341 results found
    1. Cancer Biology

    Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer

    Bahman Afsari, Albert Kuo ... Cristian Tomasetti
    A supervised methodology for mutational signatures outperforms the current standard unsupervised approach revealing new tissue-dependent mutational signatures among which some for obesity.
    1. Cancer Biology
    2. Computational and Systems Biology

    Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns

    Simon Grund Sørensen, Amruta Shrikhande ... Jakob Skou Pedersen
    Deficiencies of several DNA damage response genes can be predicted by their association with genome-wide mutation patterns.
    1. Cancer Biology
    2. Genetics and Genomics

    High-grade serous ovarian carcinoma organoids as models of chromosomal instability

    Maria Vias, Lena Morrill Gavarró ... James D Brenton
    Fifteen continuous high-grade serous ovarian carcinoma patient-derived organoids are characterized by transcriptomic, genomic, and drug sensitivity assays to reveal that they comprise communities of clonal populations and represent models of different causes of chromosomal instability and degrees of genome complexity.
    1. Cancer Biology
    2. Genetics and Genomics

    Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction

    Shixiang Wang, Zaoke He ... Xue-Song Liu
    Tumor immunogenicity is quantified with a novel method, and the resulting tumor immunogenicity score is an effective tumor-inherent biomarker for prediction of response to immune checkpoint inhibitors.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    The mutational signatures of poor treatment outcomes on the drug-susceptible Mycobacterium tuberculosis genome

    Yiwang Chen, Qi Jiang ... Qian Gao
    There are fourteen genomic variants of Mycobacterium tuberculosis that are significantly associated with poor treatment outcomes in drug-susceptible TB patients, but their predictive value is limited.
    1. Genetics and Genomics
    2. Cancer Biology

    Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

    Young Seok Ju, Ludmil B Alexandrov ... Peter J Campbell
    Identifying 1,907 mitochondrial somatic mutations from 1,675 tumor tissues provides new insights into the causes and effects of the mitochondrial genome mutations found in human cancers.
    1. Cancer Biology
    2. Computational and Systems Biology

    5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA

    Marketa Tomkova, Michael McClellan ... Benjamin Schuster-Boeckler
    Different types of epigenetic DNA modifications affect the likelihood of cytosine mutations in cancer.
    1. Cancer Biology
    2. Genetics and Genomics

    Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization

    Gabriel Renaud, Maibritt Nørgaard ... Søren Besenbacher
    Non-negative Matrix Factorization is a powerful strategy for unsupervised analysis of cell-free DNA that enables simultaneous estimation of the blood tumor fraction and the fragment length distribution of circulating tumor DNA.
    1. Cancer Biology
    2. Medicine

    Mutation analysis links angioimmunoblastic T-cell lymphoma to clonal hematopoiesis and smoking

    Shuhua Cheng, Wei Zhang ... Wayne Tam
    Comparative analysis establishes genetic links among angioimmunoblastic T-cell lymphoma (AITL), clonal hematopoiesis, and concomitant hematologic malignancies, and provides insights into the cell of origin, etiology, and biomarker discovery for AITL.
    1. Cancer Biology
    2. Genetics and Genomics

    Gallbladder adenocarcinomas undergo subclonal diversification and selection from precancerous lesions to metastatic tumors

    Minsu Kang, Hee Young Na ... Jong Seok Lee
    As the first to track clonal evolution from precancerous to metastatic lesions in gallbladder cancer patients, spatial and temporal analyses reveal how subclonal diversity in precancerous stage changes toward the metastasis, which help early detection and effective treatment of cancer.

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