The ATOM-Seq sequence capture panel can accurately predict microsatellite instability status in formalin-fixed tumour samples, alongside routine gene mutation testing.

Microsatellite instability (MSI) occurs across a number of cancers and is associated with different clinical characteristics when compared to microsatellite stable (MSS) cancers. As MSI cancers have different characteristics, routine MSI testing is now recommended for a number of cancer types including colorectal cancer (CRC). Using gene panels for sequencing of known cancer mutations is routinely performed to guide treatment decisions.

Role of klotho and fibroblast growth factor 23 in arterial calcification, thickness, and stiffness: a meta-analysis of observational studies.

This meta-analysis was conducted to clarify the role of klotho and fibroblast growth factor 23 (FGF-23) in human arterial remodeling across recent studies, in terms of arterial calcification, thickness, and stiffness. A systematic literature search was conducted on five databases for articles up to December 2023. Arterial calcification, thickness, and stiffness were determined using the calcification score and artery affected, carotid intima-media thickness (CIMT), and pulse wave velocity (PWV), respectively.

IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.

Background: Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur.

Results: Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression.

Risk factors and 26-years worldwide prevalence of endoscopic erosive esophagitis from 1997 to 2022: a meta-analysis.

Erosive esophagitis (EE) is the part of gastroesophageal reflux disease (GERD) spectrum and may progress to esophageal adenocarcinoma. Due to its progressivity and unclear prevalence, we aim to identify the factors contributing in EE to decide the need for further examination. We performed a PRISMA 2020-based systematic search through PubMed and other resources up to June 2, 2022.

Clinical characteristics, management, and outcomes of pulmonary valve myxoma: systematic review of published case reports.

Background: Cardiac myxoma is the most common type of primary cardiac tumor, with the majority located in the atrial wall. The tumor is attached to valvular structures in a few cases, of which the pulmonary valve is the least affected. Pulmonary valve myxoma may have different clinical manifestations from the more common cardiac myxomas because of its vital position.

Myocarditis and coronavirus disease 2019 vaccination: A systematic review and meta-summary of cases.

Vaccination is significant to control, mitigate, and recover from the destructive effects of coronavirus disease 2019 (COVID-19). The incidence of myocarditis following COVID-19 vaccination has been increasing and growing public concern; however, little is known about it. This study aimed to systematically review myocarditis following COVID-19 vaccination.

Model averaging in calibration of near-infrared instruments with correlated high-dimensional data.

Model averaging (MA) is a modelling strategy where the uncertainty in the configuration of selected variables is taken into account by weight-combining each estimate of the so-called 'candidate model'. Some studies have shown that MA enables better prediction, even in high-dimensional cases. However, little is known about the model prediction performance at different types of multicollinearity in high-dimensional data.

Sparse modelling of cancer patients' survival based on genomic copy number alterations.

Copy number alterations (CNA) are structural variation in the genome, in which some regions exhibit more or less than the normal two chromosomal copies. This genomic CNA profile provides critical information in tumour progression and is therefore informative for patients' survival. It is currently a statistical challenge to model patients' survival using their genomic CNA profiles while at the same time identify regions in the genome that are associated with patients' survival.

Use of shared gamma frailty model in analysis of survival data in twins.

In survival analysis, the effect of a covariate on the outcome is reported in a hazard rate. However, hazards rates are hard to interpret. Here we consider differences in survival probabilities instead.

Prediction of tumour pathological subtype from genomic profile using sparse logistic regression with random effects.

The purpose of this study is to highlight the application of sparse logistic regression models in dealing with prediction of tumour pathological subtypes based on lung cancer patients' genomic information. We consider sparse logistic regression models to deal with the high dimensionality and correlation between genomic regions. In a hierarchical likelihood (HL) method, it is assumed that the random effects follow a normal distribution and its variance is assumed to follow a gamma distribution.

Geometry-based distance for clustering amino acids.

Clustering amino acids is one of the most challenging problems in functional and structural prediction of protein. Previous studies have proposed clusters based on measurements of physical and biochemical characteristics of the amino acids such as volume, area, hydrophilicity, polarity, hydrogen bonding, shape, and charge. These characteristics, although important, are less directly related to the protein structure compared to geometrical characteristics such as dihedral angles between amino acids.

Method for Automatic Selection of Parameters in Normal Tissue Complication Probability Modeling.

Purpose: To present a fully automatic method to generate multiparameter normal tissue complication probability (NTCP) models and compare its results with those of a published model, using the same patient cohort.

Methods And Materials: Data were analyzed from 345 rectal cancer patients treated with external radiation therapy to predict the risk of patients developing grade 1 or ≥2 cystitis. In total, 23 clinical factors were included in the analysis as candidate predictors of cystitis.

A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory.

We introduce a new method to test efficiently for cospeciation in tritrophic systems. Our method utilises an analogy with electrical circuit theory to reduce higher order systems into bitrophic data sets that retain the information of the original system. We use a sophisticated permutation scheme that weights interactions between two trophic layers based on their connection to the third layer in the system.

Identification of transcript regulatory patterns in cell differentiation.

Motivation: Studying transcript regulatory patterns in cell differentiation is critical in understanding its complex nature of the formation and function of different cell types. This is done usually by measuring gene expression at different stages of the cell differentiation. However, if the gene expression data available are only from the mature cells, we have some challenges in identifying transcript regulatory patterns that govern the cell differentiation.

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.

Motivation: The role of personalized medicine and target treatment in the clinical management of cancer patients has become increasingly important in recent years. This has made the task of precise histological substratification of cancers crucial. Increasingly, genomic data are being seen as a valuable classifier.

Estimating optimal window size for analysis of low-coverage next-generation sequence data.

Motivation: Current high-throughput sequencing has greatly transformed genome sequence analysis. In the context of very low-coverage sequencing (<0.1×), performing 'binning' or 'windowing' on mapped short sequences ('reads') is critical to extract genomic information of interest for further evaluation, such as copy-number alteration analysis.

Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data.

Our main interest in supervised classification of gene expression data is to infer whether the expressions can discriminate biological characteristics of samples. With thousands of gene expressions to consider, a gene selection has been advocated to decrease classification by including only the discriminating genes. We propose to make the gene selection based on partial least squares and logistic regression random-effects (RE) estimates before the selected genes are evaluated in classification models.

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.

Motivation: Comparison of read depths from next-generation sequencing between cancer and normal cells makes the estimation of copy number alteration (CNA) possible, even at very low coverage. However, estimating CNA from patients' tumour samples poses considerable challenges due to infiltration with normal cells and aneuploid cancer genomes. Here we provide a method that corrects contamination with normal cells and adjusts for genomes of different sizes so that the actual copy number of each region can be estimated.

Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivo LPS infusion study.

Background: It is widely accepted that atherosclerosis and inflammation are intimately linked. Monocytes play a key role in both of these processes and we hypothesized that activation of inflammatory pathways in monocytes would lead to, among others, proatherogenic changes in the monocyte transcriptome. Such differentially expressed genes in circulating monocytes would be strong candidates for further investigation in disease association studies.

Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function.

Within the healthy population, there is substantial, heritable, and interindividual variability in the platelet response. We explored whether a proportion of this variability could be accounted for by interindividual variation in gene expression. Through a correlative analysis of genome-wide platelet RNA expression data from 37 subjects representing the normal range of platelet responsiveness within a cohort of 500 subjects, we identified 63 genes in which transcript levels correlated with variation in the platelet response to adenosine diphosphate and/or the collagen-mimetic peptide, cross-linked collagen-related peptide.

A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Hematopoiesis is a carefully controlled process that is regulated by complex networks of transcription factors that are, in part, controlled by signals resulting from ligand binding to cell-surface receptors. To further understand hematopoiesis, we have compared gene expression profiles of human erythroblasts, megakaryocytes, B cells, cytotoxic and helper T cells, natural killer cells, granulocytes, and monocytes using whole genome microarrays. A bioinformatics analysis of these data was performed focusing on transcription factors, immunoglobulin superfamily members, and lineage-specific transcripts.

Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype.

Platelet Glycoprotein VI (GPVI) is the activatory collagen signalling receptor that transmits an outside-in signal via the FcR gamma-chain. In Caucasians two GP6 haplotypes have been identified which encode GPVI isoforms that differ by five amino-acids. The minor haplotype is associated with a modest but statistically significant reduction in GPVI abundance and reduced downstream signalling events.

Estimation of significance thresholds for genomewide association scans.

The question of what significance threshold is appropriate for genomewide association studies is somewhat unresolved. Previous theoretical suggestions have yet to be validated in practice, whereas permutation testing does not resolve a discrepancy between the genomewide multiplicity of the experiment and the subset of markers actually tested. We used genotypes from the Wellcome Trust Case-Control Consortium to estimate a genomewide significance threshold for the UK Caucasian population.