Mads H. Rasmussen
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View article: A reference-free strategy for circulating tumor DNA detection from whole-genome sequencing data
A reference-free strategy for circulating tumor DNA detection from whole-genome sequencing data Open
Circulating tumor DNA (ctDNA) is emerging as a promising biomarker for postoperative monitoring of cancer patients. Precise estimation of circulating tumor fraction is crucial for evaluating treatment effects and timely detection of diseas…
View article: Supplementary Table S4 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S4 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S4. Information on all ddPCR assays.
View article: Data from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Data from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Purpose:Multiple clinical trials are investigating ctDNA to guide adjuvant chemotherapy (ACT) in colorectal cancer. Timely ACT initiation necessitates early ctDNA testing, but the impact of postoperative cell-free DNA (cfDNA) and ctDNA dyn…
View article: Supplementary Figure S3 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S3 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S3. Inter-patient variation in cfDNA levels.
View article: Supplementary Figure S6 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S6 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S6. Effect of input cap on ctDNA analysis.
View article: Supplementary Figure S5 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S5 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S5. Comparing ctDNA detection using droplet digital PCR (ddPCR) and UMIseq.
View article: Supplementary Table S3 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S3 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S3. Information on panel for targeted sequencing.
View article: Supplementary Table S1 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S1 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S1. National guidelines recommending early start of adjuvant chemotherapy.
View article: Supplementary Figure S8 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S8 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S8. Postoperative ctDNA level.
View article: Supplementary Figure S7 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S7 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S7. Sankey plot of change in ctDNA status between d14 and d30 sample.
View article: Supplementary Table S2 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S2 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S2. Catalog of in-house droplet digital PCR assays.
View article: Supplementary Figure S9 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S9 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S9. Turnaround time for prospective analyses by droplet digital PCR.
View article: Supplementary Table S8 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S8 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S8. Sensitivity for detection at different metastatic sites.
View article: Supplementary Figure S2 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S2 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S2. Flowchart of patient inclusion.
View article: Supplementary Figure S4 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S4 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S4. Impact of surgical procedure and complications on cfDNA elevation.
View article: Supplementary Figure S1 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Figure S1 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Figure S1. Overview of tumor-informed workflow.
View article: Supplementary Table S5 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S5 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S5. Distribution of adjuvant chemotherapy (ACT) dependent on pathological UICC stage and age.
View article: Supplementary Table S7 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S7 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S7. Surgical approach and postoperative complications.
View article: Supplementary Table S6 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer
Supplementary Table S6 from Timing of ctDNA Analysis Aimed at Guiding Adjuvant Treatment in Colorectal Cancer Open
Supplementary Table S6. Representativeness of Study Participants.
View article: The role of renal and liver function in clinical ctDNA testing
The role of renal and liver function in clinical ctDNA testing Open
Circulating tumor DNA (ctDNA) has high clinical potential in early cancer detection. The renal system and the liver are involved in clearing circulating cell free DNA (cfDNA) from the blood. Recent studies on mice show that inhibiting the …
View article: Whole‐genome sequencing of cell‐free <scp>DNA</scp> reveals <scp>DNA</scp> of tumor origin in plasma from patients with colorectal adenomas
Whole‐genome sequencing of cell‐free <span>DNA</span> reveals <span>DNA</span> of tumor origin in plasma from patients with colorectal adenomas Open
The presence of circulating tumor DNA (ctDNA) in patients with colorectal adenomas remains uncertain. Studies using tumor‐agnostic approaches report ctDNA in 10–15% of patients, though with uncertainty as to whether the signal originates f…
View article: Accurate calling of low-frequency somatic mutations by sample-specific modeling of error rates
Accurate calling of low-frequency somatic mutations by sample-specific modeling of error rates Open
Calling rare somatic variants from NGS data is more challenging than calling inherited variants, especially if the somatic variant is only present in a small fraction of the cells in the sequenced biopsy. In this case, having a good estima…
View article: Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types
Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types Open
The fragmentation patterns of whole genome sequenced cell-free DNA are promising features for tumor-agnostic cancer detection. However, systematic biases challenge their cross-cohort generalization. We introduce LIONHEART, a novel, open so…
View article: Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs
Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs Open
Circulating tumor DNA (ctDNA) is a promising cancer biomarker, but accurately detecting tumor mutations in cell-free DNA (cfDNA) is challenging due to their low frequency and sequencing errors. Our study benchmarked Mutect2, VarScan2, shea…
View article: Circulating tumour DNA and risk of recurrence in patients with asymptomatic versus symptomatic colorectal cancer
Circulating tumour DNA and risk of recurrence in patients with asymptomatic versus symptomatic colorectal cancer Open
View article: Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment
Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment Open
View article: Whole-genome Mutational Analysis for Tumor-informed Detection of Circulating Tumor DNA in Patients with Urothelial Carcinoma
Whole-genome Mutational Analysis for Tumor-informed Detection of Circulating Tumor DNA in Patients with Urothelial Carcinoma Open
Our results support the use of WGS for ultrasensitive ctDNA detection and highlight the possibility of plasma-based tracking of tumor evolution. WGS-based ctDNA detection represents a promising option for clinical use owing to the low volu…
View article: Beyond basics: Key mutation selection features for successful tumor‐informed <scp>ctDNA</scp> detection
Beyond basics: Key mutation selection features for successful tumor‐informed <span>ctDNA</span> detection Open
Tumor‐informed mutation‐based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational fe…
View article: Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA
Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA Open
Circulating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate this challenge…
View article: Error-corrected deep targeted sequencing of circulating cell-free DNA from colorectal cancer patients for sensitive detection of circulating tumor DNA
Error-corrected deep targeted sequencing of circulating cell-free DNA from colorectal cancer patients for sensitive detection of circulating tumor DNA Open
Introduction Circulating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate t…