Deep whole-genome evaluation of 494 hepatocellular carcinomas

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  • Sung, H. et al. World most cancers statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 nations. CA Most cancers J. Clin. 71, 209–249 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Llovet, J. M. et al. Hepatocellular carcinoma. Nat. Rev. Dis. Primers 7, 6 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Villanueva, A. Hepatocellular Carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • The ICGC/TCGA Pan-Most cancers Evaluation of Complete Genomes Consortium. Pan-cancer evaluation of complete genomes. Nature 578, 82–93 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Rheinbay, E. et al. Analyses of non-coding somatic drivers in 2,658 most cancers complete genomes. Nature 578, 102–111 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexandrov, L. B. et al. The repertoire of mutational signatures in human most cancers. Nature 578, 94–101 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Y. et al. Patterns of somatic structural variation in human most cancers genomes. Nature 578, 112–121 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gerstung, M. et al. The evolutionary historical past of two,658 cancers. Nature 578, 122–128 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fujimoto, A. et al. Complete-genome mutational panorama and characterization of noncoding and structural mutations in liver most cancers. Nat. Genet. 48, 500–509 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Letouze, E. et al. Mutational signatures reveal the dynamic interaction of threat elements and mobile processes throughout liver tumorigenesis. Nat. Commun. 8, 1315 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao, Q. et al. Built-in proteogenomic characterization of HBV-related hepatocellular carcinoma. Cell 179, 561–577 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sung, W. Ok. et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat. Genet. 44, 765–769 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kan, Z. et al. Complete-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 23, 1422–1433 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xue, R. et al. Variable intra-tumor genomic heterogeneity of a number of lesions in sufferers with hepatocellular carcinoma. Gastroenterology 150, 998–1008 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Schulze, Ok. et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets. Nat. Genet. 47, 505–511 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Imielinski, M., Guo, G. & Meyerson, M. Insertions and deletions goal lineage-defining genes in human cancers. Cell 168, 460–472 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity throughout 2,658 human most cancers genomes. Cell 184, 2239–2254 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martincorena, I. et al. Tumor evolution. Excessive burden and pervasive constructive choice of somatic mutations in regular human pores and skin. Science 348, 880–886 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tarabichi, M. et al. Impartial tumor evolution? Nat. Genet. 50, 1630–1633 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ng, S. W. Ok. et al. Convergent somatic mutations in metabolism genes in power liver illness. Nature 598, 473–478 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, H. et al. Extrachromosomal DNA is related to oncogene amplification and poor final result throughout a number of cancers. Nat. Genet. 52, 891–897 (2020).

  • Deshpande, V. et al. Exploring the panorama of focal amplifications in most cancers utilizing AmpliconArchitect. Nat. Commun. 10, 392 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stephens, P. J. et al. Huge genomic rearrangement acquired in a single catastrophic occasion throughout most cancers growth. Cell 144, 27–40 (2011).

    Article 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baca, S. C. et al. Punctuated evolution of prostate most cancers genomes. Cell 153, 666–677 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nik-Zainal, S. et al. The life historical past of 21 breast cancers. Cell 149, 994–1007 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cortes-Ciriano, I. et al. Complete evaluation of chromothripsis in 2,658 human cancers utilizing whole-genome sequencing. Nat. Genet. 52, 331–341 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexandrov, L. B. et al. Signatures of mutational processes in human most cancers. Nature 500, 415–421 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Satriano, L., Lewinska, M., Rodrigues, P. M., Banales, J. M. & Andersen, J. B. Metabolic rearrangements in main liver cancers: trigger and penalties. Nat. Rev. Gastroenterol. Hepatol. 16, 748–766 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guo, L. et al. Single-cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma. Gastroenterology 162, 238–252 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xue, R. et al. Genomic and transcriptomic profiling of mixed hepatocellular and intrahepatic cholangiocarcinoma reveals distinct molecular subtypes. Most cancers Cell 35, 932–947 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, S. et al. Round ecDNA promotes accessible chromatin and excessive oncogene expression. Nature 575, 699–703 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xue, R. et al. Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature 612, 141–147 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cibulskis, Ok. et al. Delicate detection of somatic level mutations in impure and heterogeneous most cancers samples. Nat. Biotechnol. 31, 213–219 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, S. et al. Strelka2: quick and correct calling of germline and somatic variants. Nat. Strategies 15, 591–594 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lawrence, M. S. et al. Mutational heterogeneity in most cancers and the seek for new cancer-associated genes. Nature 499, 214–218 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martincorena, I. et al. Common patterns of choice in most cancers and somatic tissues. Cell 171, 1029–1041 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mularoni, L., Sabarinathan, R., Deu-Pons, J., Gonzalez-Perez, A. & López-Bigas, N. OncodriveFML: a common framework to establish coding and non-coding areas with most cancers driver mutations. Genome Biol. 17, 128 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lawrence, M. S. et al. Discovery and saturation evaluation of most cancers genes throughout 21 tumour sorts. Nature 505, 495–501 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhu, H. et al. Candidate most cancers driver mutations in distal regulatory parts and long-range chromatin interplay networks. Mol. Cell 77, 1307–1321 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, M., Wu, Y., Jiang, N., Boot, A. & Rozen, S. G. mSigHdp: hierarchical Dirichlet course of combination modeling for mutational signature discovery. NAR Genom. Bioinform. 5, lqad005 (2023).

  • Boot, A. et al. In-depth characterization of the cisplatin mutational signature in human cell strains and in esophageal and liver tumors. Genome Res. 28, 654–665 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Favero, F. et al. Sequenza: allele-specific copy quantity and mutation profiles from tumor sequencing knowledge. Ann. Oncol. 26, 64–70 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic strong tumours. Nature 575, 210–216 (2019).

  • Mermel, C. H. et al. GISTIC2.0 facilitates delicate and assured localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Layer, R. M., Chiang, C., Quinlan, A. R. & Corridor, I. M. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mayakonda, A., Lin, D.-C., Assenov, Y., Plass, C. & Koeffler, H. P. Maftools: environment friendly and complete evaluation of somatic variants in most cancers. Genome Res. 28, 1747–1756 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haas, B. J. et al. Accuracy evaluation of fusion transcript detection through read-mapping and de novo fusion transcript assembly-based strategies. Genome Biol. 20, 213 (2019).

  • Turner, Ok. M. et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122–125 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • deCarvalho, A. C. et al. Discordant inheritance of chromosomal and extrachromosomal DNA parts contributes to dynamic illness evolution in glioblastoma. Nat. Genet. 50, 708–717 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tsai, S. Q. et al. CIRCLE-seq: a extremely delicate in vitro display screen for genome-wide CRISPR–Cas9 nuclease off-targets. Nat. Strategies 14, 607–614 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Koche, R. P. et al. Extrachromosomal round DNA drives oncogenic genome transforming in neuroblastoma. Nat. Genet. 52, 29–34 (2020).

  • Dobin, A. et al. STAR: ultrafast common RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Anzalone, A. V. et al. Search-and-replace genome modifying with out double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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