Roel Janssen
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View article: Kinetics of intestinal ultrasound and shear-wave elastography to assess early response in ulcerative colitis patients treated with filgotinib
Kinetics of intestinal ultrasound and shear-wave elastography to assess early response in ulcerative colitis patients treated with filgotinib Open
Background and Aims A reduction of bowel wall thickness (BWT) on intestinal ultrasound (IUS) predicts endoscopic response in ulcerative colitis (UC). Advanced techniques such as shear-wave elastography (SWE) might enhance response assessme…
View article: Submucosal hyper-echogenicity on intestinal ultrasound is associated with fat deposition and predicts treatment non-response in patients with ulcerative colitis
Submucosal hyper-echogenicity on intestinal ultrasound is associated with fat deposition and predicts treatment non-response in patients with ulcerative colitis Open
Background and Aims The submucosa is the most responsive bowel wall layer on intestinal ultrasound (IUS) when assessing treatment response in ulcerative colitis (UC). Submucosal thickening with hyper-echogenicity is observed. This study ai…
View article: Experience with a Large-Bore Vascular Closure Device in Patients Undergoing a Percutaneous Endovascular Aneurysm Repair (EVAR): A Multicentre Study
Experience with a Large-Bore Vascular Closure Device in Patients Undergoing a Percutaneous Endovascular Aneurysm Repair (EVAR): A Multicentre Study Open
The MANTA VCD is effective and safe for CFA closure in pEVAR, including in obese patients. Given rising obesity rates, the favorable outcomes in this population are encouraging and suggesting a broader applicability in large-bore percutane…
View article: An atypical case of early coronary subclavian steal syndrome after CABG managed with subclavian-subclavian crossover bypass and myocutaneous pectoralis major flap
An atypical case of early coronary subclavian steal syndrome after CABG managed with subclavian-subclavian crossover bypass and myocutaneous pectoralis major flap Open
Here we present a case of a 69-year old female patient with a rare presentation of early coronary subclavian steal syndrome (CSSS) after CABG. The steal syndrome was managed surgically with a subclavian-subclavian crossover bypass. The cas…
View article: Trends in Use and Perceptions About Triplet Chemotherapy Plus Bevacizumab for Metastatic Colorectal Cancer
Trends in Use and Perceptions About Triplet Chemotherapy Plus Bevacizumab for Metastatic Colorectal Cancer Open
The findings of this study suggest that FOLFOXIRI-B prescription rates have marginally increased in the last 5 years. Considering that most medical oncologists discuss this treatment option, the prescription rate found in this study was be…
View article: Additional file 1 of Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients
Additional file 1 of Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients Open
Additional file 1: Supplementary Tables.
View article: Additional file 2 of GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Additional file 2 of GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing Open
Additional file 2. Tables S1-S2. Table S1. Probe validation results. Table S2. Small duplication driver predictions.
View article: GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing Open
GRIDSS2 is the first structural variant caller to explicitly report single breakends - breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par wi…
View article: The mutational impact of culturing human pluripotent and adult stem cells
The mutational impact of culturing human pluripotent and adult stem cells Open
Genetic changes acquired during in vitro culture pose a risk for the successful application of stem cells in regenerative medicine. To assess the genetic risks induced by culturing, we determined all mutations in individual human stem cell…
View article: UMCUGenetics/IAP: v2.8.0
UMCUGenetics/IAP: v2.8.0 Open
Added ExomeDepth
View article: Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants
Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants Open
Background Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. Methods We applied a combinatio…
View article: Prioritization of genes driving congenital phenotypes of patients with <i>de novo</i> genomic structural variants
Prioritization of genes driving congenital phenotypes of patients with <i>de novo</i> genomic structural variants Open
Background Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients with multiple congenital abnormalities and/or intellectual disability carryi…
View article: Mutational impact of chronic alcohol use on stem cells in cirrhotic liver
Mutational impact of chronic alcohol use on stem cells in cirrhotic liver Open
Excessive alcohol consumption increases the risk of developing liver cancer, but the mechanism through which alcohol drives carcinogenesis is as yet unknown. Here, we determined the mutational consequences of chronic alcohol use on the gen…
View article: 5-Fluorouracil treatment induces characteristic T>G mutations in human cancer
5-Fluorouracil treatment induces characteristic T>G mutations in human cancer Open
5-Fluorouracil (5-FU) is a chemotherapeutic drug component that is commonly used for the treatment of solid cancers. It is proposed that 5-FU possesses anticancer properties via the interference with nucleotide synthesis and incorporation …
View article: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer Open
Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of N…
View article: MOESM1 of Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants
MOESM1 of Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants Open
Additional file 1: Table S1. Coordinates of the de novo SV breakpoint junctions detected in the 39 individuals by WGS. Table S2. List of external data sources used in this study. Table S3. Phenotype information of the 39 included patients …
View article: Mutational impact of culturing human pluripotent and adult stem cells
Mutational impact of culturing human pluripotent and adult stem cells Open
Genetic changes acquired during in vitro culture pose a potential risk for the successful application of stem cells in regenerative medicine. To assess mutation accumulation risks induced by culturing, we determined genetic aberrations in …
View article: UMCUGenetics/IAP: v2.5.0
UMCUGenetics/IAP: v2.5.0 Open
New features: IAP modules in own namespace Initial implementation of bcftools roh Sync IAP with Harwtig Pipeline v1.10 and v1.11 Add VT normalize to freebayes analysis Update freebayes filter script Update somatic melt script Check fastq.g…
View article: MutationalPatterns: comprehensive genome-wide analysis of mutational processes
MutationalPatterns: comprehensive genome-wide analysis of mutational processes Open
Base substitution catalogs represent historical records of mutational processes that have been active in a system. Such processes can be distinguished by typical characteristics, like mutation type, sequence context, transcriptional and re…