Detection and Quantification of KIT Mutations in ctDNA by Plasma Safe-SeqS

Fredebohm, Johannes; Mehnert, Daniel H.; Löber, Ann-Kathrin; Holtrup, Frank; Rahden, Vanessa van; Angenendt, Philipp; Diehl, Frank

doi:10.1007/978-3-319-42044-8_34

Cited by 15 publications

(4 citation statements)

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“…This sequencing strategy uses single-molecule barcoding before PCR amplification to reduce sequencing error and increase accuracy [19,20,21]. To our knowledge, SafeSEQ has so far been applied to plasma samples of metastatic colorectal cancer [22] and to gastrointestinal stromal tumors (GIST) patients [23].…”

Section: Introductionmentioning

confidence: 99%

Detection of TP53 and PIK3CA Mutations in Circulating Tumor DNA Using Next-Generation Sequencing in the Screening Process for Early Breast Cancer Diagnosis

Rodriguez

Córdoba

Aranda

et al. 2019

JCM

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Circulating tumor DNA (ctDNA) has emerged as a non-invasive “liquid biopsy” for early breast cancer diagnosis. We evaluated the suitability of ctDNA analysis in the diagnosis of early breast cancer after mammography findings, comparing PIK3CA and TP53 mutations between tumor biopsies and pre-biopsy circulating DNA. Matched plasma and frozen fresh tissue biopsies from patients with Breast Imaging-Reporting and Data System (BIRADS) 4c/5 mammography findings and subsequent diagnosis of primary breast cancer were analyzed using NGS TruSeq Custom Amplicon Low Input Panel (Illumina) and plasma SafeSEQ (Sysmex Inostics). The same plasma and tumor mutations were observed in eight of 29 patients (27.6%) with four in TP53 and five in PIK3CA mutations. Sequencing analysis also revealed four additional ctDNA mutations (three in TP53 and one in PIK3CA) previously not identified in three patients tissue biopsy. One of these patients had mutations in both genes. Age, tumor grade and size, immunohistochemical (IHC) subtype, BIRADS category, and lymph node positivity were significantly associated with the detectability of these blood tumor-derived mutations. In conclusion, ctDNA analysis could be used in early breast cancer diagnosis, providing critical clinical information to improve patient diagnosis.

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Section: Introductionmentioning

confidence: 99%

Detection of TP53 and PIK3CA Mutations in Circulating Tumor DNA Using Next-Generation Sequencing in the Screening Process for Early Breast Cancer Diagnosis

Rodriguez

Córdoba

Aranda

et al. 2019

JCM

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“…In contrast to duplex sequencing, these identifiers tag each template molecule. Safe-SeqS is able to detect MAF of 0.01% [ 149 ].…”

Section: Liquid Biopsy Platformsmentioning

confidence: 99%

Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges

Kolenčík

Shishido

Pitule

et al. 2020

Cancers

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Colorectal carcinoma (CRC) is characterized by wide intratumor heterogeneity with general genomic instability and there is a need for improved diagnostic, prognostic, and therapeutic tools. The liquid biopsy provides a noninvasive route of sample collection for analysis of circulating tumor cells (CTCs) and genomic material, including cell-free DNA (cfDNA), as a complementary biopsy to the solid tumor tissue. The solid biopsy is critical for molecular characterization and diagnosis at the time of collection. The liquid biopsy has the advantage of longitudinal molecular characterization of the disease, which is crucial for precision medicine and patient-oriented treatment. In this review, we provide an overview of CRC and the different methodologies for the detection of CTCs and cfDNA, followed by a discussion on the potential clinical utility of the liquid biopsy in CRC patient care, and lastly, current challenges in the field.

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“…The advantage of this approach is to limit base misincorporation errors during sequencing steps or basecalling errors, and to allow rare mutation detection on commercially available sequencers. To our knowledge, Safe-SeqS has been applied to plasma samples of metatastic colorectal cancer [76] and to GIST patients [77], but not to lung cancer patients.…”

Section: Technical Approaches For Ctdna Detection and Analysismentioning

confidence: 99%

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Vendrell

Mau-Them

Béganton

et al. 2017

IJMS

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Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.

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Detection and Quantification of KIT Mutations in ctDNA by Plasma Safe-SeqS

Cited by 15 publications

References 1 publication

Detection of TP53 and PIK3CA Mutations in Circulating Tumor DNA Using Next-Generation Sequencing in the Screening Process for Early Breast Cancer Diagnosis

Detection of TP53 and PIK3CA Mutations in Circulating Tumor DNA Using Next-Generation Sequencing in the Screening Process for Early Breast Cancer Diagnosis

Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

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