1. An, N. et al. Risk factors for brain metastases in patients with non-small-cell lung cancer. Cancer Med. 7, 6357–6364 (2018).
2. Chamberlain, M. C., Baik, C. S., Gadi, V. K., Bhatia, S. & Chow, L. Q. M. Systemic therapy of brain metastases: non-small cell lung cancer, breast cancer, and melanoma. Neuro-Oncol. 19, i1–i24 (2017).
3. Kim, M. et al. Barriers to Effective Drug Treatment for Brain Metastases: A Multifactorial Problem in the Delivery of Precision Medicine. Pharm. Res. 35, 177 (2018).
4. Nishino, M., Soejima, K. & Mitsudomi, T. Brain metastases in oncogene-driven non-small cell lung cancer. Transl. Lung Cancer Res. 8, S298–S307 (2019).
5. Tan, A. C., Itchins, M. & Khasraw, M. Brain Metastases in Lung Cancers with Emerging Targetable Fusion Drivers. Int. J. Mol. Sci. 21, E1416 (2020).
6. Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019).
7. Shih, D. J. H. et al. Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma. Nat. Genet. 52, 371–377 (2020).
8. Liu, Z. et al. Whole-exome sequencing identifies somatic mutations associated with lung cancer metastasis to the brain. Ann. Transl. Med. 9, 694 (2021).
9. Scheinin, I. et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24, 2022–2032 (2014).
10. Talevich, E., Shain, A. H., Botton, T. & Bastian, B. C. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput. Biol. 12, e1004873 (2016).
11. Tomasini, P. et al. Comparative genomic analysis of primary tumors and paired brain metastases in lung cancer patients by whole exome sequencing: a pilot study. Oncotarget 11, 4648–4654 (2020).
12. Geiss, G. K. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat. Biotechnol. 26, 317–325 (2008).
13. Brannon, A. R. et al. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions. Genome Biol. 15, 454 (2014).
14. Lee, S. Y. et al. Comparative genomic analysis of primary and synchronous metastatic colorectal cancers. PloS One 9, e90459 (2014).
15. Vignot, S. et al. Comparative analysis of primary tumour and matched metastases in colorectal cancer patients: evaluation of concordance between genomic and transcriptional profiles. Eur. J. Cancer Oxf. Engl. 1990 51, 791–799 (2015).
16. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).
17. Zhang, J. et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 346, 256–259 (2014).
18. Yates, L. R. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat. Med. 21, 751–759 (2015).
19. Yan, T. et al. Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma. Nat. Commun. 10, 1670 (2019).
20. Wang, D. et al. Multiregion Sequencing Reveals the Genetic Heterogeneity and Evolutionary History of Osteosarcoma and Matched Pulmonary Metastases. Cancer Res. 79, 7–20 (2019).
21. Wei, Q. et al. Multiregion whole-exome sequencing of matched primary and metastatic tumors revealed genomic heterogeneity and suggested polyclonal seeding in colorectal cancer metastasis. Ann. Oncol. Off. J. Eur. Soc. Med. Oncol. 28, 2135–2141 (2017).
22. Zhang, X. et al. CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples. Nat. Commun. 10, 4732 (2019).
23. Gao, R. et al. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat. Genet. 48, 1119–1130 (2016).
24. Baca, S. C. et al. Punctuated evolution of prostate cancer genomes. Cell 153, 666–677 (2013).
25. Forbes, S. A. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777–D783 (2017).
26. Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
27. Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
28. Lamouille, S., Xu, J. & Derynck, R. Molecular mechanisms of epithelial-mesenchymal transition. Nat. Rev. Mol. Cell Biol. 15, 178–196 (2014).
29. Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
30. Felder, M. et al. MUC16 (CA125): tumor biomarker to cancer therapy, a work in progress. Mol. Cancer 13, 129 (2014).
31. Cusseddu, R., Robert, A. & Côté, J.-F. Strength Through Unity: The Power of the Mega-Scaffold MACF1. Front. Cell Dev. Biol. 9, 641727 (2021).
32. Zhang, X. et al. History and progression of Fat cadherins in health and disease. OncoTargets Ther. 9, 7337–7343 (2016).
33. Greer, E. L. & Shi, Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 13, 343–357 (2012).
34. Ogryzko, V. V., Schiltz, R. L., Russanova, V., Howard, B. H. & Nakatani, Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953–959 (1996).
35. Carter, H. et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 69, 6660–6667 (2009).
36. Centore, R. C., Sandoval, G. J., Soares, L. M. M., Kadoch, C. & Chan, H. M. Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies. Trends Genet. TIG 36, 936–950 (2020).
37. Mullighan, C. G. et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235–239 (2011).
38. Ong, C.-T. & Corces, V. G. CTCF: an architectural protein bridging genome topology and function. Nat. Rev. Genet. 15, 234–246 (2014).
39. Waldman, T. Emerging themes in cohesin cancer biology. Nat. Rev. Cancer 20, 504–515 (2020).
40. Guo, Y. et al. Recent Progress in Rare Oncogenic Drivers and Targeted Therapy For Non-Small Cell Lung Cancer. OncoTargets Ther. 12, 10343–10360 (2019).
41. Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
42. Szabo, Q. et al. TADs are 3D structural units of higher-order chromosome organization in Drosophila. Sci. Adv. 4, eaar8082 (2018).
43. Brastianos, P. K. et al. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 5, 1164–1177 (2015).
44. Blasco, R. B., Patrucco, E., Mota, I., Tai, W.-T. & Chiarle, R. Comment on ‘ALK is a therapeutic target for lethal sepsis’. Sci. Transl. Med. 10, eaar4321 (2018).
45. Ambrogio, C. et al. Modeling lung cancer evolution and preclinical response by orthotopic mouse allografts. Cancer Res. 74, 5978–5988 (2014).
46. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754–1760 (2009).
47. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl. 25, 2078–2079 (2009).
48. Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).
49. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
50. Olshen, A. B., Venkatraman, E. S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostat. Oxf. Engl. 5, 557–572 (2004).
51. Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).