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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/28867605/high-throughput-and-sensitive-quantification-of-circulating-tumor-dna-by-microfluidic-based-multiplex-pcr-and-next-generation-sequencing
#1
Yinghui Guan, Oleg Mayba, Thomas Sandmann, Shan Lu, Younjeong Choi, Walter C Darbonne, Vincent Leveque, Lisa Ryner, Eric Humke, Nga Wan Rachel Tam, Sundari Sujathasarma, Anna Cheung, Richard Bourgon, Mark R Lackner, Yulei Wang
Circulating tumor DNA (ctDNA) has potential to serve as a biomarker for noninvasive monitoring of treatment response and disease progression. However, broad clinical applicability of ctDNA has been limited by the low sensitivity, throughput and patient coverage offered by existing ctDNA detection methods. Here we report the adaptation and characterization of the MMP-Seq technology for high-throughput and sensitive quantitation of ctDNA. A multiplex PCR preamplification (PreAmp) step was developed and incorporated into the MMP-seq workflow to enable low input ctDNA analysis with enhanced sensitivity...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28867604/characterization-and-genomic-localization-of-a-smad4-processed-pseudogene
#2
Christopher M Watson, Nick Camm, Laura A Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F Markham, Ian M Carr, Ruth Charlton, David T Bonthron
Like many clinical diagnostic laboratories, we undertake routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness against rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified five that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6. More detailed analysis indicated that these individuals all carried one copy of a SMAD4 processed gene...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28867603/molecular-signatures-for-tumor-classification-an-analysis-of-tcga-data
#3
Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape
Cancer classification in the clinic is primarily based on histological analysis in the proper clinical context, often supplemented by immunohistochemical and molecular studies. Recent genomic studies have shown the potential of integrated multiomics platforms for molecular classification. We performed unsupervised analyses of molecular platforms in TCGA data (n = 6216 samples) in comparison with tumor type. Our data showed that mRNA signatures and DNA methylation signatures mapped to histological diagnosis with high accuracy (95% and 88%, respectively) as individual platforms...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28866070/next-generation-sequencing-a-novel-approach-to-distinguish-multifocal-primary-lung-adenocarcinomas-from-intrapulmonary-metastases
#4
Snehal B Patel, Wendy Kadi, Ann E Walts, Alberto M Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, Jean Lopategui
Distinguishing between multiple lung primaries and intrapulmonary metastases is imperative for accurate staging. The American Joint Committee on Cancer (AJCC) criteria are routinely used for this purpose but can yield equivocal conclusions. We evaluated whether next generation sequencing (NGS) using the 50 gene AmpliSeq Cancer Hotspot Panel v2 can be used to facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). Primary-metastatic pairs showed high mutational concordance: Seven pairs shared mutations, and 1 was concordant for having no mutations...
August 30, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28860020/triplex-hrm-assay-for-the-simultaneous-assessment-of-il28b-rs12979860-abcb11-rs2287622-and-rnf7-rs16851720-genotypes-in-chronic-hepatitis-c-patients
#5
Elena Luminita Enache, Anca Sin, Liviu Sorin Enache, Ligia Bancu
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IL28B rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classical therapy...
August 28, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28822785/next-generation-sequencing-based-detection-of%C3%A2-germline-copy-number-variations-in-brca1-brca2-validation-of-a-one-step-diagnostic-work-flow
#6
Ane Y Schmidt, Thomas V O Hansen, Lise B Ahlborn, Lars Jønson, Christina W Yde, Finn C Nielsen
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2...
August 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#7
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) approximately >50 bp. Because these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required, resulting in increased labor, costs, and turnaround times...
August 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818679/improved-assays-for-agg-interruptions-in-fragile-x-premutation-carriers
#8
Bruce E Hayward, Karen Usdin
The learning disability fragile X syndrome results from the presence of >200 CGG/CCG-repeats in exon 1 of the X-linked gene FMR1. Such alleles arise by expansion from maternally transmitted FMR1 premutation alleles, alleles having 55 to 200 repeats. Expansion risk is directly related to maternal repeat number. However, AGG interruptions to the repeat tract are important modifiers of expansion risk. Thus, the ability to identify such interruptions is crucial for the appropriate genetic counseling of women who are premutation carriers...
August 14, 2017: Journal of Molecular Diagnostics: JMD
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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