Utility of serum DNA and pyrosequencing for the detection of EGFR mutations in non-small cell lung cancer

Akça, Hakan; Demiray, Aydın; Yaren, Arzu; Bir, Ferda; Köseler, Aylin; Iwakawa, Reika; Bağcı, Gülseren; Yokota, Jun

doi:10.1016/j.cancergen.2013.01.005

Cited by 41 publications

(35 citation statements)

References 25 publications

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“…In 2015, Alecensa (alectinib) and Tagrisso (osimertinib) were approved by the US Food and Drug Administration (USFDA) for personalized treatment of non-small-cell lung cancers (NSCLCs). In the past few years, studies have reported a series of achievements relevant to EGFR mutations [111], [112], [113]. The cobas® EGFR Mutation Test v2 from Roche was the first liquid biopsy test approved by the USFDA in June 2016 for the detection of EGFR exon 19 deletions or exon 21 (L858R) substitution mutations of NSCLC patients.…”

Section: Plasma Ctdna In the Clinicmentioning

confidence: 99%

Circulating Tumor DNA as Biomarkers for Cancer Detection

Han

Wang

Sun

2017

Genomics, Proteomics &Amp; Bioinformatics

193

163

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Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.

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Section: Plasma Ctdna In the Clinicmentioning

confidence: 99%

Circulating Tumor DNA as Biomarkers for Cancer Detection

Han

Wang

Sun

2017

Genomics, Proteomics &Amp; Bioinformatics

193

163

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“…This mechanism provides a rational explanation for the positive relationship between the tumor burden and the cfDNA amount observed in cancer patients. CTCs can also release DNA into the vasculature [28]. However, previous reports found that few CTCs are in the circulation (less than 10 cells in 7.5 ml peripheral blood) [29]; therefore, CTCs do not represent the primary resource of cfDNA.…”

Section: The Source and Characteristics Of Ctcs Cfdna And Exosomesmentioning

confidence: 99%

Liquid Biopsy for Cancer: Circulating Tumor Cells, Circulating Free DNA or Exosomes?

Zhang¹,

Xia

et al. 2017

Cell Physiol Biochem

204

146

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Precision medicine and personalized medicine are based on the development of biomarkers, and liquid biopsy has been reported to be able to detect biomarkers that carry information on tumor development and progression. Compared with traditional ‘solid biopsy’, which cannot always be performed to determine tumor dynamics, liquid biopsy has notable advantages in that it is a noninvasive modality that can provide diagnostic and prognostic information prior to treatment, during treatment and during progression. In this review, we describe the source, characteristics, technology for detection and current situation of circulating tumor cells, circulating free DNA and exosomes used for diagnosis, recurrence monitoring, prognosis assessment and medication planning.

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“…Pyrosequencing [20], a non-gel based, real-time, DNA sequencing-by-synthesis technique that is based on the luminometric detection of released pyrophosphate (PPi) during nucleotide incorporation, has also been used extensively for sample genotyping [21-26]. Pyrosequencing relies on a cascade of enzymatic reactions that yields detectable light, which is proportional to the incorporated nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand conformational polymorphism (SSCP), pyrosequencing and Sanger sequencing

et al. 2014

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BackgroundSingle-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirement for basic equipment accessible in most laboratories and low cost. This technique was previously used to detect rs4354668:A > C (g.-181A > C) SNP in the promoter of astroglial glutamate transporter (EAAT2) and the same approach was initially used here to investigate this promoter region in a cohort of newborns.ResultsUnexpectedly, four distinct DNA migration patterns were identified by SSCP. Sanger sequencing revealed two additional SNPs: g.-200C > A and g.-168C > T giving a rise to a total of ten EAAT2 promoter variants. SSCP failed to distinguish these variants reliably and thus pyrosequencing assays were developed. g.-168C > T was found in heterozygous form in one infant only with minor allele frequency (MAF) of 0.0023. In contrast, g.-200C > A and -181A > C were more common (with MAF of 0.46 and 0.49, respectively) and showed string evidence of linkage disequilibrium (LD). In a systematic comparison, 16% of samples were miss-classified by SSCP with 25-31% errors in the identification of the wild-type and homozygote mutant genotypes compared to pyrosequencing or Sanger sequencing. In contrast, SSCP and pyrosequencing of an unrelated single SNP (rs1835740:C > T), showed 94% concordance.ConclusionOur data suggest that SSCP cannot always detect reliably several closely located SNPs. Furthermore, caution is needed in the interpretation of the association studies linking only one of the co-inherited SNPs in the EAAT2 promoter to human diseases.

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Utility of serum DNA and pyrosequencing for the detection of EGFR mutations in non-small cell lung cancer

Cited by 41 publications

References 25 publications

Circulating Tumor DNA as Biomarkers for Cancer Detection

Circulating Tumor DNA as Biomarkers for Cancer Detection

Liquid Biopsy for Cancer: Circulating Tumor Cells, Circulating Free DNA or Exosomes?

Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand conformational polymorphism (SSCP), pyrosequencing and Sanger sequencing

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