ArticleGenome medicine2018
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing.
Article in Genome medicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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Who cites it
25 citing papers in PubMed, 42 citations in OpenAlex.
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- Comprehensive Genomic Profiling Beyond Driver Testing in Non-Squamous Non-Small Cell Lung Cancer With Known Drivers.Cancer science · 2026Article
- Feasibility of Comprehensive Genomic Profiling for Biliary Tract Cancer Using Transpapillary Biopsy Samples: A Prospective Study.Journal of hepato-biliary-pancreatic sciences · 2026Article
- tugMedi: simulator of cancer-cell evolution for personalized medicine based on the genomic data of patients.NPJ systems biology and applications · 2026Article
- Comprehensive analysis of prognosis markers with molecular features derived from pan-cancer whole-genome sequences.Human genomics · 2025Article
- Clinical utility of a comprehensive genomic profiling test for patient with advanced biliary tract cancer.International journal of clinical oncology · 2024Observational
- Dietary vitamin D intake and risk of colorectal cancer according to vitamin D receptor expression in tumors and their surrounding stroma.Journal of gastroenterology · 2024Article
- Article
- Targeting PDGF signaling of cancer-associated fibroblasts blocks feedback activation of HIF-1α and tumor progression of clear cell ovarian cancer.Cell reports. Medicine · 2024Article
- Oil blotting paper for formalin fixation increases endoscopic ultrasound-guided tissue acquisition-collected sample volumes on glass slides.Cancer medicine · 2024Article
- Feasibility of comprehensive genomic profiling using endoscopic ultrasound-guided tissue acquisition with a 22-gauge Franseen needle.DEN open · 2024Article
- Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes.NPJ genomic medicine · 2024Article
- Comparison of the novel Franseen needle versus the fine-needle aspiration needle in endoscopic ultrasound-guided tissue acquisition for cancer gene panel testing: A propensity score-matching analysis.JGH open : an open access journal of gastroenterology and hepatology · 2023Article
- Genomic features of Helicobacter pylori-naïve diffuse-type gastric cancer.The Journal of pathology · 2022Article
- Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.NAR genomics and bioinformatics · 2021Article
- A new method to accurately identify single nucleotide variants using small FFPE breast samples.Briefings in bioinformatics · 2021Article
- Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model.BMC biology · 2021Article
- Establishment and characterization of patient-derived cancer models of malignant peripheral nerve sheath tumors.Cancer cell international · 2020Article
- Establishment and characterization of novel patient-derived extraskeletal osteosarcoma cell line NCC-ESOS1-C1.Human cell · 2020Article
Corrections and comments
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Authors and funding
21 authors at 3 institutions in 1 country.
Funding
Abstract
Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.