Tag: dNdScv

KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas

Introduction The KCNQ (potassium voltage-gated channel subfamily Q) family of ion channels encode potassium transporters (1). KCNQ proteins typically repolarise the plasma membrane of a cell after depolarisation by allowing the export of potassium ions, and are therefore involved in wide-ranging biological functions including cardiac action potentials (2), neural excitability…

Continue Reading KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas

Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer

Baseline characteristics We described the baseline clinical and pathological characteristics of TNAC and LK-TNBC in Supplementary Table 1. Only stage at diagnosis was different between TNAC and LK-TNBC (P = 0.03), while no significant differences were observed in other characteristics, including nuclear grade, histologic grade, Ki-67, and status of (neo)adjuvant treatment. Somatic…

Continue Reading Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer

The evolution of non-small cell lung cancer metastases in TRACERx

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

Continue Reading The evolution of non-small cell lung cancer metastases in TRACERx

The evolution of lung cancer and impact of subclonal selection in TRACERx

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

Continue Reading The evolution of lung cancer and impact of subclonal selection in TRACERx

driver genes per sample or per group?

driver genes per sample or per group? 0 When using driver genes prediction tools such as ONCOCLUST in maftools or dNdScv, should we input the variants of per samples? or per group (same treatment/disease)? Both tutorials use input that were from multiple subjects. Is driver genes are usually described as…

Continue Reading driver genes per sample or per group?

Phenotypic plasticity and genetic control in colorectal cancer evolution

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

Continue Reading Phenotypic plasticity and genetic control in colorectal cancer evolution