Comparison of Next-Generation Sequencing and Mutation-Specific Platforms in Clinical Practice

Hinrichs, John W. J.; Blokland, W. T. M. Van; Moons, Michiel J.; Radersma, Remco D.; Loon, Joyce H. Radersma-van; Voijs, Carmen M. A. de; Rappel, Sophie B.; Koudijs, Marco J.; Besselink, Nicolle; Willems, Stefan M.; Weger, Roel A. de

doi:10.1309/ajcp40xetvyamjpy

Cited by 42 publications

(27 citation statements)

References 21 publications

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“…This is consistent with a recent case series comparing multiple NGS platforms with dedicated hotspot assays for EGFR , KRAS , and BRAF mutations using formalin-fixed, paraffin-embedded tumor. [2324] Evolving tumors can be tested in the same patient using single-gene assays after NGS has been employed. Comparing the genetic mutations in the new lesions to the known NGS results could be a method to further adjudicate tumor recurrence versus a second primary cancer.…”

Section: Discussionmentioning

confidence: 99%

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology

et al. 2017

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Background:Next-generation sequencing (NGS) with a multi-gene panel is now available for patients with lung adenocarcinoma, but the performance characteristics and clinical utility of this testing are not well-described. We present the results of an extended 467 gene panel in a series of advanced, highly selected nonsmall cell lung cancer (NSCLC) patients using a range of specimens, including predominantly small biopsy and cytology specimens.Materials and Methods:A retrospective review of 22 NSCLC biopsies sent for NGS using an extended gene panel from January 2014 to July 2015. The customized NGS panel sequences 467 cancer-associated genes with exonic and intronic sequences obtained from purified tumor DNA. Genomic alterations, patient characteristics, and success of testing were determined.Results:The majority of samples tested were metastatic lung adenocarcinoma on final pathology. Of the 22 specimens tested, 5 (22.7%) were surgical resections and 17 (77.3%) were small biopsy and cytology specimens. Twenty-one (95%) of the specimens were adequate for full sequencing and yielded a total of 204 genomic alterations (average 8.9 per tumor), of which 17 (average 0.81 per tumor) were actionable and/or clinically relevant. Genomic alterations were found most commonly in the TP53, EGFR, EPHB1, MLL3, APC, SETD2, KRAS, DNMT3A, RB1, CDKN2A, ARID1A, EP300, KDM6B, RAD50, STK11, and BRCA2 genes.Conclusions:NGS using a comprehensive gene panel was performed successfully in 95% of all NSCLC cases in this series, including 94% small biopsy and cytology specimens and 100% surgical resections. This custom assay was performed on a range of tumor specimens and demonstrates that small specimens are able to provide a similar depth of information as larger ones. As many patients present at an advanced stage and only small specimens are obtained, the information these provide has the potential for guiding treatment in highly selected patients with advanced lung adenocarcinoma.

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Section: Discussionmentioning

confidence: 99%

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology

et al. 2017

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“…360 reads/amplicon), while the Ion Torrent ™ PGM generated 4,000,000 high quality reads (ca. 1,500 reads/amplicon) [78]. This study demonstrates that, compared to Roche 454, NGS sequencing on the Ion Torrent ™ PGM platform is more informative and faster.…”

Section: Next-generation Sequencingmentioning

confidence: 96%

“…In 14 out of 25 samples, KRAS mutations that had been previously detected by Sanger sequencing combined with high-resolution melting (HRM) were detected by the Cobas ® , Rotor-Gene, and Ion Torrent ™ platforms [78]. In 10 out of these 14 samples, the Roche 454 could also detect the relevant mutations.…”

Section: Next-generation Sequencingmentioning

confidence: 99%

“…In 10 out of these 14 samples, the Roche 454 could also detect the relevant mutations. The four other “mutated” samples and one “unmutated” sample could not be analyzed with Roche 454 because of technical sequencing issues (generation of unspecific PCR products), while all of the clinically relevant EGFR mutations that had been detected with HRM and Sanger sequencing were detected with all four platforms [78]. Notably, the Roche 454 generated 53,000 high quality reads (ca.…”

Section: Next-generation Sequencingmentioning

confidence: 99%

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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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“…Although the biochemistry of the diverse platforms might be different, the workflow is similar (Shendure and Hanlee, 2008) including template preparation, sequencing and imaging, genome alignment, and assembly (Metzker, 2010). The advantages as well as disadvantages of diverse platforms (Metzker, 2010;Quail et al, 2012;Doi et al, 2014;Hinrichs et al, 2015;Hahn et al, 2016) have been reviewed. The most immediate field where NGS have been introduced into daily routine diagnostics in microbiology is surveillance and outbreak investigation.…”

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confidence: 99%

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

Ruppitsch

2016

Die Bodenkultur: Journal of Land Management, Food and Environment

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SummaryConstant confrontations with microbial threats pose major challenges to human and animal health, agricultural and food production, and public safety. Identifying pathogenic bacteria (species) and tracking strains (by series of well-characterized isolates) to their sources are especially important in outbreak investigations. Compared to the identification of the species, the identification of the source and spread of microbial infections represents a major-and many times futile-challenge. This is due to the multitude of ways microorganisms can occur and spread within healthcare facilities and in the community; how, when, and where they can contaminate the complex nutrition chain, leading to natural and man-made outbreaks. Typing is the characterization of isolates or strains below species or subspecies level. Typing of bacterial isolates is an essential procedure to identify the microbe causing the illness or to track down an outbreak to the suspected source. In the genomic era, the introduction of molecular methods has largely replaced phenotypic methods and "molecular epidemiology" has emerged as a new discipline. The current molecular typing methods can be classified into three categories: (a) PCR-based methods, (b) DNA fragment analysis-based methods, and (c) DNA sequence-based methods, including the new exciting era of high-throughput genome sequencing. Keywords

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Comparison of Next-Generation Sequencing and Mutation-Specific Platforms in Clinical Practice

Abstract: Sensitivity for detecting mutations was highly comparable among all platforms. The choice for either a dedicated genotyping platform or an NGS platform is basically a trade-off between speed and genetic information.

Cited by 42 publications

References 21 publications

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology

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

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

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