The Journal of Molecular Diagnostics: May 2017 (Volume 19, Issue 3)

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Special Article

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  Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels
Lawrence J. Jennings, Maria E. Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M.

Lubin, John Pfeifer, Robyn L. Temple-Smolkin, Karl V. Voelkerding, Marina N. Nikiforova

  Review

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  Current and Emerging Molecular Tests for Human Papillomavirus–Related Neoplasia in the

Genomic Era
Sixto M. Leal Jr., Margaret L. Gulley

  Technical Advance

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  Detection of Aberrant TERT Promoter Methylation by Combined Bisulfite Restriction Enzyme

Analysis for Cancer Diagnosis
Seungjae Lee, Sumit Borah, Armita Bahrami

  Regular Articles

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  Identification of NTRK3 Fusions in Childhood Melanocytic Neoplasms
Lu Wang, Klaus J. Busam, Ryma Benayed, Robert Cimera, Jiajing Wang, Ryan Denley, Mamta Rao,

Ruth Aryeequaye, Kerry Mullaney, Long Cao, Marc Ladanyi, Meera Hameed

  Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA
Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A. Scott

  Development and Clinical Utility of a Blood-Based Test Service for the Rapid

Identification of Actionable Mutations in Non–Small Cell Lung Carcinoma
Hestia Mellert, Trudi Foreman, Leisa Jackson, Dianna Maar, Scott Thurston, Kristina Koch,

Amanda Weaver, Samantha Cooper, Nicholas Dupuis, Ubaradka G. Sathyanarayana, Jakkie Greer,

Westen Hahn, Dawne Shelton, Paula Stonemetz, Gary A. Pestano

  Principles and Recommendations for Standardizing the Use of the Next-Generation

Sequencing Variant File in Clinical Settings
Ira M. Lubin, Nazneen Aziz, Lawrence J. Babb, Dennis Ballinger, Himani Bisht, Deanna M.

Church, Shaun Cordes, Karen Eilbeck, Fiona Hyland, Lisa Kalman, Melissa Landrum, Edward R.

Lockhart, Donna Maglott, Gabor Marth, John D. Pfeifer, Heidi L. Rehm, Somak Roy, Zivana

Tezak, Rebecca Truty, Mollie Ullman-Cullere, Karl V. Voelkerding, Elizabeth A. Worthey,

Alexander W. Zaranek, Justin M. Zook

  Haplotype Counting for Sensitive Chimerism Testing
Marija Debeljak, Evelina Mocci, Max C. Morrison, Aparna Pallavajjalla, Katie Beierl, Marie

Amiel, Michaël Noë, Laura D. Wood, Ming-Tseh Lin, Christopher D. Gocke, Alison P. Klein,

Ephraim J. Fuchs, Richard J. Jones, James R. Eshleman

  Droplet Digital PCR Is a Reliable Tool for Monitoring Minimal Residual Disease in Acute

Promyelocytic Leukemia
Claudia Brunetti, Luisa Anelli, Antonella Zagaria, Angela Minervini, Crescenzio F.

Minervini, Paola Casieri, Nicoletta Coccaro, Cosimo Cumbo, Giuseppina Tota, Luciana Impera,

Paola Orsini, Giorgina Specchia, Francesco Albano

  Targeted Next-Generation Sequencing of 51 Genes Involved in Primary Electrical Disease
Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline

M. Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints,

Jurgen Del Favero, Bart Loeys, Lut Van Laer

  Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a

Pediatric Emergency Department
Daniel T. Rogan, Mohit S. Kochar, Samuel Yang, James V. Quinn

  Utilization of Whole-Exome Next-Generation Sequencing Variant Read Frequency for

Detection of Lesion-Specific, Somatic Loss of Heterozygosity in a Neurofibromatosis Type 1

Cohort with Tibial Pseudarthrosis
Rebecca L. Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques

D'Astous, Dave Viskochil, David A. Stevenson, Rong Mao

  Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using

the CLIA Decipher Assay
Alba Torres, Mohammed Alshalalfa, Scott A. Tomlins, Nicholas Erho, Ewan A. Gibb, Jijumon

Chelliserry, Lony Lim, Lucia L.C. Lam, Sheila F. Faraj, Stephania M. Bezerra, Elai

Davicioni, Kasra Yousefi, Ashley E. Ross, George J. Netto, Edward M. Schaeffer, Tamara L.

Lotan  

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Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a Pediatric Emergency Department.
(PMID:28341587)

Rogan DT 1 ,  Kochar MS 2 ,  Yang S 3  ,  Quinn JV 4   
Affiliations
The Journal of Molecular Diagnostics : JMD [2017, 19(3):460-467]
Type:
DOI: 10.1016/j.jmoldx.2017.01.009  The Digital Object Identifier (DOI) System enables identification of digital entities
Abstract
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory PCR testing is accurate albeit slow, whereas rapid antigen testing is inaccurate. We determined the impact of bedside PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season. On ordering, ED physicians were interviewed to ascertain real-time plans if given immediate influenza/RSV PCR results for the current patient. Two groups were compared: actual management and management adjusted for mPOCT results. We compared ED length of stay (LOS), tests ordered, and antibiotic/antiviral ordering. One-hundred thirty-six respiratory PCR panels were ordered, 71 by admitting team, 61 for ED management. Of 61 ED-initiated tests, physicians indicated in 39 cases (64%) they would change patient management were bedside viral results available. Physicians would have decreased ED LOS by 33 minutes, ordered fewer tests (18%; P < 0.001) with average patient charge savings of $669, fewer antibiotics among discharged patients (17%; P = 0.043), and increased appropriate antiviral use (13%; P = 0.023). Rapid bedside ARI mPOCT PCR has the potential to decrease ED LOS, reduce diagnostic tests and patient charges, and increase appropriate use of antibiotics and antiviral agents.

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J Mol Diagn. 2017 May;19(3):366-377. doi: 10.1016/j.jmoldx.2017.01.006. Epub 2017 Mar 18.
Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era.
Leal SM Jr1, Gulley ML2.
Author information

Abstract
Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential. During oncogenesis, HPV interferes with cell cycle regulation and incites DNA damage responses that thwart apoptosis and enable mutations to accumulate. Such mutations are an adverse effect of innate and adaptive antiviral immune responses that up-regulate DNA-editing enzymes, with natural selection of cells having a chromosomally integrated viral genome lacking expression of viral proteins targeted by the immune system. Infected cancers share a similar mutation signature, reflecting the effect of apolipoprotein B mRNA-editing catalytic polypeptide enzyme DNA-editing enzymes. It is feasible that genomic tests for characteristic mutations or methylation signatures, along with tests for dysregulated HPV gene expression, add value in predicting behavior of premalignant lesions. Furthermore, these tumor markers in cell-free DNA of plasma or body fluids may one day assist in early detection or monitoring cancer burden during treatment.