Integration of Liquid Biopsies into Clinical Laboratory Applications via NGS in Cancer Diagnostics

Sonmezler, Ozge; Boğa, İbrahim; Bişgin, Atıl

doi:10.7754/clin.lab.2019.190836

Cited by 6 publications

(4 citation statements)

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“…Moreover, the co-occurrence of mutations in the 25 driver genes was compared in 97 patients from a clinical cohort and TCGA samples in order to validate their reliability in different cohorts. Ample evidence has shown that mutations of the 25 driver genes, which were identified in the present study, could promote oncogenic transformation and all of them have been detected as diagnostic NGS to facilitate precision therapeutic approaches in lung cancer ( 27 – 30 ). Among them, EGFR mutations are one of the best-characterized, which have been implicated in pathogenesis of NSCLC ( 31 ).…”

Section: Discussionmentioning

confidence: 74%

Next‑generation sequencing‑based identification of EGFR and NOTCH2 complementary mutations in non‑small cell lung cancer

Niu

Dang

et al. 2021

Oncol Lett

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Although targeted therapy has emerged as an effective treatment strategy for non-small cell lung cancer (NSCLC), some patients cannot benefit from such therapy due to the limited number of therapeutic targets. The present study aimed to identify mutated genes associated with clinicopathological characteristics and prognosis and to screen for mutations that are not concurrent with applicable drug target sites in patients with NSCLC. Tumor tissue and blood samples were obtained from 97 patients with NSCLC. A lung cancer-specific panel of 55 genes was established and analyzed using next-generation sequencing (NGS). The results obtained from the clinical cohort were compared with the NSCLC dataset from The Cancer Genome Atlas (TCGA). Subsequently, 25 driver genes were identified by taking the intersection of the 55 lung-cancer-specific genes with three databases, namely, the Catalog of Somatic Mutations in Cancer database, the Network of Cancer Genes database and Vogelstein's list. Functional annotation and protein-protein interaction analysis were conducted on these 25 driver genes. The χ 2 test and logistic regression were used to evaluate the association between mutations in the 25 driver genes and the clinicopathological characteristics of 97 patients, and phosphatase and tensin homolog (PTEN) and kirsten rat sarcoma viral oncogene homolog (KRAS) were associated with stage at diagnosis and sex, respectively, while epidermal growth factor receptor (EGFR) was associated with sex, stage at diagnosis, metastasis, CEA and CYFRA21-1. Moreover, the association between the 25 driver gene mutations and overall survival were examined using Cox regression analysis. Age and Notch homolog 2 (NOTCH2) mutations were independent prognostic factors in TCGA dataset. The correlations between statistically significant mutations in EGFR, KRAS, PTEN and NOTCH2 were further examined, both in the clinical data and TCGA dataset. There was a negative correlation between EGFR and NOTCH2 mutations (correlation coefficient, −0.078; P=0.027). Thus, the present study highlights the importance of NOTCH2 mutations and might provide novel therapeutic options for patients with NSCLC who do not harbor EGFR mutations.

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Section: Discussionmentioning

confidence: 74%

Next‑generation sequencing‑based identification of EGFR and NOTCH2 complementary mutations in non‑small cell lung cancer

Niu

Dang

et al. 2021

Oncol Lett

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“…This underlines the importance of rapidly setting up this approach in the daily clinical practice for improvement to care of lung cancer patients. Currently, LB NGS on tumor progression is beginning to be established in some comprehensive cancer centers but is not adopted as much at diagnosis and is still under heated discussion, notably for its usefulness in comparison to some targeted sequencing tests [ 21 , 156 , 157 ]. Moreover, there is still a gap between the use of LB and TB NGS at baseline in advanced NSCLC, underlying the fact that TB is still currently the best approach and the gold standard for diagnosis and detection of genetic alterations in these patients [ 158 , 159 ].…”

Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing with Liquid Biopsies from Treatment-Naïve Non-Small Cell Lung Carcinoma Patients

Hofman

2021

Cancers

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Recently, the liquid biopsy (LB), a non-invasive and easy to repeat approach, has started to compete with the tissue biopsy (TB) for detection of targets for administration of therapeutic strategies for patients with advanced stages of lung cancer at tumor progression. A LB at diagnosis of late stage non-small cell lung carcinoma (NSCLC) is also being performed. It may be asked if a LB can be complementary (according to the clinical presentation or systematics) or even an alternative to a TB for treatment-naïve advanced NSCLC patients. Nucleic acid analysis with a TB by next-generation sequencing (NGS) is gradually replacing targeted sequencing methods for assessment of genomic alterations in lung cancer patients with tumor progression, but also at baseline. However, LB is still not often used in daily practice for NGS. This review addresses different aspects relating to the use of LB for NGS at diagnosis in advanced NSCLC, including its advantages and limitations.

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“…FFPE and ctDNA samples were obtained from 278 patients between 2016-2019. Genomic and circulating tumor DNA was extracted by the methodology previously optimized in our centre (Sonmezler et al, 2020;Boga et al, 2020). Quality controls of genomic materials were assessed using Qubit 4 (Thermo Scientific, USA).…”

Section: Samplingmentioning

confidence: 99%

Real-world applications of tumor mutation burden (TMB) analysis using ctDNA and FFPE samples in various cancer types of Turkish population

Boğa

Bişgin

2022

IJERR

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Tumor mutation burden (TMB) has become one of the most popular approaches in the last decade as a molecular genetic testing strategy for cancer therapeutics that represents the somatic variations per Mbase in coding regions of the genome and which can be performed via comprehensive genomic profiling (CGP) by next generation sequencing (NGS). TMB is most commonly used to stratify the patients for immunotherapy as well as the actionable variant detection for possible other therapeutics. In this context, within this study, we share our results of the TMB score distribution of cancer patients together with distinctive diagnoses and specimens. The study was conducted from a total of 278 samples. One hundred seventy six (176) of them were formalin-fixed paraffin-embedded (FFPE) tissue samples and 102 liquid biopsy samples. Samples were sequenced using a multi-gene NGS panel consisting of 486 cancer-related genes (Illumina-NextSeq500/550). Bioinformatics analyzes were performed using an optimized in-house bioinformatics pipeline. As a result, the studies of 91.7% (n=255) among all samples were successfully performed in which total of 21 different cancer types were included. The lung cancer group was the most frequent (n=43 patients), followed by 31 colorectal cancer and 22 ovarian cancer patients. The classification of TMB scoring was very high (>50), high (20-50), moderate (5-20) and low (<5). The shared data of this study represents a cancer genome atlas-like data set for TMBs of Turkish cancer patients in relation to various cancer types and specimens in comparison with The Cancer Genome Atlas (TCGA) data.

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Integration of Liquid Biopsies into Clinical Laboratory Applications via NGS in Cancer Diagnostics

Cited by 6 publications

References 0 publications

Next‑generation sequencing‑based identification of EGFR and NOTCH2 complementary mutations in non‑small cell lung cancer

Next‑generation sequencing‑based identification of EGFR and NOTCH2 complementary mutations in non‑small cell lung cancer

Next-Generation Sequencing with Liquid Biopsies from Treatment-Naïve Non-Small Cell Lung Carcinoma Patients

Real-world applications of tumor mutation burden (TMB) analysis using ctDNA and FFPE samples in various cancer types of Turkish population

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