Other search tools

About this data

The publication data currently available has been vetted by Vanderbilt faculty, staff, administrators and trainees. The data itself is retrieved directly from NCBI's PubMed and is automatically updated on a weekly basis to ensure accuracy and completeness.

If you have any questions or comments, please contact us.

Results: 1 to 10 of 20

Publication Record

Connections

A novel real-time RT-PCR assay for influenza C tested in Peruvian children.
Howard LM, Johnson M, Gil AI, Pekosz A, Griffin MR, Edwards KM, Lanata CF, Grijalva CG, Williams JV, RESPIRA-PERU Group
(2017) J Clin Virol 96: 12-16
MeSH Terms: Child, Preschool, Female, Humans, Infant, Influenza, Human, Influenzavirus C, Male, Molecular Diagnostic Techniques, Peru, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity
Show Abstract · Added July 27, 2018
BACKGROUND - Influenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases.
OBJECTIVES - To develop a sensitive and specific real-time RT-PCR assay for ICV that allows for rapid and accurate detection in a clinical or research setting.
STUDY DESIGN - Multiple ICV sequences obtained from GenBank were analyzed, including 141 hemagglutinin-esterase (HE), 106 matrix (M), and 97 nucleoprotein (NP) sequences. Primers and probes were designed based on conserved regions. Multiple primer-probe sets were tested against multiple ICV strains.
RESULTS - The ICV M and NP genes offered the most conserved sequence regions. Primers and probes based on newer sequence data offered enhanced detection of ICV, especially for low titer specimens. An NP-targeted assay yielded the best performance and was capable of detecting 10-100 RNA copies per reaction. The NP assay detected multiple clinical isolates of ICV collected in a field epidemiology study conducted in Peru.
CONCLUSIONS - We report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.
Copyright © 2017 Elsevier B.V. All rights reserved.
0 Communities
1 Members
0 Resources
MeSH Terms
HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma: Guideline From the College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology.
Bartley AN, Washington MK, Ventura CB, Ismaila N, Colasacco C, Benson AB, Carrato A, Gulley ML, Jain D, Kakar S, Mackay HJ, Streutker C, Tang L, Troxell M, Ajani JA
(2016) Arch Pathol Lab Med 140: 1345-1363
MeSH Terms: Adenocarcinoma, Biomarkers, Tumor, Clinical Decision-Making, Combined Modality Therapy, Decision Trees, Diagnosis, Differential, Esophageal Neoplasms, Evidence-Based Medicine, Humans, Medical Oncology, Molecular Diagnostic Techniques, Molecular Targeted Therapy, Mutation, Neoplasm Grading, Neoplasm Staging, Pathology, Clinical, Receptor, ErbB-2, Societies, Medical, Stomach Neoplasms, United States
Show Abstract · Added March 14, 2018
CONTEXT - - ERBB2 (erb-b2 receptor tyrosine kinase 2 or HER2) is currently the only biomarker established for selection of a specific therapy for patients with advanced gastroesophageal adenocarcinoma (GEA). However, there are no comprehensive guidelines for the assessment of HER2 in patients with GEA.
OBJECTIVES - - To establish an evidence-based guideline for HER2 testing in patients with GEA, to formalize the algorithms for methods to improve the accuracy of HER2 testing while addressing which patients and tumor specimens are appropriate, and to provide guidance on clinical decision making.
DESIGN - - The College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology convened an expert panel to conduct a systematic review of the literature to develop an evidence-based guideline with recommendations for optimal HER2 testing in patients with GEA.
RESULTS - - The panel is proposing 11 recommendations with strong agreement from the open-comment participants.
RECOMMENDATIONS - - The panel recommends that tumor specimen(s) from all patients with advanced GEA, who are candidates for HER2-targeted therapy, should be assessed for HER2 status before the initiation of HER2-targeted therapy. Clinicians should offer combination chemotherapy and a HER2-targeted agent as initial therapy for all patients with HER2-positive advanced GEA. For pathologists, guidance is provided for morphologic selection of neoplastic tissue, testing algorithms, scoring methods, interpretation and reporting of results, and laboratory quality assurance.
CONCLUSIONS - - This guideline provides specific recommendations for assessment of HER2 in patients with advanced GEA while addressing pertinent technical issues and clinical implications of the results.
0 Communities
1 Members
0 Resources
20 MeSH Terms
Serology Enhances Molecular Diagnosis of Respiratory Virus Infections Other than Influenza in Children and Adults Hospitalized with Community-Acquired Pneumonia.
Zhang Y, Sakthivel SK, Bramley A, Jain S, Haynes A, Chappell JD, Hymas W, Lenny N, Patel A, Qi C, Ampofo K, Arnold SR, Self WH, Williams DJ, Hillyard D, Anderson EJ, Grijalva CG, Zhu Y, Wunderink RG, Edwards KM, Pavia AT, McCullers JA, Erdman DD
(2017) J Clin Microbiol 55: 79-89
MeSH Terms: Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Community-Acquired Infections, Female, Hospitalization, Humans, Infant, Infant, Newborn, Male, Middle Aged, Molecular Diagnostic Techniques, Pneumonia, Viral, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity, Serologic Tests, Young Adult
Show Abstract · Added July 27, 2018
Both molecular and serological assays have been used previously to determine the etiology of community-acquired pneumonia (CAP). However, the extent to which these methods are correlated and the added diagnostic value of serology for respiratory viruses other than influenza virus have not been fully evaluated. Using data from patients enrolled in the Centers for Disease Control and Prevention (CDC) Etiology of Pneumonia in the Community (EPIC) study, we compared real-time reverse transcription-PCR (RT-PCR) and serology for the diagnosis of respiratory syncytial virus (RSV), human metapneumovirus (HMPV), parainfluenza virus 1 to 3 (PIV1, PIV2, and PIV3), and adenovirus (AdV) infections. Of 5,126 patients enrolled, RT-PCR and serology test results were available for 2,023, including 1,087 children below the age of 18 years and 936 adults. For RSV, 287 (14.2%) patients were positive by RT-PCR and 234 (11.6%) were positive by serology; for HMPV, 172 (8.5%) tested positive by RT-PCR and 147 (7.3%) by serology; for the PIVs, 94 (4.6%) tested positive by RT-PCR and 92 (4.6%) by serology; and for AdV, 111 (5.5%) tested positive by RT-PCR and 62 (3.1%) by serology. RT-PCR provided the highest number of positive detections overall, but serology increased diagnostic yield for RSV (by 11.8%), HMPV (by 25.0%), AdV (by 32.4%), and PIV (by 48.9%). The method concordance estimated by Cohen's kappa coefficient (κ) ranged from good (for RSV; κ = 0.73) to fair (for AdV; κ = 0.27). Heterotypic seroresponses observed between PIVs and persistent low-level AdV shedding may account for the higher method discordance observed with each of these viruses. Serology can be a helpful adjunct to RT-PCR for research-based assessment of the etiologic contribution of respiratory viruses other than influenza virus to CAP.
Copyright © 2016 American Society for Microbiology.
0 Communities
1 Members
0 Resources
MeSH Terms
Targeted imaging of cancer by fluorocoxib C, a near-infrared cyclooxygenase-2 probe.
Uddin MJ, Crews BC, Ghebreselasie K, Daniel CK, Kingsley PJ, Xu S, Marnett LJ
(2015) J Biomed Opt 20: 50502
MeSH Terms: Animals, Cell Line, Tumor, Cyclooxygenase 2, Cyclooxygenase 2 Inhibitors, Female, Image Enhancement, Infrared Rays, Mice, Mice, Nude, Microscopy, Fluorescence, Molecular Diagnostic Techniques, Molecular Imaging, Molecular Probe Techniques, Neoplasms, Experimental, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added February 22, 2016
Cyclooxygenase-2 (COX-2) is a promising target for the imaging of cancer in a range of diagnostic and therapeutic settings. We report a near-infrared COX-2-targeted probe, fluorocoxib C (FC), for visualization of solid tumors by optical imaging. FC exhibits selective and potent COX-2 inhibition in both purified protein and human cancercell lines. In vivo optical imaging shows selective accumulation of FC in COX-2-overexpressing human tumor xenografts [1483 head and neck squamous cell carcinoma (HNSCC)] implanted in nude mice, while minimal uptake is detectable in COX-2-negative tumor xenografts (HCT116)or 1483 HNSCC xenografts preblocked with the COX-2-selective inhibitor celecoxib. Time course imaging studies conducted from 3 h to 7-day post-FC injection revealed a marked reduction in nonspecific fluorescent signals with retention of fluorescence in 1483 HNSCC tumors. Thus, use of FC in a delayed imaging protocol offers an approach to improve imaging signal-to-noise that should improve cancer detection in multiple preclinical and clinical settings.
0 Communities
3 Members
0 Resources
16 MeSH Terms
Methods and challenges in quantitative imaging biomarker development.
Abramson RG, Burton KR, Yu JP, Scalzetti EM, Yankeelov TE, Rosenkrantz AB, Mendiratta-Lala M, Bartholmai BJ, Ganeshan D, Lenchik L, Subramaniam RM
(2015) Acad Radiol 22: 25-32
MeSH Terms: Animals, Biomarkers, Humans, Image Interpretation, Computer-Assisted, Molecular Diagnostic Techniques, Molecular Imaging, Molecular Probe Techniques, Molecular Probes
Show Abstract · Added February 12, 2015
Academic radiology is poised to play an important role in the development and implementation of quantitative imaging (QI) tools. This article, drafted by the Association of University Radiologists Radiology Research Alliance Quantitative Imaging Task Force, reviews current issues in QI biomarker research. We discuss motivations for advancing QI, define key terms, present a framework for QI biomarker research, and outline challenges in QI biomarker development. We conclude by describing where QI research and development is currently taking place and discussing the paramount role of academic radiology in this rapidly evolving field.
Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.
0 Communities
1 Members
0 Resources
8 MeSH Terms
Clinical utility of quantitative imaging.
Rosenkrantz AB, Mendiratta-Lala M, Bartholmai BJ, Ganeshan D, Abramson RG, Burton KR, Yu JP, Scalzetti EM, Yankeelov TE, Subramaniam RM, Lenchik L
(2015) Acad Radiol 22: 33-49
MeSH Terms: Animals, Biomarkers, Evaluation Studies as Topic, Humans, Image Interpretation, Computer-Assisted, Molecular Diagnostic Techniques, Molecular Imaging, Molecular Probe Techniques, Molecular Probes
Show Abstract · Added February 12, 2015
Quantitative imaging (QI) is increasingly applied in modern radiology practice, assisting in the clinical assessment of many patients and providing a source of biomarkers for a spectrum of diseases. QI is commonly used to inform patient diagnosis or prognosis, determine the choice of therapy, or monitor therapy response. Because most radiologists will likely implement some QI tools to meet the patient care needs of their referring clinicians, it is important for all radiologists to become familiar with the strengths and limitations of QI. The Association of University Radiologists Radiology Research Alliance Quantitative Imaging Task Force has explored the clinical application of QI and summarizes its work in this review. We provide an overview of the clinical use of QI by discussing QI tools that are currently used in clinical practice, clinical applications of these tools, approaches to reporting of QI, and challenges to implementing QI. It is hoped that these insights will help radiologists recognize the tangible benefits of QI to their patients, their referring clinicians, and their own radiology practice.
Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.
0 Communities
1 Members
0 Resources
9 MeSH Terms
Comparison of 2 assays for diagnosing rotavirus and evaluating vaccine effectiveness in children with gastroenteritis.
Tate JE, Mijatovic-Rustempasic S, Tam KI, Lyde FC, Payne DC, Szilagyi P, Edwards K, Staat MA, Weinberg GA, Hall CB, Chappell J, McNeal M, Gentsch JR, Bowen MD, Parashar UD
(2013) Emerg Infect Dis 19: 1245-52
MeSH Terms: Acute Disease, Case-Control Studies, Child, Preschool, Enzyme-Linked Immunosorbent Assay, Gastroenteritis, Humans, Infant, Molecular Diagnostic Techniques, Real-Time Polymerase Chain Reaction, Rotavirus, Rotavirus Infections, Rotavirus Vaccines, Vaccination, Vaccine Potency
Show Abstract · Added May 28, 2014
We compared rotavirus detection rates in children with acute gastroenteritis (AGE) and in healthy controls using enzyme immunoassays (EIAs) and semiquantitative real-time reverse transcription PCR (qRT-PCR). We calculated rotavirus vaccine effectiveness using different laboratory-based case definitions to determine which best identified the proportion of disease that was vaccine preventable. Of 648 AGE patients, 158 (24%) were EIA positive, and 157 were also qRT-PCR positive. An additional 65 (10%) were qRT-PCR positive but EIA negative. Of 500 healthy controls, 1 was EIA positive and 24 (5%) were qRT-PCR positive. Rotavirus vaccine was highly effective (84% [95% CI 71%-91%]) in EIA-positive children but offered no significant protection (14% [95% CI -105% to 64%]) in EIA-negative children for whom virus was detected by qRT-PCR alone. Children with rotavirus detected by qRT-PCR but not by EIA were not protected by vaccination, suggesting that rotavirus detected by qRT-PCR alone might not be causally associated with AGE in all patients.
0 Communities
1 Members
0 Resources
14 MeSH Terms
Non-small cell lung cancer.
Ettinger DS, Akerley W, Borghaei H, Chang AC, Cheney RT, Chirieac LR, D'Amico TA, Demmy TL, Ganti AK, Govindan R, Grannis FW, Horn L, Jahan TM, Jahanzeb M, Kessinger A, Komaki R, Kong FM, Kris MG, Krug LM, Lennes IT, Loo BW, Martins R, O'Malley J, Osarogiagbon RU, Otterson GA, Patel JD, Pinder-Schenck MC, Pisters KM, Reckamp K, Riely GJ, Rohren E, Swanson SJ, Wood DE, Yang SC, Hughes M, Gregory KM, NCCN (National Comprehensive Cancer Network)
(2012) J Natl Compr Canc Netw 10: 1236-71
MeSH Terms: Algorithms, Biomarkers, Tumor, Carcinoma, Non-Small-Cell Lung, Clinical Laboratory Techniques, Humans, Lung Neoplasms, Medical Oncology, Molecular Diagnostic Techniques, Neoplasm Metastasis, Neoplasm Staging, Practice Guidelines as Topic, Prognosis, Recurrence
Show Abstract · Added June 26, 2014
Most patients with non-small cell lung cancer (NSCLC) are diagnosed with advanced cancer. These guidelines only include information about stage IV NSCLC. Patients with widespread metastatic disease (stage IV) are candidates for systemic therapy, clinical trials, and/or palliative treatment. The goal is to identify patients with metastatic disease before initiating aggressive treatment, thus sparing these patients from unnecessary futile treatment. If metastatic disease is discovered during surgery, then extensive surgery is often aborted. Decisions about treatment should be based on multidisciplinary discussion.
0 Communities
1 Members
0 Resources
13 MeSH Terms
Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials.
Lovly CM, Dahlman KB, Fohn LE, Su Z, Dias-Santagata D, Hicks DJ, Hucks D, Berry E, Terry C, Duke M, Su Y, Sobolik-Delmaire T, Richmond A, Kelley MC, Vnencak-Jones CL, Iafrate AJ, Sosman J, Pao W
(2012) PLoS One 7: e35309
MeSH Terms: Cell Line, Tumor, Clinical Trials as Topic, DNA Mutational Analysis, Eligibility Determination, GTP-Binding Protein alpha Subunits, GTP-Binding Protein alpha Subunits, Gq-G11, Genetic Testing, Humans, Male, Melanoma, Molecular Diagnostic Techniques, Nerve Tissue Proteins, Point Mutation, Proto-Oncogene Proteins B-raf, Proto-Oncogene Proteins c-kit, Proto-Oncogene Proteins p21(ras), Skin Neoplasms
Show Abstract · Added September 3, 2013
PURPOSE - Knowledge of tumor mutation status is becoming increasingly important for the treatment of cancer, as mutation-specific inhibitors are being developed for clinical use that target only sub-populations of patients with particular tumor genotypes. Melanoma provides a recent example of this paradigm. We report here development, validation, and implementation of an assay designed to simultaneously detect 43 common somatic point mutations in 6 genes (BRAF, NRAS, KIT, GNAQ, GNA11, and CTNNB1) potentially relevant to existing and emerging targeted therapies specifically in melanoma.
METHODS - The test utilizes the SNaPshot method (multiplex PCR, multiplex primer extension, and capillary electrophoresis) and can be performed rapidly with high sensitivity (requiring 5-10% mutant allele frequency) and minimal amounts of DNA (10-20 nanograms). The assay was validated using cell lines, fresh-frozen tissue, and formalin-fixed paraffin embedded tissue. Clinical characteristics and the impact on clinical trial enrollment were then assessed for the first 150 melanoma patients whose tumors were genotyped in the Vanderbilt molecular diagnostics lab.
RESULTS - Directing this test to a single disease, 90 of 150 (60%) melanomas from sites throughout the body harbored a mutation tested, including 57, 23, 6, 3, and 2 mutations in BRAF, NRAS, GNAQ, KIT, and CTNNB1, respectively. Among BRAF V600 mutations, 79%, 12%, 5%, and 4% were V600E, V600K, V600R, and V600M, respectively. 23 of 54 (43%) patients with mutation harboring metastatic disease were subsequently enrolled in genotype-driven trials.
CONCLUSION - We present development of a simple mutational profiling screen for clinically relevant mutations in melanoma. Adoption of this genetically-informed approach to the treatment of melanoma has already had an impact on clinical trial enrollment and prioritization of therapy for patients with the disease.
3 Communities
8 Members
0 Resources
17 MeSH Terms
NCCN Clinical Practice Guidelines Occult primary.
Ettinger DS, Agulnik M, Cates JM, Cristea M, Denlinger CS, Eaton KD, Fidias PM, Gierada D, Gockerman JP, Handorf CR, Iyer R, Lenzi R, Phay J, Rashid A, Saltz L, Shulman LN, Smerage JB, Varadhachary GR, Zager JS, Zhen WK, National Comprehensive Cancer Network
(2011) J Natl Compr Canc Netw 9: 1358-95
MeSH Terms: Adenocarcinoma, Algorithms, Antibodies, Antineoplastic Combined Chemotherapy Protocols, Carcinoma, Female, Humans, Lymphatic Metastasis, Male, Medical Oncology, Molecular Diagnostic Techniques, Neoplasms, Unknown Primary, Practice Guidelines as Topic, Societies, Medical, United States
Show Abstract · Added March 15, 2013
Occult primary tumors, or cancers of unknown primary (CUPs), are defined as histologically proven metastatic malignant tumors whose primary site cannot be identified during pretreatment evaluation. They have a wide variety of clinical presentations and a poor prognosis in most patients. Patients with occult primary tumors often present with general complaints, such as anorexia and weight loss. Clinical absence of primary tumor, early dissemination, aggressiveness, and unpredictability of metastatic pattern are characteristic of these tumors. Life expectancy is very short, with a median survival of 6 to 9 months. In most patients, occult primary tumors are refractory to systemic treatments, and chemotherapy is only palliative and does not significantly improve long-term survival. However, certain clinical presentations of these tumors are associated with a better prognosis. Special pathologic studies can identify subsets of patients with tumor types that are more responsive to chemotherapy. Treatment options should be individualized for this selected group of patients to achieve improved response and survival rates.
0 Communities
1 Members
0 Resources
15 MeSH Terms