Diagnostic yield of targeted next generation sequencing in various cancer types: An information-theoretic approach

Hagemann, Ian S.; O'Neill, Patrick; Erill, Ivan; Pfeifer, John D.

doi:10.1016/j.cancergen.2015.05.030

Cited by 9 publications

(7 citation statements)

References 47 publications

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“…In our population, we identified a higher percentage of KRAS mutations (37.9% vs 28% and 26%) and fewer EGFR mutations (11.1% vs 14% and 20%) than reported by Hageman et al and Dogan et al, respectively [9] , [10] . This may be due to different prevalence of smoking and ethnicity in the different sample sets or selection bias of the various populations or testing methods (for instance, we tested multiple samples from the same patient in several instances).…”

Section: Discussionsupporting

confidence: 48%

Clinical Genotyping of Non–Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

et al. 2016

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Detection of somatic mutations in non–small cell lung cancers (NSCLCs), especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM) and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips). We identified variants with the Ion Torrent Variant Caller Plugin, and Golden Helix's SVS software was used for annotation and prediction of the significance of the variants. Three hundred ninety-eight samples were successfully sequenced (12.1% failure rate). In all, 633 variants in 41 genes were detected with a median of 2 (range of 0 to 7) variants per sample. Mutations detected in BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA were considered potentially actionable and were identified in 237 samples, most commonly in KRAS (37.9%), EGFR (11.1%), BRAF (4.8%), and PIK3CA (4.3%). In our patient population, all mutations in EGFR, KRAS, and BRAF were mutually exclusive. The Ion Torrent Ampliseq technology can be utilized on small biopsy and cytology specimens, requires very little input DNA, and can be applied in clinical laboratories for genotyping of NSCLC. This targeted next-generation sequencing approach allows for detection of common and also rare mutations that are clinically actionable in multiple patients simultaneously.

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Section: Discussionsupporting

confidence: 48%

Clinical Genotyping of Non–Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

et al. 2016

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“…In a study to determine if results from NGS are useful for detecting mutations in tumor tissues, Hagemann et al analyzed the mutations revealed from NGS from the five most common cancer types and calculated a Shannon entropy level for each tumor type to determine if NGS revealed new information. High levels of Shannon entropy indicate analytic utility, while low levels indicate that a variable provides no new or useful information [49]. In this study, Shannon entropy levels for these cancer types from highest to lowest were colorectal cancer, high grade glioma, non-small cell lung cancer, pancreatic cancer, and sarcomas/soft tissue tumors [49].…”

Section: Next-generation Sequencingmentioning

confidence: 94%

“…High levels of Shannon entropy indicate analytic utility, while low levels indicate that a variable provides no new or useful information [49]. In this study, Shannon entropy levels for these cancer types from highest to lowest were colorectal cancer, high grade glioma, non-small cell lung cancer, pancreatic cancer, and sarcomas/soft tissue tumors [49]. These results suggest that for some major cancer types, including lung cancer, NGS has analytic utility and could provide useful information in cancer diagnosis without being redundant.…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer

et al. 2016

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Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.

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“…Hagemann et al designed an experiment to verify the results from NGS analysis based on in situ tissue. 53 Results suggested that NGS analysis provides reliable reference information for NSCLC diagnosis. In the field of lung cancer study, NGS has the advantage of detecting unknown mutated sites, while ddPCR focuses on individual known mutated sites.…”

Section: Next-generation Sequencing Detection For Lung Cancer Diagnosmentioning

confidence: 96%

Liquid Biopsy Promotes Non-Small Cell Lung Cancer Precision Therapy

Lü

Han

2018

Technol Cancer Res Treat

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The range of potential applications of liquid biopsies for non-small cell lung cancer management is expanded by the use of circulating tumor deoxyribonucleic acid and circulating tumor cells. Principal studies have demonstrated the predictive accuracy of droplet digital polymerase chain reaction detection, next-generation sequencing, and circulating tumor cells detection in patients with non-small cell lung cancer. The translational potential of these liquid biopsy technologies promotes the improvement of sensitivity and specificity in genomic and molecular methods. Here, we highlight the realities and challenges associated with the use of liquid biopsies for the detection of non-small cell lung cancer in patients. However, liquid biopsy technologies including circulating tumor cells detection, droplet digital polymerase chain reaction detection, and next-generation sequencing detection for precision therapy in non-small cell lung cancer will show substantive clinical applications in the future.

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Diagnostic yield of targeted next generation sequencing in various cancer types: An information-theoretic approach

Cited by 9 publications

References 47 publications

Clinical Genotyping of Non–Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

Clinical Genotyping of Non–Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer

Liquid Biopsy Promotes Non-Small Cell Lung Cancer Precision Therapy

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