MutationalPatterns: the one stop shop for the analysis of mutational processes
F Manders, AM Brandsma, J de Kanter, M Verheul… - BMC genomics, 2022 - Springer
Background The collective of somatic mutations in a genome represents a record of
mutational processes that have been operative in a cell. These processes can be …
mutational processes that have been operative in a cell. These processes can be …
Mutant collagen COL11A1 enhances cancerous invasion
Collagens are the most abundant proteins in the body and comprise the basement
membranes and stroma through which cancerous invasion occurs; however, a pro …
membranes and stroma through which cancerous invasion occurs; however, a pro …
Visual intratumor heterogeneity and breast tumor progression
Simple Summary This study investigates the role of visual intratumor heterogeneity (ITH) in
breast cancer progression. By analyzing histologic images from the Carolina Breast Cancer …
breast cancer progression. By analyzing histologic images from the Carolina Breast Cancer …
Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms
Background Organoids are 3-dimensional experimental models that summarize the
anatomical and functional structure of an organ. Although a promising experimental model …
anatomical and functional structure of an organ. Although a promising experimental model …
Exome sequencing of 628,388 individuals identifies common and rare variant associations with clonal hematopoiesis phenotypes
Clonal hematopoiesis (CH) refers to the expansion of certain blood cell lineages and has
been associated with aging and adverse health outcomes. Here, we use exome sequence …
been associated with aging and adverse health outcomes. Here, we use exome sequence …
MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data
LN Singh, B Ennis, B Loneragan, NL Tsao… - PLoS Computational …, 2021 - journals.plos.org
The growing number of next-generation sequencing (NGS) data presents a unique
opportunity to study the combined impact of mitochondrial and nuclear-encoded genetic …
opportunity to study the combined impact of mitochondrial and nuclear-encoded genetic …
Identification of neoantigens in oesophageal adenocarcinoma
Oesophageal adenocarcinoma (OAC) has a relatively poor long‐term survival and limited
treatment options. Promising targets for immunotherapy are short peptide neoantigens …
treatment options. Promising targets for immunotherapy are short peptide neoantigens …
Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss
MA Lewis, J Schulte, L Matthews, KI Vaden Jr… - PLoS …, 2023 - journals.plos.org
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic
component. Although to date over 150 genes have been identified as contributing to human …
component. Although to date over 150 genes have been identified as contributing to human …
Clonal haematopoiesis of indeterminate potential and atrial fibrillation: an east Asian cohort study
Abstract Background and Aims Both clonal haematopoiesis of indeterminate potential
(CHIP) and atrial fibrillation (AF) are age-related conditions. This study investigated the …
(CHIP) and atrial fibrillation (AF) are age-related conditions. This study investigated the …
Integrative proteogenomics using ProteomeGenerator2
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis
of genetic variation and transcription, enabling population-scale studies of human biology …
of genetic variation and transcription, enabling population-scale studies of human biology …