell, Rory Miles, Simon Carne, David Wooldridge, Carmen Manso, Nicola Hennessy, Daniel Bailey, Steven T Pullan, Saheer Gharbia, Richard Vipond
Extraction of viral RNA and the storage of sample material are extremely important factors in the detection and whole genome sequencing (WGS) of viral pathogens. Although PCR-based detection methods focus on small amplicons, viral WGS applications require RNA of high quality and integrity for adequate sequence coverage and depth. This study examined the fitness of one manual and four automated RNA extraction platforms commonly used in diagnostic laboratories for use in metagenomic sequencing, how the practice of storing sample material in Qiagen buffer AVL before extraction affected the integrity of viral RNA and its suitability for use in amplicon-based WGS methods, and how the addition of Triton X-100 to buffer AVL affected the capability of the extraction platforms and the integrity of viral RNA in stored samples...
December 29, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28027945/next-generation-assessment-of-erbb2-human%C3%A2-epidermal-growth-factor-receptor-2-amplification-status-clinical-validation-in-the-context-of-a-hybrid-capture-based-comprehensive-solid-tumor-genomic-profiling-assay
#6
Dara S Ross, Ahmet Zehir, Donavan T Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F Hechtman, Yelena Y Janjigian, Britta Weigelt, Pedram Razavi, David M Hyman, José Baselga, Michael F Berger, Marc Ladanyi, Maria E Arcila
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to patients' treatment plans. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling...
December 24, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28024947/clinical-genomic-profiling-of-a-diverse-array-of-oncology-specimens-at-a-large-academic-cancer-center-identification-of-targetable-variants-and-experience-with-reimbursement
#7
Anthony N Sireci, Vimla S Aggarwal, Andrew T Turk, Tatyana Gindin, Mahesh M Mansukhani, Susan J Hsiao
Large cancer panels are being increasingly used in the practice of precision medicine to generate genomic profiles of tumors with the goal of identifying targetable variants and guiding eligibility for clinical trials. To facilitate identification of mutations in a broad range of solid and hematological malignancies, a 467-gene oncology panel (Columbia Combined Cancer Panel) was developed in collaboration with pathologists and oncologists and is currently available and in use for clinical diagnostics. Herein, we share our experience with this testing in an academic medical center...
December 23, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28017569/a-targeted-high-throughput-next-generation-sequencing-panel-for-clinical-screening-of-mutations-gene-amplifications-and-fusions-in-solid-tumors
#8
Rajyalakshmi Luthra, Keyur P Patel, Mark J Routbort, Russell R Broaddus, Jonathan Yau, Crystal Simien, Wei Chen, David Z Hatfield, L Jeffrey Medeiros, Rajesh R Singh
Clinical next-generation sequencing (NGS) assay choice requires careful consideration of panel size, inclusion of appropriate markers, ability to detect multiple genomic aberration types, compatibility with low quality and quantity of nucleic acids, and work flow feasibility. Herein, in a high-volume clinical molecular diagnostic laboratory, we have validated a targeted high-multiplex PCR-based NGS panel (OncoMine Comprehensive Assay) coupled with high-throughput sequencing using Ion Proton sequencer for routine screening of solid tumors...
December 22, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28012713/accurate-quantification-of-t-cells-by-measuring-loss-of-germline-t-cell-receptor-loci-with-generic-single-duplex-droplet-digital-pcr-assays
#9
Willem H Zoutman, Rogier J Nell, Mieke Versluis, Debby van Steenderen, Rajshri N Lalai, Jacoba J Out-Luiting, Mark J de Lange, Maarten H Vermeer, Anton W Langerak, Pieter A van der Velden
Quantifying T cells accurately in a variety of tissues of benign, inflammatory, or malignant origin can be of great importance in a variety of clinical applications. Flow cytometry and immunohistochemistry are considered to be gold-standard methods for T-cell quantification. However, these methods require fresh, frozen, or fixated cells and tissue of a certain quality. In addition, conventional and droplet digital PCR (ddPCR), whether followed by deep sequencing techniques, have been used to elucidate T-cell content by focusing on rearranged T-cell receptor (TCR) genes...
December 21, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27993330/standards-and-guidelines-for-the-interpretation-and-reporting-of-sequence-variants-in-cancer-a-joint-consensus-recommendation-of-the-association-for-molecular-pathology-american-society-of-clinical-oncology-and-college-of-american-pathologists
#10
REVIEW
Marilyn M Li, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, Cindy L Vnencak-Jones, Daynna J Wolff, Anas Younes, Marina N Nikiforova
Widespread clinical laboratory implementation of next-generation sequencing-based cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencing-based cancer testing and establish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was convened by the Association for Molecular Pathology with liaison representation from the American College of Medical Genetics and Genomics, American Society of Clinical Oncology, and College of American Pathologists...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27993329/an-mrna-gene-expression-based-signature-to-identify-fgfr1-amplified-estrogen-receptor-positive-breast-tumors
#11
Jingqin Luo, Shuzhen Liu, Samuel Leung, Alejandro A Gru, Yu Tao, Jeremy Hoog, Julie Ho, Sherri R Davies, D Craig Allred, Andrea L Salavaggione, Jacqueline Snider, Elaine R Mardis, Torsten O Nielsen, Matthew J Ellis
Fibroblast growth factor receptor 1 (FGFR1) amplification drives poor prognosis and is an emerging therapeutic target. We sought to construct a multigene mRNA expression signature to efficiently identify FGFR1-amplified estrogen receptor-positive (ER(+)) breast tumors. Five independent breast tumor series were analyzed. Genes discriminative for FGFR1 amplification were screened transcriptome-wide by receiver operating characteristic analyses. The METABRIC series was leveraged to construct/evaluate four approaches to signature composition...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27993328/diagnostic-quality-assurance-pilot-a-model-to-demonstrate-comparative-laboratory-test-performance-with-an-oncology-companion-diagnostic-assay
#12
EDITORIAL
Barbara Zehnbauer, Catherine Lofton-Day, John Pfeifer, Elizabeth Shaughnessy, Lindee Goh
This Editorial highlights a model demonstrating laboratory test performance with a companion diagnostic assay.
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27939865/pitx2-dna-methylation-as-biomarker-for-individualized-risk-assessment-of-prostate-cancer-in-core-biopsies
#13
Barbara Uhl, Heidrun Gevensleben, Yuri Tolkach, Verena Sailer, Michael Majores, Maria Jung, Sebastian Meller, Johannes Stein, Jörg Ellinger, Dimo Dietrich, Glen Kristiansen
Hypermethylation of the paired-like homeodomain transcription factor 2 (PITX2) gene is a strong predictor of the risk of biochemical recurrence in patients with prostate cancer (PCa) after radical prostatectomy. We investigate whether PITX2 methylation is feasible for individualized risk assessment in prostate core biopsies before surgery. A quantitative, methylation-specific real-time PCR was used to measure PITX2 in three cohorts: i) matched samples of neoplastic and nonneoplastic tissue from 24 patients with PCa, ii) a well-characterized cohort of 300 patients with PCa after radical prostatectomy, and iii) core biopsy specimens from 32 patients with PCa and 31 patients with benign prostatic disease...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27916435/analytical-validation-of-androgen-receptor-splice-variant-7-detection-in-a-clinical-laboratory-improvement-amendments-clia-laboratory-setting
#14
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...
January 2017: 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
#15
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%...
January 2017: 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
#16
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)...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863262/in-silico-proficiency-testing-for-clinical-next-generation-sequencing
#17
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...
January 2017: 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
#18
Cristina Jiménez, María Jara-Acevedo, Luis A Corchete, David Castillo, Gonzalo R Ordóñez, María E Sarasquete, Noemí Puig, Joaquín Martínez-López, María I Prieto-Conde, María García-Álvarez, María C 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...
January 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863260/applications-of-dna-based-liquid-biopsy-for-central-nervous-system-neoplasms
#19
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...
January 2017: 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
#20
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...
January 2017: Journal of Molecular Diagnostics: JMD
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