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Characterizing mutation-treatment effects using clinico-genomics data of 78,287 patients with 20 types of cancers.
Nat Commun
December 2024
Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
Evaluating the effectiveness of cancer treatments in relation to specific tumor mutations is essential for improving patient outcomes and advancing the field of precision medicine. Here we represent a comprehensive analysis of 78,287 U.S.
View Article and Find Full Text PDFPrecise identification of somatic and germline variants in the absence of matched normal samples.
Brief Bioinform
November 2024
The Department of Medical Oncology, Jilin Cancer Hospital, No. 1066, Jinhu Road, Changchun, 130012, China.
Somatic variants play a crucial role in the occurrence and progression of cancer. However, in the absence of matched normal controls, distinguishing between germline and somatic variants becomes challenging in tumor samples. The existing tumor-only genomic analysis methods either suffer from limited performance or insufficient interpretability due to an excess of features.
View Article and Find Full Text PDFIndividualized Cell-Free DNA Monitoring With Chromosomal Junctions for Mesothelioma.
JTO Clin Res Rep
December 2024
Mayo Clinic, Rochester, Minnesota.
Introduction: The spatially complex nature of mesothelioma and interventions like pleurodesis, surgery, and radiation often complicate imaging-based assessment. Further, cell-free DNA (cfDNA) based monitoring strategies are inadequate for mesothelioma, given the presence of a few recurring nonsynonymous somatic variants. However, patient-specific chromosomal rearrangements are commonly found in mesothelioma.
View Article and Find Full Text PDFBiomarker potential of plasma cell-free DNA for cholangiocarcinoma.
Heliyon
December 2024
Research Group in Multidimensional Health and Disease (MHD), Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.
Background: To prevent the development of cholangiocarcinoma, an effective screening opisthorchiasis viverrini and/or differential diagnosis of and the cholangiocarcinoma is crucial needed. The level and quality of cfDNA in plasma are being investigated for their potential role as biomarkers in cholangiocarcinoma.
Methods: The study enrolled 43 healthy controls (N), 36 -infected subjects (OV), and 36 cholangiocarcinoma patients (CCA).
Multi-omics analysis-based clinical and functional significance of a novel prognostic and immunotherapeutic gene signature derived from amino acid metabolism pathways in lung adenocarcinoma.
Front Immunol
December 2024
Molecular Pathology & Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan.
Background: Studies have shown that tumor cell amino acid metabolism is closely associated with lung adenocarcinoma (LUAD) development and progression. However, the comprehensive multi-omics features and clinical impact of the expression of genes associated with amino acid metabolism in the LUAD tumor microenvironment (TME) are yet to be fully understood.
Methods: LUAD patients from The Cancer Genome Atlas (TCGA) database were enrolled in the training cohort.
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