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

Kamps, Rick; Brandão, Rita D.; Bosch, Bianca Jc van den; Paulussen, Aimée D C; Xanthoulea, Sofia; Blok, Marinus J.; Romano, Andrea

doi:10.3390/ijms18020308

Cited by 397 publications

(313 citation statements)

References 301 publications

(353 reference statements)

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“…With the development of nextgeneration sequencing (NGS), a technology capable of simultaneously sequencing millions of DNA fragments without previous sequence knowledge, increases in the positive rate of ctDNA mutation detection have become feasible (10). NGS has been widely used in genetic analysis of patients with various tumors including GIST because of the advantages of higher reliability and lower costs (10,11).…”

Section: Introductionmentioning

confidence: 99%

Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

Chen

Shao³

et al. 2018

Molecular Cancer Therapeutics

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Gastrointestinal stromal tumors (GIST) are the most common mesenchymal tumor of digestive tract. In the past, tissue biopsy was the main method for the diagnosis of GISTs. Although, circulating tumor DNA (ctDNA) detection by next-generation sequencing (NGS) may be a feasible and replaceable method for diagnosis of GISTs. We retrospectively analyzed the data for ctDNA and tissue DNA detection from 32 advanced GIST patients. We found that NGS obviously increased the positive rate of ctDNA detection. ctDNA detection identified rare mutations that were not detected in tissue DNA detection. Tumor size and Ki-67 were significant influencing factors of the positive rate of ctDNA detection and concordance between ctDNA and tissue DNA detection. In all patients, the concordance rate between ctDNA and tissue DNA detection was 71.9%, with moderate concordance, but the concordance was strong for patients with tumor size > 10 cm or Ki-67 > 5%. Tumor size, mitotic figure, Ki-67, and ctDNA mutation type were the significant influencing factors of prognosis, but only tumor size and ctDNA mutation type, were the independent prognostic factors for advanced GIST patients. We confirmed that ctDNA detection by NGS is a feasible and promising method for the diagnosis and prognosis of advanced GIST patients.

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Section: Introductionmentioning

confidence: 99%

Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

Chen

Shao³

et al. 2018

Molecular Cancer Therapeutics

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“…Clinical application of Next Generation Sequencing (NGS) has enhanced molecular profiling capacity (Kamps et al., 2017). NGS sequencing methods are now commonly used in personalized clinical cancer care (Chang et al., 2017; Green et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

“…NGS sequencing methods are now commonly used in personalized clinical cancer care (Chang et al., 2017; Green et al., 2016). However, NGS also yields increasing numbers of variants that predominantly are of unknown significance and compounds the challenge of variant interpretation (Good, Ainscough, McMichael, Su, & Griffith, 2014; Kamps et al., 2017). As clinical analysis of large volumes of patient variant data becomes increasingly difficult, inconsistencies increase both in variant interpretation and reporting between laboratories (Harrison et al., 2017).…”

Section: Introductionmentioning

confidence: 99%

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards

et al. 2018

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Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant‐associated knowledge are central problems that arise with increased usage of clinical next‐generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open‐source platform supporting crowdsourced and expert‐moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field‐by‐field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group‐level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.

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“…NGS technology enables the simultaneous sequencing of a large number of target genes and provides early detection and diagnostic markers to develop NGS-based cancer molecular diagnosis [41][42][43].…”

Section: Advantages Of Ngs Technologiesmentioning

confidence: 99%

“…such as ATM, CHEK2, PALB2, and TP53, have also been shown to confer high BC risk [43]. Therefore, a multiplegene sequencing panel was developed using NGS, which contained 68 genes including BRCA1, BRCA2, ATM, and TP53.…”

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confidence: 99%

The applications of massive parallel sequencing (next-generation sequencing) in research and molecular diagnosis of human genetic diseases

Nguyen¹,

Le²,

Nguyen³

et al. 2018

VJSTE

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Abstract:Next-generation sequencing (NGS) is a high throughput sequencing technology, which has revolutionized both basic and clinical research of the human genetic disorders. This technology is also called massively parallel sequencing (MPS) due to its ability to generate a huge amount of output data in a cost-and time-effective manner. NGS is widely utilized for different sequencing applications such as targeted sequencing (a group of candidate genes), exome sequencing (all coding regions), and whole genome sequencing (the entire human genome). With NGS, a variety of genomic aberrations can be screened simultaneously such as common and rare variants, structural variations (amplifications and deletion), copy-number variation, and fusion transcripts. NGS technologies combined with advanced bioinformatic analysis have tremendously expanded our knowledge. On the one hand, the basic research area involves direct use of NGS to identify novel variations and determine human disease mechanisms. On the other hand, clinical research is being advanced by highthroughput genetic tests with high resolution and clinically relevant genetic information for molecular diagnoses of human disorders. In this communication, we introduce NGS technologies and review a few key areas where NGS has made a significant impact, with an emphasis on the application of NGS to the identification of the molecular bases of human genetic diseases.

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

Cited by 397 publications

References 301 publications

Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards

The applications of massive parallel sequencing (next-generation sequencing) in research and molecular diagnosis of human genetic diseases

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