Structural variations in cancer and the 3D genome

Tallman, M. S. et al. All-trans-retinoic acid in acute promyelocytic leukemia. N. Engl. J. Med. 337, 1021–1028 (1997).

CAS  PubMed  Article  Google Scholar 

Slamon, D. J. et al. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N. Engl. J. Med. 344, 783–792 (2001).

CAS  PubMed  Article  Google Scholar 

Druker, B. J. et al. Efficacy and safety of a specific inhibitor of the BCR–ABL tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med. 344, 1031–1037 (2001).

CAS  PubMed  Article  Google Scholar 

Wala, J. A. et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 28, 581–591 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gong, T., Hayes, V. M. & Chan, E. K. F. Detection of somatic structural variants from short-read next-generation sequencing data. Brief. Bioinform 22, bbaa056 (2021).

PubMed  Article  Google Scholar 

Weischenfeldt, J. et al. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat. Genet. 49, 65–74 (2016).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Bandopadhayay, P. et al. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat. Genet. 48, 273–282 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Northcott, P. A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428–434 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Newman, S. et al. Genomes for kids: the scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing. Cancer Discov. https://doi.org/10.1158/2159-8290.CD-20-1631 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Staaf, J. et al. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nat. Med. 25, 1526–1533 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Duncavage, E. J. et al. Genome sequencing as an alternative to cytogenetic analysis in myeloid cancers. N. Engl. J. Med. 384, 924–935 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Cho, S. W. et al. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell 173, 1398–1412.e22 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Morton, A. R. et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell 179, 1330–1341.e13 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Chiang, C. et al. The impact of structural variation on human gene expression. Nat. Genet. 49, 692–699 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Audano, P. A. et al. Characterizing the major structural variant alleles of the human genome. Cell 176, 663–675.e19 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Merker, J. D. et al. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genet. Med. 20, 159–163 (2018).

CAS  PubMed  Article  Google Scholar 

Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007).

CAS  PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).

Article  CAS  Google Scholar 

Spielmann, M., Lupiáñez, D. G. & Mundlos, S. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453–467 (2018).

CAS  PubMed  Article  Google Scholar 

Fudenberg, G., Getz, G., Meyerson, M. & Mirny, L. A. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol. 29, 1109–1113 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).

CAS  PubMed  PubMed Central  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

Scheble, V. J. et al. ERG rearrangement is specific to prostate cancer and does not occur in any other common tumor. Mod. Pathol. 23, 1061–1067 (2010).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Zheng, H. & Xie, W. The role of 3D genome organization in development and cell differentiation. Nat. Rev. Mol. Cell Biol. 20, 535–550 (2019).

CAS  PubMed  Article  Google Scholar 

Bintu, B. et al. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Mirny, L. A. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 19, 37–51 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Meaburn, K. J. & Misteli, T. Cell biology: chromosome territories. Nature 445, 379–781 (2007).

CAS  PubMed  Article  Google Scholar 

Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Boyle, S. et al. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum. Mol. Genet. 10, 211–219 (2001).

CAS  PubMed  Article  Google Scholar 

Szabo, Q., Bantignies, F. & Cavalli, G. Principles of genome folding into topologically associating domains. Sci. Adv. 5, eaaw1668 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Strom, A. R. et al. Phase separation drives heterochromatin domain formation. Nature 547, 241–245 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

de Wit, E. et al. CTCF binding polarity determines chromatin looping. Mol. Cell 60, 676–684 (2015).

PubMed  Article  CAS  Google Scholar 

Symmons, O. et al. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 24, 390–400 (2014).

CAS  PubMed  PubMed Central  Article 

留言 (0)

沒有登入
gif