Noninvasive diagnosis and monitoring of mutations by deep sequencing of circulating tumor DNA in esophageal squamous cell carcinoma

Luo, Hui; Li, Hong; Hu, Zhaoyang; Wu, Hongjin; Liu, Cheng‐Lin; Liu, Ying; Zhang, Xiaoyan; Lin, Ping; Hou, Qiang; Ding, Guohui; Wang, Yan; Li, Shuang; Wei, Dongkai; Qiu, Feng; Li, Yixue; Wu, Shixiu

doi:10.1016/j.bbrc.2016.02.011

Cited by 45 publications

(42 citation statements)

References 19 publications

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“…In addition, TP53 R273H mutation was shown in three sub-regions of patient E111 with VAF of 22.98%, 42.86% and 34.79% respectively, but only 0.93% in cfDNA. This observation agreed with a previous study that one ESCC patient had a TP53 N1311 mutation with VAF of 52.9 % in tumor and 1.3% in cfDNA from preoperative plasma [43]. One possible explanation could be that the colonies of tumor cells with driver mutations are resistant to apoptosis, and rarely release mutated DNA fragments to plasma.…”

Section: Discussionsupporting

confidence: 93%

Detection of somatic mutations in circulating cell-free DNA from patients with esophageal squamous cell carcinoma

Yuan

Wang

Geng

et al. 2020

Preprint

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Background: The aim of this study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) from patients with esophageal squamous cell carcinoma (ESCC). Methods: Paired multi-regional tumor tissues, cfDNA and white blood cells (WBCs) collected from five ESCC patients before treatment from a prospective study (NCT02395705). Of them, samples from Cohort 1 (E102 and E110) were sequenced by whole-exome sequencing (WES) and those from Cohort 2 (E104, E111 and E121) were sequenced by targeted captured sequencing with a panel of 560 cancer-related genes respectively. To call somatic single nucleotide variations (SNVs) by comparing the solid tumor or cfDNA with matched WBCs, the minimal variant allele frequency (VAFmin) as 0.1% and P value <0.05 were allowed. Results: Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were successfully sequenced. In Cohort 1, 596 (596/712, 83%) and 562 (562/796, 71%) were heterogeneous SNVs in E102 and E110 respectively. There was a statistically significant linear relationship between the VAFs for tumor and cfDNA (R2 = 0.78, P <0.0001). In Cohort 2, 296 (296/323, 92%), 384 (384/423, 91%) and 331 (331/357, 93%) were heterogeneous SNVs in E104, E111 and E121respectively. cfDNA could recover an average of 60.7% (31/51; range, 35.7%-76.2%) of somatic mutations present in matched solid tumors. The correlation of VAFs between cfDNA and matched solid tumor was significantly positive (r2 =0.92, P <0.0001).Conclusions: Both sequencing approaches revealed the highly intratumoral heterogeneity in ESCC and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA. Further validation in cfDNA is required to define its potential utility for ESCC in clinical practice. Trial registrationAll patients selected in this study were from the registered clinical trial from ClinicalTrials.gov (NCT02395705). Date of registration: March 24, 2015.

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Section: Discussionsupporting

confidence: 93%

Detection of somatic mutations in circulating cell-free DNA from patients with esophageal squamous cell carcinoma

Yuan

Wang

Geng

et al. 2020

Preprint

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“…To reduce the sequencing errors confound with rare mutations, a NGS method termed Duplex sequencing was developed these years and may be useful in future plasma sequencing (45)(46)(47). In addition, given the capability of NGS test to detect variants with low MAF, the correlation between the NGS clinical report and the effect of targeted therapy still need further assessment (48). Finally, our NCP assay can give more mutation information and thus expand the treatment choices for patients, but more efforts still need to be done for future cancer diagnostics.…”

Section: Discussionmentioning

confidence: 99%

Development and validation of an ultra-high sensitive next-generation sequencing assay for molecular diagnosis of clinical oncology

She

Zhu

et al. 2016

International Journal of Oncology

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Abstract. Dramatic improvements in the understanding of oncogenes have spurred the development of molecular target therapies, which created an exigent need for comprehensive and rapid clinical genotyping. Next-generation sequencing (NGS) assay with increased performance and decreased cost is becoming more widely used in clinical diagnosis. However, the optimization and validation of NGS assay remain a challenge, especially for the detection of somatic variants at low mutant allele fraction (MAF). In the present study, we developed and validated the Novogene Comprehensive Panel (NCP) based on targeted capture for NGS analysis. Due to the high correlation between SNV/INDEL detection performance and target coverage, here we focused on these two types of variants for our deep sequencing strategy. To validate the capability of NCP in single-nucleotide variant (SNV) and small insert and deletion (INDEL) detection, we implemented a practical validation strategy with pooled cell lines, deep sequencing of pooled samples (>2000X average unique coverage across target region) achieving >99% sensitivity and high specificity (positive predictive value, PPV >99%) for all types of variations with expected MAF >5%. Furthermore, given the high sensitivity and that false positive may exist in this assay, we confirmed its accuracy of variants with MAF <5% using 35 formalin-fixed and paraffin-embedded (FFPE) tumor specimens by QuantStudio 3D Digital PCR (dPCR; Life Technologies) and obtained a high consistency (32 of 35 mutations detected by NGS were verified). We also used the amplification refractory mutation system (ARMS) to verify the variants with a MAF in a broad range of 2-63% detected in 33 FFPE samples and reached a 100% PPV for this assay. As a potential clinical diagnosis tool, NCP can robustly and comprehensively analyze clinical-related genes with high sensitivity and low cost.

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“…ctDNA analysis of patients with squamous cell carcinoma (SCC) of the esophagus with the use of a 90gene panel was associated with sensitivity of 94% and 75%, respectively, when detecting ≥1 or ≥2 mutant genes, suggesting that ctDNA analysis can help monitor treatment effect in these patients [32]. In multivariate analysis, a higher plasma cyclin D1 (CCND1; 11q13) to dopamine receptor D2 (DRD2; 11q22-23) ratio (C/D ratio) was significantly correlated with worse prognosis [33].…”

Section: Esophageal Carcinomamentioning

confidence: 99%

Circulating tumor DNA analysis in the era of precision oncology

et al. 2020

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The spatial and temporal genomic heterogeneity of various tumor types and advances in technology have stimulated the development of circulating tumor DNA (ctDNA) genotyping. ctDNA was developed as a non-invasive, cost-effective alternative to tumor biopsy when such biopsy is associated with significant risk, when tumor tissue is insufficient or inaccessible, and/or when repeated assessment of tumor molecular abnormalities is needed to optimize treatment. The role of ctDNA is now well established in the clinical decision in certain alterations and tumors, such as the epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer and the v-Ki-ras2 kirsten rat sarcoma viral oncogene homolog (KRAS) mutation in colorectal cancer. The role of ctDNA analysis in other tumor types remains to be validated. Evolving data indicate the association of ctDNA level with tumor burden, and the usefulness of ctDNA analysis in assessing minimal residual disease, in understanding mechanisms of resistance to treatment, and in dynamically guiding therapy. ctDNA analysis is increasingly used to select therapy. Carefully designed clinical trials that use ctDNA analysis will increase the rate of patients who receive targeted therapy, will elucidate our understanding of evolution of tumor biology and will accelerate drug development and implementation of precision medicine. In this article we provide a critical overview of clinical trials and evolving data of ctDNA analysis in specific tumors and across tumor types.

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Noninvasive diagnosis and monitoring of mutations by deep sequencing of circulating tumor DNA in esophageal squamous cell carcinoma

Cited by 45 publications

References 19 publications

Detection of somatic mutations in circulating cell-free DNA from patients with esophageal squamous cell carcinoma

Detection of somatic mutations in circulating cell-free DNA from patients with esophageal squamous cell carcinoma

Development and validation of an ultra-high sensitive next-generation sequencing assay for molecular diagnosis of clinical oncology

Circulating tumor DNA analysis in the era of precision oncology

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