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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/28807814/development-of-a-chromosomal-microarray-test-for-the-detection-of-abnormalities-in-formalin-fixed-paraffin-embedded-products-of-conception-specimens
#1
Troy J Gliem, Umut Aypar
Testing the products of conception (POC) provides information regarding the cause of fetal loss, and helps determine the recurrence risk for future losses and chromosome abnormalities in subsequent pregnancies. Historically, the Mayo Clinic Cytogenetics Laboratory performed targeted fluorescent in situ hybridization (FISH) testing to identify aneuploidy of only certain chromosomes in formalin-fixed, paraffin-embedded (FFPE) POC samples. Chromosomal microarray (CMA) studies utilizing the Affymetrix OncoScan™ FFPE Assay can detect copy number changes across the genome...
August 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28807813/norovirus-loads-in-stool-specimens-of-cancer-patients-with-norovirus-gastroenteritis
#2
Taojun He, Tracy A McMillen, Yuanyuan Qiu, Liang Hua Chen, Xuedong Lu, Xiao-Li Pang, Mini Kamboj, Yi-Wei Tang
In immunocompromised patients with norovirus (NoV) gastroenteritis, the relationship between fecal NoV load and clinical complications has not been examined. In this study, a validated real-time quantitative PCR (qPCR) assay was used to determine viral loads NoV genogroup I and II (GI and GII) in NoV positive stool specimens of cancer patients. A total of 234 specimens from 152 patients were positive for NoV, including 201 of GII and 33 of GI. Geometric mean of logarithmic copies (GMLC) per gram of stool (w/w) of NoV-GII were 9...
August 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28807812/evaluation-and-clinical-validation-of-two-field-deployable-reverse-transcription-insulated-isothermal-pcr-assays-for-the-detection-of-the-middle-east-respiratory-syndrome-coronavirus
#3
Yun Young Go, Yeon-Sook Kim, Shinhye Cheon, Sangwoo Nam, Keun Bon Ku, Meehyein Kim, Nam Hyuk Cho, Hyun Park, Pei-Yu Alison Lee, Yu-Chun Lin, Yun-Long Tsai, Hwa-Tang Thomas Wang, Udeni B R Balasuriya
Middle East respiratory syndrome (MERS) is an emerging zoonotic viral respiratory disease that was first identified in Saudi Arabia in 2012. In 2015, the largest MERS outbreak outside of the Middle East region occurred in the Republic of Korea. The rapid nosocomial transmission of MERS-coronavirus (MERS-CoV) in Korean healthcare settings highlighted the importance and urgent need for a rapid and reliable on-site diagnostic assay to implement effective control and preventive measures. Here, we describe the evaluation and validation of two newly developed reverse transcription-insulated isothermal PCR (RT-iiPCR) methods targeting the ORF1a and upE genes of MERS-CoV...
August 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28807811/clinical-validation-of-a-genome-wide-dna-methylation-assay-for-molecular-diagnosis-of-imprinting-disorders
#4
Erfan Aref-Eshghi, Laila C Schenkel, Hanxin Lin, Cindy Skinner, Peter Ainsworth, Guillaume Paré, Victoria Siu, David Rodenhiser, Charles Schwartz, Bekim Sadikovic
Genomic imprinting involves a DNA methylation-dependent and parent-of-origin-specific regulation of gene expression. Clinical assays for imprinting disorders are genomic locus-, disorder-, and molecular defect-specific. We aimed to clinically validate a genome-wide approach for simultaneous testing of common imprinting disorders in a single assay. Using genome-wide DNA methylation arrays, epigenetic profiles from peripheral blood of patients with Angelman, Prader-Willi, Beckwith-Wiedemann, and Silver-Russell syndrome were compared to a reference cohort of 361 unaffected individuals...
August 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28802831/validation-of-a-targeted-rna-sequencing-assay-for-kinase-fusion-detection-in-solid-tumors
#5
Julie W Reeser, Dorrelyn Martin, Jharna Miya, Esko A Kautto, Ezra Lyon, Eliot Zhu, Michele R Wing, Amy Smith, Matthew Reeder, Eric Samorodnitsky, Hannah Parks, Karan R Naik, Joseph Gozgit, Nicholas Nowacki, Kurtis D Davies, Marileila Varella-Garcia, Lianbo Yu, Aharon G Freud, Joshua Coleman, Dara L Aisner, Sameek Roychowdhury
Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93...
August 8, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28743024/a-method-to-evaluate-the-quality-of-clinical-gene-panel-sequencing-data-for-single-nucleotide-variant-detection
#6
Chung Lee, Joon S Bae, Gyu H Ryu, Nayoung K D Kim, Donghyun Park, Jongsuk Chung, Sungkyu Kyung, Je-Gun Joung, Hyun-Tae Shin, Seung-Ho Shin, Younglan Kim, Byung S Kim, Hojun Lee, Kyoung-Mee Kim, Jung-Sun Kim, Woong-Yang Park, Dae-Soon Son
Customized gene-panel tests, based on next-generation sequencing, have demonstrated their usefulness in a plethora of clinical settings. As with other clinical diagnostic techniques, gene-panel sequencing for clinical purposes requires precise quality control (QC) measures to ensure its reliability. Only detected variants are currently recorded in clinical reports; however, identifying whether a nondetected variant is a true or false negative is regarded essential in a clinical setting and, thus, a comprehensive QC measure is in demand...
July 22, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28736296/a-new-targeted-cftr-mutation-panel-based-on-next-generation-sequencing-technology
#7
Marco Lucarelli, Luigi Porcaro, Alice Biffignandi, Lucy Costantino, Valentina Giannone, Luisella Alberti, Sabina Maria Bruno, Carlo Corbetta, Erminio Torresani, Carla Colombo, Manuela Seia
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we tested the clinical and laboratory validity of an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population...
July 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28736295/digital-multiplex-ligation-dependent-probe-amplification-for-detection-of-key-copy-number-alterations-in-t-and-b-cell-lymphoblastic-leukemia
#8
Anne Benard-Slagter, Ilse Zondervan, Karel de Groot, Farzaneh Ghazavi, Virinder Sarhadi, Pieter Van Vlierberghe, Barbara De Moerloose, Claire Schwab, Kim Vettenranta, Christine J Harrison, Sakari Knuutila, Jan Schouten, Tim Lammens, Suvi Savola
Recurrent and clonal genetic alterations are characteristic of different subtypes of T- and B-cell lymphoblastic leukemia (ALL), and several subtypes are strong independent predictors of patient outcome. A next-generation sequencing-based multiplex ligation-dependent probe amplification variant (digitalMLPA) has been developed enabling simultaneous detection of copy number alterations (CNAs) of up to 1000 target sequences. This novel digitalMLPA assay was designed and optimized to detect CNAs of 56 key target genes and regions in ALL...
July 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28732216/development-of-hla-b-57-01-genotyping-real-time-pcr-with-optimized-hydrolysis-probe-design
#9
Hou-Sung Jung, Gregory J Tsongalis, Joel A Lefferts
HLA-B*57:01 genotyping before abacavir (ABC) administration is a standard of care to avoid ABC-driven hypersensitivity reactions. Several HLA-B*57:01 tests have been developed, each with advantages and disadvantages. Some have limited accuracy, require special instrumentation, and/or are labor intensive and expensive. We developed a novel hydrolysis probe-based real-time PCR method of HLA-B*57:01 genotyping. Primer and probes were designed based on published sequence variations in exon 3 of HLA-B that distinguish HLA-B*57:01 from ABC-insensitive alleles such as HLA-B*57:03 and HLA-B*58:01...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28732215/a-method-for-next-generation-sequencing-of-paired-diagnostic-and-remission-samples-to-detect-mitochondrial-dna-mutations-associated-with-leukemia
#10
Ilaria S Pagani, Chung H Kok, Verity A Saunders, Mark B Van der Hoek, Susan L Heatley, Anthony P Schwarer, Christopher N Hahn, Timothy P Hughes, Deborah L White, David M Ross
Somatic mitochondrial DNA (mtDNA) mutations have been identified in many human cancers, including leukemia. To identify somatic mutations, it is necessary to have a control tissue from the same individual for comparison. When patients with leukemia achieve remission, the remission peripheral blood may be a suitable and easily accessible control tissue, but this approach has not previously been applied to the study of mtDNA mutations. We have developed and validated a next-generation sequencing approach for the identification of leukemia-associated mtDNA mutations in 26 chronic myeloid leukemia patients at diagnosis using either nonhematopoietic or remission blood samples as the control...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28732214/crispr-cas9-technology-based-xenograft-tumors-as-candidate-reference-materials-for-multiple-eml4-alk-rearrangements-testing
#11
Rongxue Peng, Rui Zhang, Guigao Lin, Xin Yang, Ziyang Li, Kuo Zhang, Jiawei Zhang, Jinming Li
The echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (EML4-ALK) rearrangement is an important biomarker that plays a pivotal role in therapeutic decision making for non-small-cell lung cancer (NSCLC) patients. Ensuring accuracy and reproducibility of EML4-ALK testing by fluorescence in situ hybridization, immunohistochemistry, RT-PCR, and next-generation sequencing requires reliable reference materials for monitoring assay sensitivity and specificity...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28732213/comparison-of-blood-collection-tubes-from-three-different-manufacturers-for-the-collection-of-cell-free-dna-for-liquid-biopsy-mutation-testing
#12
Christina Alidousty, Danielle Brandes, Carina Heydt, Svenja Wagener, Maike Wittersheim, Stephan Christian Schäfer, Barbara Holz, Sabine Merkelbach-Bruse, Reinhard Büttner, Jana Fassunke, Anne Maria Schultheis
The improvement in sensitive techniques has allowed the detection of tumor-specific aberrations in circulating tumor (ct) DNA. Amplification-refractory mutation system PCR has been used for the analysis of ctDNA to detect resistance-causing mutations in the epidermal growth factor receptor gene (eg, EGFR T790M) in lung cancer patients. So far, Streck tubes have been widely used as standard blood collection tubes. Here, we compared blood collection tubes manufactured by Streck with tubes from Roche and Qiagen regarding their utility in stabilizing ctDNA in plasma samples...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28727985/comparative-study-and-analytical-verification-of-pcr-methods-for-the-diagnosis-of-congenital-chagas-disease
#13
Carolina Inés Cura, Juan Carlos Ramírez, Marcelo Rodríguez, Constanza Lopez-Albízu, Lucía Irazu, Karenina Scollo, Sergio Sosa-Estani
Congenital infection is currently the first cause of new cases of Chagas disease in Argentina and nonendemic areas worldwide. Its diagnosis is of utmost importance to guarantee curative treatment. To improve such diagnosis, a transfer process of PCR tests to the national laboratory network has been initiated. We performed a comparative study of four PCR assays [two end-point PCR and two duplex real-time quantitative PCR (qPCR) procedures] to detect Trypanosoma cruzi DNA in blood samples. Because satellite DNA and kinetoplastid DNA qPCR methods have the best performance and the use of two different molecular targets for confirmatory purposes has been recommended, these methods selected to perform the transfer process and, in consequence, subjected to an analytical verification protocol based on international guidelines...
July 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28727984/gba-analysis-in-next-generation-era-pitfalls-challenges-and-possible-solutions
#14
Stefania Zampieri, Silvia Cattarossi, Bruno Bembi, Andrea Dardis
Mutations in the gene encoding the lysosomal enzyme acid β-glucosidase (GBA) are responsible for Gaucher disease and represent the main genetic risk factor for developing Parkinson disease. In past years, next-generation sequencing (NGS) technology has been applied for the molecular analysis of the GBA gene, both as a single gene or as part of gene panels. However, the presence of complex gene-pseudogene rearrangements, resulting from the presence of a highly homologous pseudogene (GBAP1) located downstream of the GBA gene, makes NGS analysis of GBA challenging...
July 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#15
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28623087/highly-multiplex-real-time-pcr-based-screening-for-blood-borne-pathogens-on-an-openarray-platform
#16
Elena Grigorenko, Carolyn Fisher, Sunali Patel, Valerie Winkelman, Phillip Williamson, Caren Chancey, Germán Añez, Maria Rios, Victoria Majam, Sanjai Kumar, Robert Duncan
Molecular diagnostics are increasingly used in the blood bank industry. A device that can combine simultaneous detection of multiple targets with the flexibility of inclusion of emerging pathogens is desirable for testing blood products. A highly multiplexed blood-borne pathogen panel (BBPP) using dual-label probe chemistry (TaqMan assays) was developed for simultaneous detection and discrimination of 17 viral pathogens in human plasma samples and 13 bacterial and protozoan pathogens in human blood samples on the OpenArray platform...
June 12, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28645444/npm1-for-mrd-droplet-like-it-s-hot
#17
Gerald B W Wertheim, Adam Bagg
This commentary highlights the article by Mencia-Trinchant et al that describes a novel digital PCR assay for sensitive detection of minimal residual disease in NPM1 mutated acute myeloid leukemia.
July 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28552549/pheoseq-a-targeted-next-generation-sequencing-assay-for-pheochromocytoma-and-paraganglioma-diagnostics
#18
Maria Currás-Freixes, Elena Piñeiro-Yañez, Cristina Montero-Conde, María Apellániz-Ruiz, Bruna Calsina, Veronika Mancikova, Laura Remacha, Susan Richter, Tonino Ercolino, Natalie Rogowski-Lehmann, Timo Deutschbein, María Calatayud, Sonsoles Guadalix, Cristina Álvarez-Escolá, Cristina Lamas, Javier Aller, Julia Sastre-Marcos, Conxi Lázaro, Juan C Galofré, Ana Patiño-García, Amparo Meoro-Avilés, Judith Balmaña-Gelpi, Paz De Miguel-Novoa, Milagros Balbín, Xavier Matías-Guiu, Rocío Letón, Lucía Inglada-Pérez, Rafael Torres-Pérez, Juan M Roldán-Romero, Cristina Rodríguez-Antona, Stephanie M J Fliedner, Giuseppe Opocher, Karel Pacak, Esther Korpershoek, Ronald R de Krijger, Laurent Vroonen, Massimo Mannelli, Martin Fassnacht, Felix Beuschlein, Graeme Eisenhofer, Alberto Cascón, Fátima Al-Shahrour, Mercedes Robledo
Genetic diagnosis is recommended for all pheochromocytoma and paraganglioma (PPGL) cases, as driver mutations are identified in approximately 80% of the cases. As the list of related genes expands, genetic diagnosis becomes more time-consuming, and targeted next-generation sequencing (NGS) has emerged as a cost-effective tool. This study aimed to optimize targeted NGS in PPGL genetic diagnostics. A workflow based on two customized targeted NGS assays was validated to study the 18 main PPGL genes in germline and frozen tumor DNA, with one of them specifically directed toward formalin-fixed paraffin-embedded tissue...
July 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28525762/minimal-residual-disease-monitoring-of-acute-myeloid-leukemia-by-massively-multiplex-digital-pcr-in-patients-with-npm1-mutations
#19
Nuria Mencia-Trinchant, Yang Hu, Maria Antonina Alas, Fatima Ali, Bas J Wouters, Sangmin Lee, Ellen K Ritchie, Pinkal Desai, Monica L Guzman, Gail J Roboz, Duane C Hassane
The presence of minimal residual disease (MRD) is widely recognized as a powerful predictor of therapeutic outcome in acute myeloid leukemia (AML), but methods of measurement and quantification of MRD in AML are not yet standardized in clinical practice. There is an urgent, unmet need for robust and sensitive assays that can be readily adopted as real-time tools for disease monitoring. NPM1 frameshift mutations are an established MRD marker present in half of patients with cytogenetically normal AML. However, detection is complicated by the existence of hundreds of potential frameshift insertions, clonal heterogeneity, and absence of sequence information when the NPM1 mutation is identified using capillary electrophoresis...
July 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28502727/concordance-between-research-sequencing-and-clinical-pharmacogenetic-genotyping-in-the-emerge-pgx-study
#20
Laura J Rasmussen-Torvik, Berta Almoguera, Kimberly F Doheny, Robert R Freimuth, Adam S Gordon, Hakon Hakonarson, Jared B Hawkins, Ammar Husami, Lynn C Ivacic, Iftikhar J Kullo, Michael D Linderman, Teri A Manolio, Aniwaa Owusu Obeng, Renata Pellegrino, Cynthia A Prows, Marylyn D Ritchie, Maureen E Smith, Sarah C Stallings, Wendy A Wolf, Kejian Zhang, Stuart A Scott
There has been extensive debate about both the necessity of orthogonal confirmation of next-generation sequencing (NGS) results in Clinical Laboratory Improvement Amendments-approved laboratories and return of research NGS results to participants enrolled in research studies. In eMERGE-PGx, subjects underwent research NGS using PGRNseq and orthogonal targeted genotyping in clinical laboratories, which prompted a comparison of genotyping results between platforms. Concordance (percentage agreement) was reported for 4077 samples tested across nine combinations of research and clinical laboratories...
July 2017: Journal of Molecular Diagnostics: JMD
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