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Sökning: WFRF:(Filges Stefan 1991)

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  • Bjursten, Sara, et al. (författare)
  • Response to BRAF/MEK Inhibition in A598_T599insV BRAF Mutated Melanoma
  • 2019
  • Ingår i: Case Reports in Oncology. - : S. Karger AG. - 1662-6575. ; 12:3, s. 872-879
  • Tidskriftsartikel (refereegranskat)abstract
    • Approximately 50% of patients with metastatic melanoma harbor an activating BRAF mutation. Tumors with activating mutation BRAF gene proliferate excessively and can be treated with targeted BRAF-inhibitors in combination with MEK inhibitors. The most common BRAF mutation occurs at amino acid position 600. Other BRAF mutations are rare and their predictive value for treatment response to BRAF/MEK inhibition is low. Here, we report on a patient with a BRAF A598_T599insV mutated melanoma, a mutation that has only been described in one previous melanoma patient in which the treatment response to BRAF/MEK inhibition was transient. Our patient had a large ulcerated metastasis that showed a durable complete response implying that BRAF/MEK inhibition should be considered a treatment option for this mutation. We analyzed circulating cell-free tumor DNA (ctDNA) carrying the BRAF A598_T599insV mutation throughout treatment. The allele frequency of BRAF A598_T599insV decreased during regression of the tumors, indicating that this method has potential to monitor treatment response. Our case demonstrates durable response to BRAF/MEK inhibition in a melanoma patient carrying a BRAF A598_T599insV mutation. In addition, we show that allele frequency analysis of A598_T599insV mutation in blood using ultrasensitive sequencing can be used to monitor treatment response.
  • Crescitelli, Rossella, 1985, et al. (författare)
  • Extracellular vesicle DNA from human melanoma tissues contains cancer-specific mutations
  • 2022
  • Ingår i: Frontiers in Cell and Developmental Biology. - : Frontiers Media SA. - 2296-634X. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • Liquid biopsies are promising tools for early diagnosis and residual disease monitoring in patients with cancer, and circulating tumor DNA isolated from plasma has been extensively studied as it has been shown to contain tumor-specific mutations. Extracellular vesicles (EVs) present in tumor tissues carry tumor-derived molecules such as proteins and nucleic acids, and thus EVs can potentially represent a source of cancer-specific DNA. Here we identified the presence of tumor-specific DNA mutations in EVs isolated from six human melanoma metastatic tissues and compared the results with tumor tissue DNA and plasma DNA. Tumor tissue EVs were isolated using enzymatic treatment followed by ultracentrifugation and iodixanol density cushion isolation. A panel of 34 melanoma-related genes was investigated using ultra-sensitive sequencing (SiMSen-seq). We detected mutations in six genes in the EVs (BRAF, NRAS, CDKN2A, STK19, PPP6C, and RAC), and at least one mutation was detected in all melanoma EV samples. Interestingly, the mutant allele frequency was higher in DNA isolated from tumor-derived EVs compared to total DNA extracted directly from plasma DNA, supporting the potential role of tumor EVs as future biomarkers in melanoma.
  • Egyud, M., et al. (författare)
  • Detection of Circulating Tumor DNA in Plasma: A Potential Biomarker for Esophageal Adenocarcinoma
  • 2019
  • Ingår i: Annals of Thoracic Surgery. - : Elsevier BV. - 0003-4975. ; 108:2, s. 343-349
  • Tidskriftsartikel (refereegranskat)abstract
    • Background. Recent literature has demonstrated the potential of "liquid biopsy" and detection of circulating tumor (ct)DNA as a cancer biomarker. However, to date there is a lack of data specific to esophageal adenocarcinoma (EAC). This study was conducted to determine how detection and quantification of ctDNA changes with disease burden in patients with EAC and evaluate its potential as a biomarker in this population. Methods. Blood samples were obtained from patients with stage I to IV EAC. Longitudinal blood samples were collected from a subset of patients. Imaging studies and pathology reports were reviewed to determine disease course. Tumor samples were sequenced to identify mutations. Mutations in plasma DNA were detected using custom, barcoded, patient-specific sequencing libraries. Mutations in plasma were quantified, and associations with disease stage and response to therapy were explored. Results. Plasma samples from a final cohort of 38 patients were evaluated. Baseline plasma samples were ctDNA positive for 18 patients (47%) overall, with tumor allele frequencies ranging from 0.05% to 5.30%. Detection frequency of ctDNA and quantity of ctDNA increased with stage. Data from longitudinal samples indicate that ctDNA levels correlate with and precede evidence of response to therapy or recurrence. Conclusions. ctDNA can be detected in plasma of EAC patients and correlates with disease burden. Detection of ctDNA in early-stage EAC is challenging and may limit diagnostic applications. However, our data demonstrate the potential of ctDNA as a dynamic biomarker to monitor treatment response and disease recurrence in patients with EAC. (C) 2019 by The Society of Thoracic Surgeons
  • Egyud, Matthew, et al. (författare)
  • Plasma circulating tumor DNA as a potential tool for disease monitoring in head and neck cancer.
  • 2019
  • Ingår i: Head & neck. - : Wiley. - 1097-0347 .- 1043-3074. ; 41:5, s. 1351-1358
  • Tidskriftsartikel (refereegranskat)abstract
    • Recommendations for perioperative therapy in head and neck cancer are not explicit and recurrence occurs frequently. Circulating tumor DNA is an emerging cancer biomarker, but has not been extensively explored for detection of recurrence in head and neck cancer.Patients diagnosed with head and neck squamous cell carcinoma were recruited into the study protocol. Tumors were sequenced to identify patient-specific mutations. Mutations were then identified in plasma circulating tumor DNA from pre-treatment blood samples and longitudinally during standard follow-up. Circulating tumor DNA status during follow-up was correlated to disease recurrence.Samples were taken from eight patients. Tumor mutations were verified in seven patients. Baseline circulating tumor DNA was positive in six patients. Recurrence occurred in four patients, two of whom had detectable circulating tumor DNA prior to recurrence.Circulating tumor DNA is a potential tool for disease and recurrence monitoring following curative therapy in head and neck cancer, allowing for better prognostication, and/or modification of treatment strategies.
  • Elliott, Kerryn, et al. (författare)
  • Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers.
  • 2018
  • Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 14:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions, in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor (TF) binding sites. While sometimes interpreted as functional driver events, these mutations are commonly believed to be due to locally inhibited DNA repair. Here, we first show that low-dose UV light induces mutations preferably at a known ETS promoter hotspot in cultured cells even in the absence of global or transcription-coupled nucleotide excision repair (NER). Further, by genome-wide mapping of cyclobutane pyrimidine dimers (CPDs) shortly after UV exposure and thus before DNA repair, we find that ETS-related mutation hotspots exhibit strong increases in CPD formation efficacy in a manner consistent with tumor mutation data at the single-base level. Analysis of a large whole genome cohort illustrates the widespread contribution of this effect to recurrent mutations in melanoma. While inhibited NER underlies a general increase in somatic mutation burden in regulatory elements including ETS sites, our data supports that elevated DNA damage formation at specific genomic bases is at the core of the prominent promoter mutation hotspots seen in skin cancers, thus explaining a key phenomenon in whole-genome cancer analyses.
  • Filges, Stefan, 1991, et al. (författare)
  • Digital Quantification of Chemical Oligonucleotide Synthesis Errors
  • 2021
  • Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 67:10, s. 1384-1394
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Chemically synthesized oligonucleotides are vital to most nucleic acids-based technologies and several applications are sensitive to oligonucleotide sequence errors. However, it is challenging to identify and quantify the types and amount of errors in synthetic oligonucleotides. METHODS: We applied a digital sequencing approach using unique molecular identifiers to quantify errors in chemically synthesized oligonucleotides from multiple manufacturers with different synthesis strategies, purity grades, batches, and sequence context. RESULTS: We detected both deletions and substitutions in chemical oligonucleotide synthesis, but deletions were 7 times more common. We found that 97.2% of all analyzed oligonucleotide molecules were intact across all manufacturers and purity grades, although the number of oligonucleotide molecules with deletions ranged between 0.2% and 11.7% for different types. Different batches of otherwise identical oligonucleotide types also varied significantly, and batch effect can impact oligonucleotide quality more than purification. We observed a bias of increased deletion rates in chemically synthesized oligonucleotides toward the 5'-end for 1 out of 2 sequence configurations. We also demonstrated that the performance of sequencing assays depends on oligonucleotide quality. CONCLUSIONS: Our data demonstrate that manufacturer, synthesis strategy, purity, batch, and sequence context all contribute to errors in chemically synthesized oligonucleotides and need to be considered when choosing and evaluating oligonucleotides. High-performance oligonucleotides are essential in numerous molecular applications, including clinical diagnostics.
  • Filges, Stefan, 1991, et al. (författare)
  • Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes.
  • 2019
  • Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Liquid biopsy and detection of tumor-associated mutations in cell-free circulating DNA often requires the ability to identify single nucleotide variants at allele frequencies below 0.1%. Standard sequencing protocols cannot achieve this level of sensitivity due to background noise from DNA damage and polymerase induced errors. Addition of unique molecular identifiers allows identification and removal of errors responsible for this background noise. Theoretically, high fidelity enzymes will also reduce error rates in barcoded NGS but this has not been thoroughly explored. We evaluated the impact of polymerase fidelity on the magnitude of error reduction at different steps of barcoded NGS library construction. We find that barcoding itself displays largest impact on error reduction, even with low fidelity polymerases. Use of high fidelity polymerases in the barcoding step of library construction further suppresses error in barcoded NGS, and allows detection of variant alleles below 0.1% allele frequency. However, the improvement in error correction is modest and is not directly proportional to polymerase fidelity. Depending on the specific application, other polymerase characteristics such as multiplexing capacity, PCR efficiency, buffer requirements and ability to amplify targets with high GC content may outweigh the relatively small additional decrease in error afforded by ultra-high fidelity polymerases.
  • Filges, Stefan, 1991 (författare)
  • Next generation molecular diagnostics using ultrasensitive sequencing
  • 2022
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Massively parallel sequencing enables the exploration of the genetic heterogeneity within microbial, viral and tumor cell populations. Detecting circulating tumor DNA in blood and other body fluids has the potential to revolutionize molecular diagnostics. However, these liquid biopsies typically contain only minute amounts of highly degraded DNA and standard sequencing approaches lack the resolution to detect rare genetic variants. The overall goal of this thesis was to develop an ultrasensitive sequencing approach with single molecule resolution that requires only minimal amounts of material. To this end, we developed the simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing protocol (SiMSen-Seq). SiMSen-Seq achieves ultrasensitive detection of nucleotide variants by attaching unique molecular identifiers to target DNA molecules using PCR primers. SiMSen-Seq is enabled by highly optimized reaction conditions and the use of a stem-loop structure that prevents the UMI from forming non-specific PCR products. We showed that ultrasensitive variant detection is attained mainly by using UMI, while gains in sensitivity from using high-fidelity polymerases were minor. We also demonstrated that oligonucleotide quality is essential in numerous molecular applications, including SiMSen-Seq. Next generation diagnostics tools also demand optimized preanalytical conditions to achieve the necessary variant detection sensitivity, while remaining fast, simple, and cost efficient. Therefore, we established a workflow for cell-free DNA analysis and developed quantitative PCR-based quality controls to evaluate each experimental step. We also developed a bioinformatics pipeline for processing any type of targeted sequencing data containing unique molecular identifiers, including barcode clustering, error correction, variant calling, and visualization. Next, we used SiMSen-Seq in applications requiring ultrasensitive mutant detection. We first employed SiMSen-Seq to experimentally confirm that UV light rapidly induces highly recurrent mutations within a specific promotor motif. These mutations remained sub-clonal even after weeks of cell culture, arguing against a tumor-driving role. Our results highlight the importance of sequence context for the interpretation of somatic variants in cancer. We also showed that ctDNA can be used as a clinical biomarker for tumor burden and to monitor treatment efficacy in uveal melanoma. Patients with high ctDNA levels had worse overall survival, demonstrating the clinical utility of circulating tumor-DNA-based liquid biopsy analysis. In conclusion, we showed that SiMSen-Seq is a simple, flexible, low-DNA input protocol that enables rare variant detection to address a multitude of clinical and basic research questions.
  • Fredriksson, Nils Johan, 1979-, et al. (författare)
  • Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature
  • 2017
  • Ingår i: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 13:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Sequencing of whole tumor genomes holds the promise of revealing functional somatic regulatory mutations, such as those described in the TERT promoter. Recurrent promoter mutations have been identified in many additional genes and appear to be particularly common in melanoma, but convincing functional data such as influence on gene expression has been more elusive. Here, we show that frequently recurring promoter mutations in melanoma occur almost exclusively at cytosines flanked by a distinct sequence signature, TTCCG, with TERT as a notable exception. In active, but not inactive, promoters, mutation frequencies for cytosines at the 5' end of this ETS-like motif were considerably higher than expected based on a UV trinucleotide mutational signature. Additional analyses solidify this pattern as an extended context-specific mutational signature that mediates an exceptional position-specific vulnerability to UV mutagenesis, arguing against positive selection. We further use ultra-sensitive amplicon sequencing to demonstrate that cell cultures exposed to UV light quickly develop subclonal mutations specifically in affected positions. Our findings have implications for the interpretation of somatic mutations in regulatory regions, and underscore the importance of genomic context and extended sequence patterns to accurately describe mutational signatures in cancer.
  • He, H. J., et al. (författare)
  • Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements
  • 2019
  • Ingår i: Journal of Molecular Diagnostics. - : Elsevier BV. - 1525-1578. ; 21:4, s. 658-676
  • Tidskriftsartikel (refereegranskat)abstract
    • We conducted a multilaboratory assessment to determine the suitability of a new commercially available reference material with 40 cancer variants in a background of wild-type DNA at four different variant allele frequencies (VAFs): 2%, 0.50%, 0.125%, and 0%. The variants include single nucleotides, insertions, deletions, and two structural variations selected for their clinical importance and to challenge the performance of next-generation sequencing (NGS) methods. Fragmented DNA was formulated to simulate the size distribution of circulating wild-type and tumor DNA in a synthetic plasma matrix. DNA was extracted from these samples and characterized with different methods and multiple laboratories. The various extraction methods had differences in yield, perhaps because of differences in chemistry. Digital PCR assays were used to measure VAFs to compare results from different NGS methods. Comparable VAFs were observed across the different NGS methods. This multilaboratory assessment demonstrates that the new reference material is an appropriate tool to determine the analytical parameters of different measurement methods and to ensure their quality assurance.
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