CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations.

The quality control and filtration of cancer somatic mutations (CAMs), including the elimination of false positives due to technical bias and the selection of key mutation candidates, are crucial steps for downstream analysis in cancer genomics. However, due to diverse needs and the lack of standardized filtering criteria, the filtering strategies applied vary from study to study, often resulting in reduced efficiency, accuracy, and reproducibility. Here, we present CaMutQC, a heuristic quality control and soft-filtering R/Bioconductor package designed specifically for CAMs.

Myeloid-derived itaconate suppresses cytotoxic CD8 T cells and promotes tumour growth.

The tumour microenvironment possesses mechanisms that suppress anti-tumour immunity. Itaconate is a metabolite produced from the Krebs cycle intermediate cis-aconitate by the activity of immune-responsive gene 1 (IRG1). While it is known to be immune modulatory, the role of itaconate in anti-tumour immunity is unclear.

Comprehensive profiling of 1015 patients' exomes reveals genomic-clinical associations in colorectal cancer.

The genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 of which mutate in 14.

A novel diagnostic nomogram based on serological and ultrasound findings for preoperative prediction of malignancy in patients with ovarian masses.

Objective: To develop a novel diagnostic nomogram model to predict malignancy in patients with ovarian masses.

Methods: In total, 1277 patients with ovarian masses were retrospectively analyzed. Receiver operating characteristic (ROC) analysis was performed to identify valuable predictive factors.

Trastuzumab plus docetaxel and capecitabine as a first-line treatment for HER2-positive advanced gastric or gastroesophageal junction cancer: a phase II, multicenter, open-label, single-arm study.

Gastric cancer (GC) is the second most common cancer in China. The ToGA study showed that trastuzumab in combination with fluoropyrimidine plus cisplatin prolonged overall survival (OS) in patients with human epidermal growth factor receptor 2 (HER2)-positive advanced GC (AGC). However, some patients may not be able to receive this regimen.

Germline mutational profile of Chinese patients under 70 years old with colorectal cancer.

Background: Inherited susceptibility accounts for nearly one-third of colorectal cancer (CRC) predispositions and has an 80%-100% lifetime risk of this disease. However, there are few data about germline mutations of hereditary CRC-related genes in Chinese patients with CRC. This study aimed to assess the prevalence of gene mutations related to cancer susceptibility among Chinese patients with CRC, differences between Chinese and Western patients, and the phenotype-genotype correlation.