Highly sensitive detection method of retinoblastoma genetic predisposition and biomarkers
Retinoblastoma is a malignant tumor of the infant retina. Nearly half of patients are predisposed to retinoblastoma by a germline RB1 pathogenic variant. Non-hereditary retinoblastoma is mainly caused by inactivation of both RB1 alleles at a somatic level. Several polymorphisms have been reported as biomarkers of retinoblastoma risk, aggressiveness or invasion. The most informative genetic testing is obtained from tumor DNA. Historically, access to tumor DNA has been warranted by the frequent indication of enucleation, which has decreased due to advances in conservative approaches. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 14, 2021 Category: Pathology Authors: Jessica Le Gall, Catherine Dehainault, Camille Benoist, Alexandre Matet, Livia Lumbroso-Le Rouic, Isabelle Aerts, Irene Jim énez, Gudrun Schleiermacher, Claude Houdayer, François Radvanyi, Eleonore Frouin, Victor Renault, François Doz, Dominique Stoppa Source Type: research

Rare Variants in RPPH1 qPCR Control Assay Binding Sites Result in Incorrect Copy Number Calls
Real-time quantitative PCR (qPCR) using RPPH1 as a reference gene is a standard method for assessment and validation of genomic copy number variations (CNVs). However, variants in the reference amplicon may cause errors, which was investigated here. While conducting CNV validations for birth defects research studies, 13/1,634 specimens with multiple loci that appeared to be present as 3 copies were unexpectedly detected. This apparent trisomy was hypothesized to be an amplification artifact caused by a variant in the RPPH1 amplicon. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 14, 2021 Category: Pathology Authors: Robert J. Sicko, Paul A. Romitti, Marilyn L. Browne, Lawrence C. Brody, Colleen F. Stevens, James L. Mills, Michele Caggana, Denise M. Kay Tags: Regular Article Source Type: research

Evaluating Targeted Next-Generation Sequencing (NGS) Assays and Reference Materials for NTRK Fusion Detection
Neurotrophic tyrosine receptor kinase (NTRK1/2/3) gene fusions are oncogenic drivers in ∼0.3% of solid tumors. High-quality testing to identify patients with NTRK fusion-positive tumors who could benefit from TRK inhibitors is recommended, but the current NTRK testing landscape, including next-generation sequencing (NGS), is fragmented and availability of assays varies widely.The ana lytical and clinical performance of four commonly available RNA-based NGS assays, Archer’s FusionPlex Lung panel (AFL), Illumina’s TruSight Oncology 500 (TSO500), as well as Thermo Fisher’s Oncomine Precision Assay (OPA) ...
Source: Journal of Molecular Diagnostics - October 14, 2021 Category: Pathology Authors: Christina Bormann Chung, Jeeyun Lee, Marc Barritault, Pierre-Paul Bringuier, Zhaolin Xu, Weei-Yuarn Huang, Andrea Beharry, Joseph Castillo, Jason Christiansen, Jennifer C. Lin, Brandon S. Sheffield Source Type: research

Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group
The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as a number of other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians and patients in the ability to generate, communicate, consume and use genomic test...
Source: Journal of Molecular Diagnostics - October 14, 2021 Category: Pathology Authors: Alexis B. Carter, Lynne V. Abruzzo, Julie Woolworth Hirschhorn, Dan Jones, Danielle C. Jordan, Mehdi Nassiri, Shuji Ogino, Nimesh R. Patel, Christopher G. Suciu, Robyn L. Temple-Smolkin, Ahmet Zehir, Somak Roy Tags: Perspectives Source Type: research

Immunoglobulin Gene Clonality Analysis using Next-Generation Sequencing for Improved Minimal Residual Disease Detection with Significant Prognostic Value in Multiple Myeloma Patients
Next-generation sequencing (NGS) of rearranged immunoglobulin genes is an effective technology for identifying pathological clonal cells in multiple myeloma (MM) and tracking minimal residual disease (MRD). The clinical effect of implementing NGS in immunoglobulin gene clonality analysis was evaluated via a retrospective chart review. We enrolled a total of 312 patients diagnosed with MM. Immunoglobulin gene clonality was determined by fragment analysis using BIOMED-2 multiplex PCR assays (Invivoscribe Technologies) and by NGS using the LymphoTrack IGH FR1 Assay and LymphoTrack IGK Assay (Invivoscribe Technologies). (Sourc...
Source: Journal of Molecular Diagnostics - October 14, 2021 Category: Pathology Authors: Jihye Ha, Hyeonah Lee, Saeam Shin, Hyunsoo Cho, Haerim Chung, Ji Eun Jang, Soo-Jeong Kim, June-Won Cheong, Seung-Tae Lee, Jin Seok Kim, Jong Rak Choi Tags: Regular Article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 1, 2021 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 1, 2021 Category: Pathology Source Type: research

Efficient Detection of Severe Acute Respiratory Syndrome  Coronavirus 2 (SARS-CoV-2) from Exhaled Breath
Severe acute respiratory syndrome –coronavirus 2 (SARS-CoV-2) is transmitted through airborne particles in exhaled breath, causing severe respiratory disease, coronavirus disease–2019 (COVID-19), in some patients. Samples for SARS-CoV-2 testing are typically collected by nasopharyngeal swab, with the virus detected by PCR; howev er, patients can test positive for 3 months after infection. Without the capacity to assay SARS-CoV-2 in breath, it is not possible to learn the risk for transmission from infected individuals. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 29, 2021 Category: Pathology Authors: Chaorui Duan, Luke Buerer, Jing Wang, Samuel Kaplan, Gavin Sabalewski, Gregory D. Jay, Sean Monaghan, Andrea E. Arena, William G. Fairbrother Tags: Regular article Source Type: research

A magnetic modulation biosensing-based molecular assay for rapid and highly sensitive clinical diagnosis of COVID-19
Rapid and sensitive detection of human pathogens, such as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is an urgent and challenging task for clinical laboratories. Currently, the gold standard test for SARS-CoV-2-specific ribonucleic acid (RNA) is based on reverse transcription quantitative polymerase chain reaction (RT-qPCR), which relies on target amplification by Taq polymerase and uses a fluorescent resonance energy transfer (FRET)-based hydrolysis probe. Although this method is accurate and specific, it is also time consuming. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 29, 2021 Category: Pathology Authors: Michael Margulis, Oran Erster, Shira Roth, Michal Mandelboim, Amos Danielli Tags: Regular Article Source Type: research

Measurable residual disease monitoring of SPAG6, ST18, PRAME, and XAGE1A expression in peripheral blood may detect imminent relapse in childhood acute myeloid leukemia
Overexpressed genes may be applicable for monitoring of measurable residual disease (MRD) in childhood acute myeloid leukemia (AML) patients without a leukemia-specific target. The normal expression of five leukemia-associated genes (SPAG6, ST18, MSLN, PRAME, XAGE1A) was defined in children without hematologic disease (n=53) and children with suspected infection (n=90). Gene expression at AML diagnosis (n=50) and during follow-up (n=21) was compared with child-specific reference values. At AML diagnosis, 34/50 children (68%) had high expression of at least one of the five genes, and so did 16/31 children (52%) without a le...
Source: Journal of Molecular Diagnostics - September 29, 2021 Category: Pathology Authors: Anne-Sofie Skou, Kristian L øvvik Juul-Dam, Maria Hansen, Birgitte Lausen, Svea Stratmann, Linda Holmfeldt, Anni Aggerholm, Charlotte Guldborg Nyvold, Hans Beier Ommen, Henrik Hasle Tags: Regular Article Source Type: research

Efficient detection of SARS-CoV-2 from exhaled breath.
SARS-CoV-2 is transmitted through airborne particles in exhaled breath, causing severe respiratory disease. SARS-CoV-2 is typically collected by nasopharyngeal swab and detected by PCR; however, patients can test positive for 3 months after infection. Without the ability to assay SARS-CoV-2 in human breath, it is not possible to learn the transmission risk from infected individuals. To detect virus in breath, the Bubbler - a breathalyzer that reverse transcribes RNA from airborne SARS-CoV-2 particles into a sample-specific barcoded cDNA was developed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 29, 2021 Category: Pathology Authors: Chaorui Duan, Luke Buerer, Jing Wang, Samuel Kaplan, Gavin Sabalewski, Gregory D. Jay, Sean Monaghan, Andrea E. Arena, William G. Fairbrother Tags: Regular Article Source Type: research

DNA Methylation-Based Classification of Small B-Cell Lymphomas
In this study, we hypothesize that DNA methylation array profiling can assist with the classification of SBCLs, including MZLs. Extramedullary SBCLs, including challenging cases, were reviewed internally for pathology consensus and profiled. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 22, 2021 Category: Pathology Authors: Daniel Xia, Alberto Jose Leon, Jiong Yan, Anjali Silva, Mehran Bakhtiari, Rosemarie Tremblay-LeMay, Shamini Selvarajah, Peter Sabatini, Phedias Diamandis, Trevor Pugh, Robert Kridel, Jan Delabie Tags: Regular article Source Type: research

Two-Stage Hierarchical Group Testing Strategy to Increase SARS-CoV-2 Testing Capacity at an Institution of Higher Education: A Retrospective Analysis
Population testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is necessary owing to the potential for viral transmission from asymptomatic cases, yet scarcity of reagents and equipment has increased the cost-prohibitive implementation of screening campaigns at institutions of higher education. Significant analytical sensitivities of nucleic acid amplification methods permit sample pooling to increase testing capacity. Statistical models compared optimal testing configuration for pools of 3, 5, and 10 samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 22, 2021 Category: Pathology Authors: Troy J. Ganz, Rachel Donner, Kevin M. Hines, Markus L. Waithe-Alleyne, Deirdre L. Slate, Gyorgy Abel, Jared R. Auclair Tags: Regular Article Source Type: research

DNA methylation-based classification of small B-cell lymphomas: a proof-of-principle study
In this study, we hypothesize that DNA methylation array profiling can assist with the classification of SBCLs, including MZLs. Extramedullary SBCLs, including challenging cases, were reviewed internally for pathology consensus and profiled. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 22, 2021 Category: Pathology Authors: Daniel Xia, Alberto Jose Leon, Jiong Yan, Anjali Silva, Mehran Bakhtiari, Rosemarie Tremblay-LeMay, Shamini Selvarajah, Peter Sabatini, Phedias Diamandis, Trevor Pugh, Robert Kridel, Jan Delabie Tags: Regular Article Source Type: research

Dmg26
In this study, we examined the exonic sequences of 26 genes reported to be mutated in>1% of patients with myeloma using a custom panel. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 21, 2021 Category: Pathology Authors: Samuel D. Cutler, Philipp Knopf, Clinton J.V. Campbell, Andrea Thoni, Mohamed Abou El Hassan, Nicholas Forward, Darrell White, Julie Wagner, Marissa Goudie, Jeanette E. Boudreau, Barry E. Kennedy, Shashi Gujar, Daniel Gaston, Manal O. Elnenaei Tags: Regular article Source Type: research

Clinical Implications of a Targeted RNA-Sequencing Panel in the Detection of Gene Fusions in Solid Tumors
The detection of recurrent gene fusions can help confirm diagnoses in solid tumors, particularly when the morphology and staining are unusual or nonspecific, and can guide therapeutic decisions. Although fluorescence in situ hybridization and PCR are often used to identify fusions, the rearrangement must be suspected, with only a few prioritized probes run. We hypothesized that the Illumina TruSight RNA Fusion Panel, which detects fusions of 507 genes and their partners, would uncover fusions with greater sensitivity than other approaches, leading to changes in diagnosis, prognosis, or therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 21, 2021 Category: Pathology Authors: Lulu Sun, Samantha N. McNulty, Michael J. Evenson, Xiaopei Zhu, Joshua Robinson, Patrick R. Mann, Eric J. Duncavage, John D. Pfeifer Tags: Regular article Source Type: research

Clinical Implications of a Targeted RNA Sequencing Panel in the Detection of Gene Fusions in Solid Tumors
The detection of recurrent gene fusions can help confirm diagnoses in solid tumors, particularly when the morphology and staining are unusual or nonspecific, and can guide therapeutic decisions. While fluorescence in situ hybridization (FISH) and PCR are often used to identify fusions, the rearrangement must be suspected, with only a few prioritized probes run. We hypothesized that the Illumina TruSight RNA Fusion Panel, which detects fusions of 507 genes and their partners, would uncover fusions with greater sensitivity than other approaches, leading to changes in diagnosis, prognosis, or therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 21, 2021 Category: Pathology Authors: Lulu Sun, Samantha N. McNulty, Michael J. Evenson, Xiaopei Zhu, Joshua Robinson, Patrick R. Mann, Eric J. Duncavage, John D. Pfeifer Tags: Regular Article Source Type: research

Predicted immunogenicity of CDK12 biallelic loss-of-function tumors varies across cancer types
CDK12 biallelic inactivation is associated with a distinct genomic signature of focal tandem duplications (FTDs). Gene fusions resulting from FTDs increase neoantigen load, raising interest in CDK12 as a biomarker of response to immune checkpoint inhibitors (ICIs). Despite evidence of FTDs in multiple CDK12-altered cancer types, notably for prostate and ovarian, report of fusion-associated neoantigen load is limited to prostate cancer. Molecular profiles were retrospectively reviewed for CDK12-biallelic (CDK12-biLOF) and -monoallelic loss-of-function (CDK12-monoLOF) in a primary cohort of>9,000 tumors, representing 39 c...
Source: Journal of Molecular Diagnostics - September 21, 2021 Category: Pathology Authors: Andrew Elliott, Jian Zhang, Qing Zhang, Jeffrey Swensen, Daniel Martin, Joanne Xiu, Daniel M. Geynisman, Daniel Vaena, Thomas J. Herzog, Robert W. Holloway, Wafik S. El-Deiry, David Spetzler, Elisabeth Heath, Phillip Stafford, W. Michael Korn Tags: Regular Article Source Type: research

DMG26: A Targeted Sequencing Panel for Mutation Profiling to Address Gaps in the Prognostication of Multiple Myeloma
In this study, we examined the exonic sequences of 26 genes reported to be mutated in>1% of myeloma patients using a custom panel. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 21, 2021 Category: Pathology Authors: Samuel D. Cutler, Philipp Knopf, Clinton JV. Campbell, Andrea Thoni, Mohamed Abou El Hassan, Nicholas Forward, Darrell White, Julie Wagner, Marissa Goudie, Jeanette E. Boudreau, Barry E. Kennedy, Shashi Gujar, Daniel Gaston, Manal O. Elnenaei Tags: Regular Article Source Type: research

Whole-Genome Sequencing Reveals Large ATP8B1 Deletion/Duplications as Second Mutations Missed by Exome-Based Sequencing
This study sought second pathogenic variants in ATP8B1 by whole-genome sequencing (WGS) in four unrelated low γ-glutamyl transpeptidase cholestasis patients in whom clinical suspicion of PFIC1 was high and gene-panel or Sanger sequencing had identified only one pathogenic variant in ATP8B1. Sanger sequencing confirmed WGS findings and determined the origin of each variant. Novel nonrecurrent structural var iants in three patients (patient 1 to patient 3) were identified in trans: g.55396652_55403080del (6427-bp deletion), g.55335906_55346620dup (10,715-bp duplication), and g.55362063_55364293dup (2231-bp duplication)...
Source: Journal of Molecular Diagnostics - September 17, 2021 Category: Pathology Authors: Ye Yang, Jing Zhang, Li-Ting Li, Yi-Ling Qiu, Jing-Yu Gong, Mei-Hong Zhang, Cai-Hua Li, Jian-She Wang Tags: Regular article Source Type: research

Whole-genome sequencing reveals large ATP8B1 deletion / duplications as “second mutations” missed by exome-based sequencing
This study sought second pathogenic variants in ATP8B1 by whole-genome sequencing (WGS) in 4 unrelated low-GGT cholestasis patients in whom clinical suspicion of PFIC1 was high and gene-panel or Sanger sequencing had identified only one pathogenic variant in ATP8B1. Sanger sequencing confirmed WGS findings and determined the origin of each variant. Novel non-recurrent structural variants in 3 patients (P1 – P3) were identified in trans: g.55396652_55403080del (6427bp deletion), g.55335906_55346620dup (10,715bp duplication), and g.55362063_55364293dup (2231bp duplication). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 17, 2021 Category: Pathology Authors: Ye Yang, Jing Zhang, Li-Ting Li, Yi-Ling Qiu, Jing-Yu Gong, Mei-Hong Zhang, Cai-Hua Li, Jian-She Wang Source Type: research

Temporary Regulatory Deviations and the Coronavirus Disease 2019 (COVID-19) PCR Labeling Update Study Indicate What Laboratory-Developed Test Regulation by the US Food and Drug Administration (FDA) Could Look Like
The coronavirus disease 2019 (COVID-19) response necessitated innovations and a series of regulatory deviations that also affected laboratory-developed tests (LDTs). To examine real-world consequences and specify regulatory paradigm shifts, legislative proposals were aligned on a common timeline with Emergency Use Authorization (EUA) of LDTs and the US Food and Drug Administration (FDA)-orchestrated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) labeling update study. The initial EUA adoption by LDT developers shows that the FDA can have oversight over LDTs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 16, 2021 Category: Pathology Authors: Hetal D. Marble, Adam Z. Bard, Mark M. Mizrachi, Jochen K. Lennerz Tags: Perspectives Source Type: research

Extraction-Free Rapid Cycle Quantitative RT-PCR and Extreme RT-PCR for SARS-CoV-2 Virus Detection
This study explored the kinetic limitations of extraction-free rapid cycle quantitative real-time RT-PCR for SARS-CoV-2 virus detection using the commercially available capillary-based LightCycler. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Joseph C. Lownik, Grayson Way, Jared S. Farrar, Rebecca K. Martin Tags: Regular article Source Type: research

Molecular Testing in Breast Cancer
This article provides an overview of currently available molecular assays and testing modalities that have prognostic, predictive, and therapeutic value. These include multigene assays for invasive breast cancer (Oncotype DX, MammaPrint, Prosigna, and Breast Cancer Index) and ductal carcinoma in situ (Oncotype DX DCIS and DCISionRT) and companion tests to detect PIK3CA mutations and NTRK fusions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Lulu Sun, Ariel Wu, Gregory R. Bean, Ian S. Hagemann, Chieh-Yu Lin Tags: Review Source Type: research

Automated Detection of Arm-level Alterations for Individual Cancer Patients in the clinical setting
Copy number alterations (CNAs) are genetic events that promote tumor initiation and progression and are used in clinical care as diagnostic, prognostic and predictive biomarkers. Based on the length of the alteration, they are roughly classified as “focal” and “arm-level” alterations. While genome-wide techniques to detect arm-level alterations are gaining momentum in hospital laboratories, the high precision and novelty of these techniques pose new challenges: There is no consensus on the definition of an arm-level alteration and a la ck of tools to compute them for individual patients. (Source: Jo...
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Yann Christinat, Prasad Chaskar, Sophie Cl ément, Liza Ho, Mélinda Charrier, Thomas McKee, Petros Tsantoulis Tags: Regular Article Source Type: research

Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection
This study explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Joseph C. Lownik, Grayson Way, Jared S. Farrar, Rebecca K. Martin Source Type: research

Development and Validation of StrataNGS, a Multiplex PCR, Semiconductor Sequencing-Based Comprehensive Genomic Profiling Test
Despite widespread use in targeted tumor testing, multiplex PCR/semiconductor (Ion Torrent) sequencing-based assessment of all comprehensive genomic profiling (CGP) variant classes has been limited. Here we describe the development and validation of StrataNGS, a 429 gene, multiplex PCR/semiconductor sequencing-based CGP laboratory developed test performed on co-isolated DNA and RNA from FFPE tumor specimens with ≥ 2mm2 tumor surface area. Validation was performed in accordance with MolDX CGP validation guidelines using 1,986 clinical FFPE samples and an in-house developed optimized bioinformatics pipeline. (Source: Jour...
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Scott A. Tomlins, Daniel H. Hovelson, Paul Harms, Stephanie Drewery, Jayson Falkner, Andrew Fischer, Jennifer Hipp, Kat Kwiatkowski, Lorena Lazo de la Vega, Khalis Mitchell, Travis Reeder, Javed Siddiqui, Hana Vakil, D. Bryan Johnson, Daniel R. Rhodes Source Type: research

Accuracy of Xpert Carba-R Assay for the Diagnosis of Carbapenemase-Producing Organisms from Rectal Swabs and Clinical Isolates: A Meta-Analysis of Diagnostic Studies
The Cepheid Xpert Carba-R assay has demonstrated a promising value for the detection of carbapenemase-producing organisms (CPOs), but its diagnostic performance remains unclear. Studies were retrieved from Cochrane Library, EMBASE and PubMed databases according to pre-determined selection criteria. The specificity, sensitivity, negative likelihood ratio, positive likelihood ratio and area under the summary receiver operating characteristic curves (AUC) of Xpert Carba-R were analyzed by STATA v13.0. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Yuanyuan Bai, Yingying Hao, Chunhong Shao, Yueling Wang, Yan Jin Tags: Regular Article Source Type: research

Clinical Whole Genome Sequencing for Clarithromycin and Amikacin Resistance Prediction and Subspecies Identification of Mycobacterium abscessus
Mycobacterium abscessus infections are an emerging healthcare concern in patients with chronic pulmonary diseases, leading to high morbidity and mortality. One major challenge is resistance to clarithromycin, a cornerstone antibiotic with high efficacy. Therefore, treatment is primarily guided by phenotypic susceptibility results of clarithromycin, which requires extended incubation to assess for inducible resistance. Resistance mechanisms for clarithromycin include induction of erm(41) and mutations in the 23S rRNA gene (rrl). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Susan Realegeno, Ruel Mirasol, Omai B. Garner, Shangxin Yang Tags: Regular Article Source Type: research

Paired somatic-germline testing of 15 polyposis and colorectal cancer –predisposing genes highlights the role of APC mosaicism in de novo familial adenomatous polyposis
Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome responsible for 1% of colorectal cancers. Up to 90% of classical FAP are caused by inactivating mutations in APC, and mosaicism has been previously reported in 20% of de novo cases, usually linked to milder phenotypic manifestations. To explore the prevalence of mosaicism in 11 unsolved cases of classical FAP and to evaluate the diagnostic yield of somatic testing. Paired samples of colorectal polyps, tumors and/or mucosa were analyzed using a custom NGS panel targeting 15 polyposis and colorectal cancer-predisposing genes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Paula Rofes, Sara Gonz ález, Matilde Navarro, José Marcos Moreno-Cabrera, Ares Solanes, Esther Darder, Estela Carrasco, Sílvia Iglesias, Mónica Salinas, Carolina Gómez, Àngela Velasco, Noemí Tuset, Mar Varela, Gemma Llort, Teresa Ramon y Cajal, Èl Tags: Regular Article Source Type: research

CRISPR/Cas advancement in molecular diagnostics and signal readout approaches
We present here the major three Cas-effectors (Cas9, Cas12 and Cas13) and their significance in various detection assays. The CRISPR/Cas detection strategies based on their target hybridization, cleavage activity, sensor capabilities and signal readout methods are discussed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Md Zohaib Ahmed, Purav Badani, Raj Reddy, Geetesh Mishra Tags: Review Source Type: research

Molecular Testing in Breast Cancer: Current Status and Future Directions
This article provides an overview of currently available molecular assays and testing modalities that have prognostic, predictive, and therapeutic value. These include multi-gene assays for invasive breast cancer (Oncotype DX, MammaPrint, Prosigna, and Breast Cancer Index) and ductal carcinoma in situ (Oncotype DX DCIS and DCISionRT), and companion tests to detect PIK3CA mutations and NTRK fusions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Lulu Sun, Ariel Wu, Gregory R. Bean, Ian S. Hagemann, Chieh-Yu Lin Tags: Review Source Type: research

Optimization of sources of circulating cell-free DNA variability for downstream molecular analysis
Circulating cell-free DNA (ccfDNA) is increasingly used as a cancer biomarker for prognostication, as a correlate for tumor volume, or as input for downstream molecular analysis. Determining optimal blood processing and ccfDNA quantification are crucial for ccfDNA to serve as an accurate biomarker as it moves into the clinical realm. Whole blood was collected from 50 subjects, processed to plasma, and used immediately or frozen at -80 °C. Plasma ccfDNA was extracted and concentration was assessed by qPCR, Qubit, and ddPCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Jacob E. Till, Taylor A. Black, Caren Gentile, Aseel Abdalla, Zhuoyang Wang, Hareena K. Sangha, Jacquelyn J. Roth, Robyn Sussman, Stephanie S. Yee, Mark H. O ’Hara, Jeffrey C. Thompson, Charu Aggarwal, Wei-Ting Hwang, Kojo S.J. Elenitoba-Johnson, Erica Tags: Regular Article Source Type: research

PCR-free shallow whole genome sequencing for chromosomal copy number detection from plasma of cancer patients is an efficient alternative to the conventional PCR-based approach
Somatic copy number alterations (SCNAs) can be detected in cell-free DNA (cfDNA) by shallow whole genome sequencing (sWGS). Polymerase chain reaction (PCR) is typically included in library preparations but a PCR-free method could serve as a high throughput alternative. To evaluate a PCR-free method for research and diagnostics, archival peripheral blood or bone marrow plasma samples collected in EDTA- or lithium heparin-containing tubes were collected from patients with: non-small cell lung cancer (n=10 longitudinal samples; 4 patients), B-cell lymphoma (n=31), acute myeloid leukemia (n=15) or from healthy donors (n=14). (...
Source: Journal of Molecular Diagnostics - August 25, 2021 Category: Pathology Authors: Jamie J. Beagan, Esther E.E. Drees, Phylicia Stathi, Paul P. Eijk, Laura Meulenbroeks, Floortje Kessler, Jaap M. Middeldorp, D. Michiel Pegtel, Jos ée M. Zijlstra, Daoud Sie, Daniëlle A.M. Heideman, Erik Thunnissen, Linda Smit, Daphne de Jong, Florent M Tags: Regular Article Source Type: research

Correction
There is an error in the title of the recently published Commentary entitled, “Transitioning From T-Cell Clonality Testing to High-Throughput Sequencing” (Volume 23, pages 781–783 of the July 2021 issue of The Journal of Molecular Diagnostics; DOI:https://doi.org/10.1016/j.jmoldx.2021.05.005). Due to an error during the proof correction process, an edit requested by the authors was mistakenly overlooked. The correct title of this Commentary is: “Transitioning T-Cell Clonality Testing to High-Throughput Sequencing”, the word “From” has been removed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 24, 2021 Category: Pathology Tags: Correction Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 24, 2021 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 24, 2021 Category: Pathology Source Type: research

Evaluation of a Commercial Multiplexed Molecular Lower Respiratory Panel at a Tertiary Care Cancer Center
This study evaluated the analytical performance of the LRT on bronchoalveolar lavages (BAL) fluids and bronchial washings (BW) in a cancer patient population and retrospectively determined cl inical impact on therapy. Sensitivity and specificity of LRT on BAL and BW compared to bacterial culture and susceptibilities was calculated. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 23, 2021 Category: Pathology Authors: Melvil í Cintrón, Rawlica Sumner, Tracy McMillen, Peter A. Mead, N. Esther Babady Source Type: research

Development of Cooperative Primer-based Real-time PCR Assays for the Detection of Plasmodium malariae and Plasmodium ovale
In this study, SYBR Green-based real-time PCR assays were developed for the detection of P. malariae and P. ovale using cooperative primers that significantly limit the formation and propagation of primer-dimers. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 19, 2021 Category: Pathology Authors: Felix Ansah, Jonathan Suurbaar, Derrick Darko, Nsoh Godwin Anabire, Samuel O. Blankson, Bright K.S. Domson, Alamissa Soulama, Paulina Kpasra, Jersley D. Chirawurah, Lucas Amenga-Etego, Prosper Kanyong, Gordon A. Awandare, Yaw Aniweh Tags: Regular Article Source Type: research

Correction
In the article entitled, “Simultaneous Screening of the FRAXA and FRAXE Loci for Rapid Detection of FMR1 CGG and/or AFF2 CCG Repeat Expansions by Triplet-Primed PCR” (Volume 23, pages 941–951 of the August 2021 issue of The Journal of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2021.04.015) the author s noticed that a requested edit from the proof stage was not implemented into the final version of the manuscript. This is a typesetting error and was not a mistake on the part of the authors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Tags: Correction Source Type: research

The Application of Targeted RNA Sequencing for KMT2A –Partial Tandem Duplication Identification and Integrated Analysis of Molecular Characterization in Acute Myeloid Leukemia
In this study, we developed a targeted RNA-based next-generation sequencing panel, together with single primer enrichment and unique molecular identifiers, to identify KMT2A-PTD as well as AML-related gene fusions and other driver mutations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Authors: Bing Dai, Hao Yu, Tingting Ma, Yichen Lei, Jiyue Wang, Yunxiang Zhang, Jing Lu, Han Yan, Lu Jiang, Bing Chen Tags: Regular article Source Type: research

Corrections
In the article entitled, “Simultaneous Screening of the FRAXA and FRAXE Loci for Rapid Detection of FMR1 CGG and/or AFF2 CCG Repeat Expansions by Triplet-Primed PCR” (Volume 23, pages 941–951 of the August 2021 issue of The Journal of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2021.04.015) the author s noticed that a requested edit from the proof stage was not implemented into the final version of the manuscript. This is a typesetting error and was not a mistake on the part of the authors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Tags: Correction Source Type: research

The Application of Targeted RNA Sequencing for KMT2A Partial Tandem Duplication Identification and Integrated Analysis of Molecular Characterization in Acute Myeloid Leukemia
In this study, we developed a targeted RNA-based NGS panel, together with single primer enrichment and unique molecular identifiers (UMI), to identify KMT2A-PTD, as well as AML-related gene fusions and other driver mutations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Authors: Bing Dai, Hao Yu, Tingting Ma, Yichen Lei, Jiyue Wang, Yunxiang Zhang, Jing Lu, Han Yan, Lu Jiang, Bing Chen Tags: Regular Article Source Type: research

Validation, Implementation, and Clinical Utility of Whole Genome Sequence-Based Bacterial Identification in the Clinical Microbiology Laboratory
The application of next-generation sequencing (NGS) extends from microbial identification to epidemiological insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical labs lies in implementation and validation of such complex technology and data analysis. Here, we describe a validation study of using whole-genome sequencing (WGS) for pan-bacterial identification (ID) in a clinical laboratory setting, and discuss the clinical relevance. A diverse set of 125 bacterial isolates, including a subset of isolates without genus (25) and/or species (10) IDs, were analyzed by de novo assembl...
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Authors: Travis K. Price, Susan Realegeno, Ruel Mirasol, Allison Tsan, Sukantha Chandrasekaran, Omai B. Garner, Shangxin Yang Tags: Regular Article Source Type: research

Validation of Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy (FSHD)
The molecular diagnosis of FSHD relies on detecting contractions of the unique D4Z4 repeat array at the chromosome 4q35 locus in the presence of a permissive 4q35A haplotype. Long, intact DNA molecules are required for accurate sizing of D4Z4 repeats. We validated the use of optical genome mapping to determine size and haplotype of D4Z4 alleles for FSHD analysis. The cohort included 36 unique DNA specimens from fresh blood samples or archived agarose plugs. High-molecular weight DNA underwent sequence-specific labeling followed by separation and image analysis with data collection on the Saphyr system (Bionano Genomics, Sa...
Source: Journal of Molecular Diagnostics - August 9, 2021 Category: Pathology Authors: Aaron A. Stence, Jon G. Thomason, Jonathan A. Pruessner, Ramakrishna R. Sompallae, Anthony N. Snow, Deqin Ma, Steven A. Moore, Aaron D. Bossler Tags: Regular Article Source Type: research

Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation
Modern genomic sequencing tests often interrogate large numbers of genes. Identification of appropriate reference materials for development, validation studies, and quality assurance of these tests poses a significant challenge for laboratories. It is difficult to develop and maintain expert knowledge to identify all variants that must be validated to ensure analytic and clinical validity. Additionally, it is usually not possible to procure appropriate and characterized genomic DNA reference materials containing the number and scope of variants required. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 8, 2021 Category: Pathology Authors: Emma Wilcox, Steven M. Harrison, Edward Lockhart, Karl Voelkerding, Ira M. Lubin, ClinGen Expert Panels, Heidi L. Rehm, Lisa Kalman, Birgit Funke Tags: Regular article Source Type: research

Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation: A ClinGen and GeT-RM Collaborative Project
Modern genomic sequencing tests often interrogate large numbers of genes. Identification of appropriate reference materials for development, validation studies, and quality assurance of these tests poses a significant challenge for laboratories. It is difficult to develop and maintain expert knowledge to identify all variants that must be validated to assure analytic and clinical validity. Additionally, it is usually not possible to procure appropriate and characterized genomic DNA reference materials containing the number and scope of variants required. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 8, 2021 Category: Pathology Authors: Emma Wilcox, Steven M. Harrison, Edward Lockhart, Karl Voelkerding, Ira M. Lubin, ClinGen Expert Panels, Heidi L. Rehm, Lisa Kalman, Birgit Funke Tags: Regular Article Source Type: research

Practical Considerations for Using RNA Sequencing in Management of B-Lymphoblastic Leukemia
Despite the immense genetic heterogeneity of B-lymphoblastic leukemia [or precursor B-cell acute lymphoblastic leukemia (B-ALL)], RNA sequencing (RNA-Seq) could comprehensively interrogate its genetic drivers, assigning a specific molecular subtype in>90% of patients. However, study groups have only started to use RNA-Seq. For  broader clinical use, technical, quality control, and appropriate performance validation are needed. We describe the development and validation of an RNA-Seq workflow for subtype classification, TPMT/NUDT15/TP53 variant discovery, and immunoglobulin heavy chain (IGH) disease clone ident...
Source: Journal of Molecular Diagnostics - August 5, 2021 Category: Pathology Authors: Winnie Hui Ni Chin, Zhenhua Li, Nan Jiang, Evelyn Huizi Lim, Joshua Yew Suang Lim, Yi Lu, Kean Hui Chiew, Shirley Kow Yin Kham, Bernice Ling Zhi Oh, Ah Moy Tan, Hany Ariffin, Jun J. Yang, Allen Eng-Juh Yeoh Tags: Regular article Source Type: research

Practical Considerations for Using RNA Sequencing in Management of B-Cell Acute Lymphoblastic Leukemia
Despite the immense genetic heterogeneity of B-cell acute lymphoblastic leukemia (ALL), RNA sequencing (RNA-Seq) could comprehensively interrogate its genetic drivers, assigning a specific molecular subtype in>90% of patients. However, study groups have only started to use RNA-Seq. For  broader clinical use, technical, quality control, and appropriate performance validation are needed. We describe the development and validation of an RNA-Seq workflow for subtype classification, TPMT/NUDT15/TP53 variant discovery, and IGH disease clone identification for Malaysia-Singapore ALL se quencing (ALL-Seq) 2020. (Sourc...
Source: Journal of Molecular Diagnostics - August 5, 2021 Category: Pathology Authors: Winnie H. Ni Chin, Zhenhua Li, Nan Jiang, Evelyn H. Lim, Joshua Y. Suang Lim, Yi Lu, Kean H. Chiew, Shirley K. Yin Kham, Bernice L. Zhi Oh, Ah M. Tan, Hany Ariffin, Jun J. Yang, Allen Eng-Juh Yeoh Tags: Regular article Source Type: research

Validation, implementation, and clinical impact of the Oncomine Myeloid targeted-amplicon DNA and RNA ion semiconductor sequencing assay
We present validation of the Thermo Fisher Oncomine Myeloid NGS Panel (OMP), targeting 40 genes and 29 fusion drivers recurrently mutated in myeloid malignancies. The study includes data from a sample exchange between two Canadian hospitals demonstrating high concordance for detection of DNA and RNA aberrations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 5, 2021 Category: Pathology Authors: Christina K. Ferrone, Henry Wong, Laura Semenuk, Barnaba Werunga, Brooke Snetsinger, Xiao Zhang, Grace Zhang, Janet Lui, Guillaume Richard-Carpentier, Susan Crocker, David Good, Annette E. Hay, Graeme Quest, Nancy Carson, Harriet E. Feilotter, Michael J. Tags: Regular Article Source Type: research