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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/30165206/noninvasive-molecular-monitoring-in-multiple-myeloma-patients-using-cell-free-tumor-dna-a-pilot-study
#1
Giulia Biancon, Silvia Gimondi, Antonio Vendramin, Cristiana Carniti, Paolo Corradini
Novel treatments for multiple myeloma (MM) have increased rates of complete response, raising interest in more accurate methods to evaluate residual disease. Cell-free tumor DNA (cfDNA) analysis may represent a minimally invasive approach complementary to multiparameter flow cytometry (MFC) and molecular methods on bone marrow aspirates. A sequencing approach using the Ion Torrent Personal Genome Machine was applied to identify clonal IGH gene rearrangements in tumor plasma cells (PCs) and in serial plasma samples of 25 patients with MM receiving second-line therapy...
August 28, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30165205/a-head-to-head-analytical-comparison-of-cobas-4800-hpv-papillocheck-hpv-screening-and-lmnx-genotyping-kit-hpv-gp-for-detection-of-human-papillomavirus-dna-in-cervical-and-cervicovaginal-swabs
#2
Hana Jaworek, Vladimira Koudelakova, Jiri Drabek, Jana Vrbkova, Blazena Zborilova, Ivana Oborna, Jana Brezinova, Radim Marek, Karel Huml, Peter Vanek, Marian Hajduch
High-risk human papillomavirus (hrHPV) infection is a cause of cervical cancer development. The addition of hrHPV testing to cervical cancer screening and monitoring of cervical intraepithelial neoplasia treatment improves the efficacy of screening and treatment, respectively. Self-sampling for hrHPV testing seems a promising tool for increasing patient participation in cervical cancer screening. In this project, 1198 cervical swabs obtained by physicians and 176 cervicovaginal swabs obtained by self-sampling (not collected in parallel) were analyzed for the presence of 14 hrHPV genotypes using three commercially available assays in comparison...
August 28, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30165204/effects-of-collection-and-processing-procedures-on-plasma-circulating-cell-free-dna-from-cancer-patients
#3
Bente Risberg, Dana W Y Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James Morris, Vincent Plagnol, Nitzan Rosenfeld, Carlos Caldas, James D Brenton, Davina Gale
Circulating tumor DNA (ctDNA) offers new opportunities for noninvasive cancer management. Detecting ctDNA in plasma is challenging because it constitutes only a minor fraction of the total cell-free DNA (cfDNA). Pre-analytical factors affect cfDNA levels contributed from leukocyte lysis, hence the ability to detect low-frequency mutant alleles. This study investigates the effects of the delay in processing, storage temperatures, different blood collection tubes, centrifugation protocols, and sample shipment on cfDNA levels...
August 28, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30142445/diagnostic-targeted-sequencing-panel-for-hepatocellular-carcinoma-genomic-screening
#4
Viola Paradiso, Andrea Garofoli, Nadia Tosti, Manuela Lanzafame, Valeria Perrina, Luca Quagliata, Matthias S Matter, Stefan Wieland, Markus H Heim, Salvatore Piscuoglio, Charlotte K Y Ng, Luigi M Terracciano
Commercially available targeted panels miss genomic regions frequently altered in hepatocellular carcinoma (HCC). We sought to design and benchmark a sequencing assay for genomic screening in HCC. We designed an AmpliSeq custom panel targeting all exons of 33 protein-coding and two long noncoding RNA genes frequently mutated in HCC, TERT promoter, and nine genes with frequent copy number alterations. By using this panel, the profiling of DNA from fresh-frozen (n = 10, 1495×) and/or formalin-fixed, paraffin-embedded (FFPE) tumors with low-input DNA (n = 36, 530×) from 39 HCCs identified at least one somatic mutation in 90% of the cases...
August 22, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30138725/analytical-validation-of-clinical-whole-genome-and-transcriptome-sequencing-of-patient-derived-tumors-clinical-application-of-whole-genome-sequencing-for-reporting-targetable-variants-in-cancer
#5
Kazimierz O Wrzeszczynski, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Heather Geiger, Dina Manaa, Ferrah London, Dino Robinson, Xiaolan Fang, David Lin, Michelle F Lamendola-Essel, Depinder Khaira, Esra Dikoglu, Anne-Katrin Emde, Nicolas Robine, Minita Shah, Kanika Arora, Olca Basturk, Umesh Bhanot, Alex Kentsis, Mahesh M Mansukhani, Govind Bhagat, Vaidehi Jobanputra
We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded on for establishing performance validation applicable to whole-genome sequencing...
August 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30138727/clinical-significance-of-dna-variants-in-chronic-myeloid-neoplasms-a-report-of-the-association-for-molecular-pathology
#6
REVIEW
Rebecca F McClure, Mark D Ewalt, Jennifer Crow, Robyn L Temple-Smolkin, Mrudula Pullambhatla, Rachel Sargent, Annette S Kim
To address the clinical relevance of small DNA variants in chronic myeloid neoplasms (CMNs), an Association for Molecular Pathology Working Group comprehensively reviewed published literature, summarized key findings that support clinical utility, and defined critical gene inclusions for high-throughput sequencing testing panels. This review highlights the biological complexity of CMNs [including myelodysplastic syndromes, myeloproliferative neoplasms, entities with overlapping features (myelodysplastic syndromes/myeloproliferative neoplasms), and systemic mastocytosis], the genetic heterogeneity within diagnostic categories, and similarities between apparently disparate diagnostic entities...
August 20, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30138726/validation-of-a-long-read-pcr-assay-for-sensitive-detection-and-sizing-of-c9orf72-hexanucleotide-repeat-expansions
#7
EunRan Suh, Kaitlyn Grando, Vivianna M Van Deerlin
A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal degeneration. Accurate determination and quantitation of the repeat length is critical in both clinical and research settings. However, because of the complexity of the C9orf72 expansion with high GC content, large size of repeats, and high rate of insertions/deletions (indels) and sequence variations in the flanking regions, molecular genetic analysis of the locus is challenging...
August 20, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30138724/oncokids-a-comprehensive-next-generation-sequencing-panel-for-pediatric-malignancies
#8
Matthew C Hiemenz, Dejerianne G Ostrow, Tracy M Busse, Jonathan Buckley, Dennis T Maglinte, Moiz Bootwalla, James Done, Jianling Ji, Gordana Raca, Alex Ryutov, Xinjie Xu, Chao Jie Zhen, Jeffrey M Conroy, Florette K Hazard, Joshua L Deignan, Beverly Rogers, Amanda L Treece, David M Parham, Xiaowu Gai, Alexander R Judkins, Timothy J Triche, Jaclyn A Biegel
The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes...
August 20, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30096382/high-throughput-copy-number-profiling-by-digital-multiplex-ligation-dependent-probe-amplification-in-multiple-myeloma
#9
Szabolcs Kosztolanyi, Richard Kiss, Lilit Atanesyan, Ambrus Gango, Karel de Groot, Maryvonne Steenkamer, Pal Jakso, Andras Matolcsy, Bela Kajtar, Laszlo Pajor, Karoly Szuhai, Suvi Savola, Csaba Bodor, Donat Alpar
Multiple myeloma (MM) is a genetically heterogeneous disease with a diverse clinical outcome. Copy number alterations (CNAs), including whole chromosome and subchromosomal gains and losses, are common contributors of the pathogenesis and have demonstrated prognostic impact in MM. We tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA), a novel technique combining MLPA and next-generation sequencing, to detect disease-related CNAs. Copy number status at 371 genomic loci was simultaneously analyzed in 56 diagnostic bone marrow samples, which were also examined by conventional MLPA and interphase fluorescence in situ hybridization (iFISH)...
August 8, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30096381/curating-clinically-relevant-transcripts-for-the-interpretation-of-sequence-variants
#10
Marina T DiStefano, Sarah E Hemphill, Brandon J Cushman, Mark J Bowser, Elizabeth Hynes, Andrew R Grant, Rebecca K Siegert, Andrea M Oza, Michael A Gonzalez, Sami S Amr, Heidi L Rehm, Ahmad N Abou Tayoun
Variant interpretation depends on accurate annotations using biologically relevant transcripts. We have developed a systematic strategy for designating primary transcripts and have applied it to 109 hearing loss-associated genes that were divided into three categories. Category 1 genes (n = 38) had a single transcript; category 2 genes (n = 32) had multiple transcripts, but a single transcript was sufficient to represent all exons; and category 3 genes (n = 38) had multiple transcripts with unique exons...
August 8, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30055348/describing-the-reportable-range-is-important-for-reliable-treatment-decisions-a-multiple-laboratory-study-for-molecular-tumor-profiling-using-next-generation-sequencing
#11
Véronique Tack, Lien Spans, Ed Schuuring, Cleo Keppens, Karen Zwaenepoel, Patrick Pauwels, Jeroen Van Houdt, Elisabeth M C Dequeker
Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. No significant differences in performance were observed between analyses with NGS and traditional techniques...
July 26, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30055350/next-generation-sequencing-using-s1-nuclease-for-poor-quality-formalin-fixed-paraffin-embedded-tumor-specimens
#12
Sung-Min Chun, Chang O Sung, Hyejoon Jeon, Tae-Im Kim, Ji-Young Lee, Whan Park, Yujin Kim, Deokhoon Kim, Se J Jang
Next-generation sequencing (NGS) testing of formalin-fixed, paraffin-embedded (FFPE) tissues is widely used in clinical diagnosis. However, the failure of high-quality DNA library construction, a critical step for NGS, often limits NGS application for FFPE tissues, particularly for old FFPE tissues. The aim was to develop a high-quality DNA library construction method optimized for NGS of FFPE specimens. DNA library construction was developed for FFPE specimens by using S1 nuclease and compared with the Covaris method-the widely accepted DNA library construction protocol...
July 25, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30055349/benchmarking-of-amplicon-based-next-generation-sequencing-panels-combined-with-bioinformatics-solutions-for-germline-brca1-and-brca2-alteration-detection
#13
Julie A Vendrell, Paul Vilquin, Marion Larrieux, Charles Van Goethem, Jérôme Solassol
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs)...
July 25, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29981866/comprehensive-validation-of-cytology-specimens-for-next-generation-sequencing-and-clinical-practice-experience
#14
Agnes Balla, Ken J Hampel, Mukesh K Sharma, Catherine E Cottrell, Nikoletta Sidiropoulos
Biopsy specimens are subjected to an expanding portfolio of assays that regularly include mutation profiling via next-generation sequencing (NGS). Specimens derived via fine-needle aspiration, a common biopsy technique, are subjected to a variety of cytopreparatory methods compared with surgical biopsies that are almost uniformly processed as formalin-fixed, paraffin-embedded tissue. Therefore, the fine-needle aspiration-derived specimens most commonly accepted for molecular analysis are cell blocks (CBs), because they are processed most similarly to surgical biopsy tissue...
July 6, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30146005/laboratory-information-systems-and-instrument-software-lack-basic-functionality-for-molecular-laboratories
#15
Charles Myers, Matthew Swadley, Alexis B Carter
Laboratory information systems (LISs) have some basic functionality necessary for molecular workflow that is glaringly absent. This study determined functionality gaps of LISs in molecular laboratories and the associated impact to workflow, efficiency, and security by collecting anonymous survey data from clinical laboratory professionals. A 34-question survey (30 required + 4 optional) was compiled using an online survey tool. Participants were recruited through several professional molecular society listservs and given 4 weeks to complete the survey...
September 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/30139549/molecular-analysis-of-gene-fusions-in-bone-and-soft-tissue-tumors-by-anchored-multiplex-pcr-based-targeted-next-generation-sequencing
#16
Suk Wai Lam, Anne-Marie Cleton-Jansen, Arjen H G Cleven, Dina Ruano, Tom van Wezel, Karoly Szuhai, Judith V M G Bovée
Molecular assays for translocation detection in bone and soft tissue tumors have gradually been incorporated into routine diagnostics. However, conventional methods such as fluorescence in situ hybridization (FISH) and reverse transcriptase-PCR come with several drawbacks. In this study, the applicability of a novel technique termed anchored multiplex PCR (AMP) for next-generation sequencing (NGS), using the Archer FusionPlex Sarcoma kit, aimed at 26 genes, was evaluated and compared with FISH and reverse transcriptase-PCR...
September 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29981867/multiple-ways-to-detect-idh2-mutations-in-angioimmunoblastic-t-cell-lymphoma-from-immunohistochemistry-to-next-generation-sequencing
#17
Aurélie Dupuy, François Lemonnier, Virginie Fataccioli, Nadine Martin-Garcia, Cyrielle Robe, Romain Pelletier, Elsa Poullot, Anissa Moktefi, Karima Mokhtari, Marie C Rousselet, Alexandra Traverse-Glehen, Richard Delarue, Olivier Tournilhac, Marie H Delfau-Larue, Corinne Haioun, Nicolas Ortonne, Christiane Copie-Bergman, Laurence de Leval, Anaïs Pujals, Philippe Gaulard
Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma associated with chemoresistance and a poor prognosis. Various nonsynonymous mutations in the R172 residue of IDH2 are present in 20% to 30% of AITL patients. In addition to their diagnostic value, these mutations are potentially targetable, especially by isocitrate dehydrogenase (IDH) 2 inhibitor, and therefore their identification in a routine setting is clinically relevant. However, in AITL, the neoplastic cells may be scarce, making the identification of molecular anomalies difficult...
September 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29959025/characterization-of-108-genomic-dna-reference-materials-for-11-human-leukocyte-antigen-loci-a-get-rm-collaborative-project
#18
Maria P Bettinotti, Deborah Ferriola, Jamie L Duke, Timothy L Mosbruger, Nikolaos Tairis, Lawrence Jennings, Lisa V Kalman, Dimitri Monos
The highly polymorphic human leukocyte antigen (HLA) genes, located in the human major histocompatibility complex, encode the class I and II antigen-presenting molecules, which are centrally involved in the immune response. HLA typing is used for several clinical applications, such as transplantation, pharmacogenetics, and diagnosis of autoimmune disease. HLA typing is highly complex because of the homology of HLA genes and pseudogenes and the extensive polymorphism in the population. The Centers for Disease Control and Prevention established the Genetic Testing Reference Materials Coordination Program (GeT-RM) in partnership with the genetics community to improve the availability of genomic DNA reference materials necessary for quality assurance of genetic laboratory testing...
September 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29959024/determining-performance-metrics-for-targeted-next-generation-sequencing-panels-using-reference-materials
#19
Megan H Cleveland, Justin M Zook, Marc Salit, Peter M Vallone
The National Institute of Standards and Technology has developed reference materials for five human genomes. DNA aliquots are available for purchase, and the data, analyses, and high-confidence small variant and homozygous reference calls are freely available on the web. These reference materials are useful for evaluating whole-genome sequencing methods and also can be used to benchmark targeted sequencing panels, which are used commonly in clinical settings. This article describes how to use the Genome in a Bottle samples to obtain performance metrics on any germline-targeted sequencing panel of interest, as well as the limitations of the reference materials...
September 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29959023/evaluation-of-a-hepatitis-c-virus-core-antigen-assay-in-plasma-and-dried-blood-spot-samples
#20
François M J Lamoury, Behzad Hajarizadeh, Angelica Soker, Danica Martinez, Camelia Quek, Philip Cunningham, Beth Catlett, Gavin Cloherty, Philippa Marks, Janaki Amin, Jason Grebely, Gregory J Dore, Tanya L Applegate
Simplified, affordable tools to diagnose active hepatitis C virus (HCV) infection are needed to scale up treatment. This study evaluated the analytical performance of HCV core antigen (HCVcAg) detection in samples of plasma and dried venous blood spots (DBSs). Paired plasma and DBS samples were prepared from remnant diagnostic samples, and plasma HCV RNA and HCVcAg were quantified. Sensitivity and specificity for HCVcAg (>3 fmol/L) at two HCV RNA thresholds (≥15 and ≥3000 IU/mL) were calculated. Of 120 paired samples tested, 25 had nonquantifiable HCV RNA and 95 had quantifiable HCV RNA...
September 2018: Journal of Molecular Diagnostics: JMD
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