Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data

Cimino, Patrick J.; Zhao, Guoyan; Wang, David; Sehn, Jennifer K.; Lewis, James S.; Duncavage, Eric J.

doi:10.1016/j.yexmp.2014.03.010

Cited by 45 publications

(37 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Oncologist directed NGS was performed as previously described (Cimino et al, 2014b). Between 300 and 750 ng of total genomic DNA (as determined by Qubit, Life Technologies, Grand Island, NY) was extracted from formalin-fixed paraffin-embedded (FFPE) tissue from each of the cases and was first fragmented to approximately 200–300 base pairs using a Covaris E210 instrument (Covaris Inc, Woburn, MA).…”

Section: Methodsmentioning

confidence: 99%

A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel

Cimino¹,

Bredemeyer²,

Abel³

et al. 2015

Experimental and Molecular Pathology

Self Cite

View full text Add to dashboard Cite

With the advent of large-scale genomic analysis, the genetic landscape of glioblastoma (GBM) has become more clear, including characteristic genetic alterations in EGFR. In routine clinical practice, genetic alterations in GBMs are identified using several disparate techniques that consume already limited amounts of tissue and add to overall testing costs. In this study, we sought to determine if the full spectrum of EGFR mutations in GBMs could be detected using a single next generation sequencing (NGS) based oncology assay in 34 consecutive cases. Using a battery of informatics tools to identify single nucleotide variants, insertions and deletions, and amplification (including variants EGFRvIII and EGFRvV), twenty-one of the 34 (62%) individuals had had at least one alteration in EGFR by sequencing, consistent with published datasets. Mutations detected include several single nucleotide variants, amplification (confirmed by fluorescence in situ hybridization), and the variants EGFRvIII and EGFRvV (confirmed by multiplex ligation-dependent probe amplification). Here we show that a single NGS assay can identify the full spectrum of relevant EGFR mutations. Overall, sequencing based diagnostics have the potential to maximize the amount of genetic information obtained from GBMs and simultaneously reduce the total time, required specimen material, and costs associated with current multimodality studies.

show abstract

Section: Methodsmentioning

confidence: 99%

A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel

Cimino¹,

Bredemeyer²,

Abel³

et al. 2015

Experimental and Molecular Pathology

Self Cite

View full text Add to dashboard Cite

show abstract

“…King and Gerber have recently reviewed the methods available for translatome profiling [308]. NGS has been used to detect microsatellite instability [309], to study and diagnose mitochondrial diseases [310], and to detect pathogens in human biological specimens [311]. …”

Section: Other Applications and Future Directionsmentioning

confidence: 99%

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Kamps

Brandão

Bosch

et al. 2017

IJMS

374

294

View full text Add to dashboard Cite

Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.

show abstract

“…Emerging genomic studies suggest that pathogens may be implicated in more tumors than was historically appreciated. 24 Extension to other oncogenic viruses, such as EBV, HHV8, HTLV1, HBV, and Merkel cell polyomavirus, should be explored. Evaluation of premalignant lesions is also feasible.…”

Section: Discussionmentioning

confidence: 99%

Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing

Montgomery¹,

Parker

Eberhard

et al. 2016

Applied Immunohistochemistry &Amp; Molecular Morphology

View full text Add to dashboard Cite

Human papillomaviruses (HPV) are oncogenic DNA viruses implicated in squamous cell carcinomas of several anatomic sites, as well as endocervical adenocarcinomas. Identification of HPV is an actionable finding in some carcinomas, potentially influencing tumor classification, prognosis, and management. We incorporated capture probes for oncogenic HPV strains 16 and 18 into a broader next-generation sequencing (NGS) panel designed to identify actionable mutations in solid malignancies. A total of 21 head and neck, genitourinary and gynecological squamous cell carcinomas and endocervical adenocarcinomas were sequenced as part of the UNCSeq project. Using p16 immunohistochemical results as the gold standard, we set a cutoff for proportion of aligned HPV reads that maximized performance of our NGS assay (92% sensitive, 100% specific for HPV). These results suggest that sequencing of oncogenic pathogens can be incorporated into targeted NGS panels, extending the clinical utility of genomic assays.

show abstract

Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data

Cited by 45 publications

References 50 publications

A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel

A wide spectrum of EGFR mutations in glioblastoma is detected by a single clinical oncology targeted next-generation sequencing panel

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing

Contact Info

Product

Resources

About