[ad_1]
Hruban, R. H., Goggins, M., Parsons, J. & Kern, S. E. Progression model for pancreatic cancer. Clin. Cancer Res. 6, 2969–2972 (2000).
Siegel, R. L., Miller, K. D., Hannah, F. E. & Jemal, A. Cancer statistics, 2022. CA 72, 7–33 (2022).
Ryan, D. P., Hong, T. S. & Bardeesy, N. Pancreatic adenocarcinoma. N. Engl. J. Med. 371, 1039–1049 (2014).
Takaori, K., Kobashi, Y., Matsusue, S., Matsui, K. & Yamamoto, T. Clinicopathological features of pancreatic intraepithelial neoplasias and their relationship to intraductal papillary-mucinous tumors. J. Hepatobiliary Pancreat. Surg. 10, 125–136 (2003).
Hruban, R. H. et al. An illustrated consensus on the classification of pancreatic intraepithelial neoplasia and intraductal papillary mucinous neoplasms. Am. J. Surg. Pathol. 28, 977–987 (2004).
Kanda, M. et al. Presence of somatic mutations in most early-stage pancreatic intraepithelial neoplasia. Gastroenterology 142, 730–733.e739 (2012).
Hong, S. M. et al. Genome-wide somatic copy number alterations in low-grade PanINs and IPMNs from individuals with a family history of pancreatic cancer. Clin. Cancer Res. 18, 4303–4312 (2012).
Andea, A., Sarkar, F. & Adsay, V. N. Clinicopathological correlates of pancreatic intraepithelial neoplasia: a comparative analysis of 82 cases with and 152 cases without pancreatic ductal adenocarcinoma. Mod. Pathol. 16, 996–1006 (2003).
Makohon-Moore, A. P. et al. Precancerous neoplastic cells can move through the pancreatic ductal system. Nature 561, 201–205 (2018).
Kiemen, A. L. et al. CODA: quantitative 3D reconstruction of large tissues at cellular resolution. Nat. Methods 19, 1490–1499 (2022).
Hosoda, W. et al. Genetic analyses of isolated high-grade pancreatic intraepithelial neoplasia (HG-PanIN) reveal paucity of alterations in TP53 and SMAD4. J. Pathol. 242, 16–23 (2017).
Opitz, F. V., Haeberle, L., Daum, A. & Esposito, I. Tumor microenvironment in pancreatic intraepithelial neoplasia. Cancers 13, 6188 (2021).
Hata, T. et al. Genome-wide somatic copy number alterations and mutations in high-grade pancreatic intraepithelial neoplasia. Am. J. Pathol. 188, 1723–1733 (2018).
Chhoda, A., Lu, L., Clerkin, B. M., Risch, H. & Farrell, J. J. Current approaches to pancreatic cancer screening. Am. J. Pathol. 189, 22–35 (2019).
Fischer, C. G. et al. Intraductal papillary mucinous neoplasms arise from multiple independent clones, each with distinct mutations. Gastroenterology 157, 1123–1137.e1122 (2019).
Wu, J. et al. Recurrent GNAS mutations define an unexpected pathway for pancreatic cyst development. Sci. Transl. Med. 3, 92ra66 (2011).
Felsenstein, M. et al. IPMNs with co-occurring invasive cancers: neighbours but not always relatives. Gut 67, 1652–1662 (2018).
Connor, A. A. et al. Integration of genomic and transcriptional features in pancreatic cancer reveals increased cell cycle progression in metastases. Cancer Cell 35, 267–282.e267 (2019).
Makohon-Moore, A. P. et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nat. Genet. 49, 358–366 (2017).
Shi, C. et al. KRAS2 mutations in human pancreatic acinar-ductal metaplastic lesions are limited to those with PanIN: implications for the human pancreatic cancer cell of origin. Mol. Cancer Res. 7, 230–236 (2009).
Qu, C. et al. Detection of early-stage hepatocellular carcinoma in asymptomatic HBsAg-seropositive individuals by liquid biopsy. Proc. Natl Acad. Sci. USA 116, 6308–6312 (2019).
Wang, P. et al. Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection. Sci. Transl. Med. 14, eabp8704 (2022).
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
Moore, L. et al. The mutational landscape of human somatic and germline cells. Nature 597, 381–386 (2021).
Aguirre, A. J. et al. High-resolution characterization of the pancreatic adenocarcinoma genome. Proc. Natl Acad. Sci. USA 101, 9067–9072 (2004).
Murphy, S. J. et al. Integrated genomic analysis of pancreatic ductal adenocarcinomas reveals genomic rearrangement events as significant drivers of disease. Cancer Res. 76, 749–761 (2016).
Waddell, N. et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature 518, 495–501 (2015).
Zheng, L., Niknafs, N., Wood, L. D., Karchin, R. & Scharpf, R. B. Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinformatics 38, 3677–3683 (2022).
Baker, A.-M. et al. Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. Nat. Commun. 8, 1998 (2017).
Amano, T. et al. Number of polyps detected is a useful indicator of quality of clinical colonoscopy. Endosc. Int. Open 6, E878–E884 (2018).
Müller, A. D. & Sonnenberg, A. Prevention of colorectal cancer by flexible endoscopy and polypectomy. A case-control study of 32,702 veterans. Ann. Intern. Med. 123, 904–910 (1995).
Rohan, T. E., Henson, D. E., Franco, E. L. & Albores-Saavedra, J. in Cancer Epidemiology and Prevention (eds Schottenfeld, D. & Fraumeni, J. F.) 21–46 (Oxford Univ. Press, 2006).
Williams, A. R., Balasooriya, B. A. & Day, D. W. Polyps and cancer of the large bowel: a necropsy study in Liverpool. Gut 23, 835–842 (1982).
Pollock, P. M. et al. High frequency of BRAF mutations in nevi. Nat. Genet. 33, 19–20 (2003).
Kumar, R., Angelini, S., Snellman, E. & Hemminki, K. BRAF mutations are common somatic events in melanocytic nevi. J. Invest. Dermatol. 122, 342–348 (2004).
Ichii-Nakato, N. et al. High frequency of BRAFV600E mutation in acquired nevi and small congenital nevi, but low frequency of mutation in medium-sized congenital nevi. J. Invest. Dermatol. 126, 2111–2118 (2006).
Cooke, K. R., Spears, G. F. & Skegg, D. C. Frequency of moles in a defined population. J. Epidemiol. Community Health 39, 48–52 (1985).
Schäfer, T., Merkl, J., Klemm, E., Wichmann, H. E. & Ring, J. The epidemiology of nevi and signs of skin aging in the adult general population: results of the KORA-survey 2000. J. Invest. Dermatol. 126, 1490–1496 (2006).
Bryant, K. L., Mancias, J. D., Kimmelman, A. C. & Der, C. J. KRAS: feeding pancreatic cancer proliferation. Trends Biochem. Sci 39, 91–100 (2014).
Chen, Z., Chen, M., Fu, Y. & Zhang, J. The KRAS signaling pathway’s impact on the characteristics of pancreatic cancer cells. Pathol. Res. Pract. 248, 154603 (2023).
Matsuda, Y. et al. The prevalence and clinicopathological characteristics of high-grade pancreatic intraepithelial neoplasia: autopsy study evaluating the entire pancreatic parenchyma. Pancreas 46, 658–664 (2017).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Gabow, H. N. & Myers, E. W. Finding all spanning trees of directed and undirected graphs. SIAM J. Comput. 7, 280–287 (1978).
Niknafs, N., Beleva-Guthrie, V., Naiman, D. Q. & Karchin, R. SubClonal hierarchy inference from somatic mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing. PLoS Comput. Biol. 11, e1004416 (2015).
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).
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).
Bergstrom, E. N. et al. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 20, 685 (2019).
Islam, S. M. A. et al. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genomics 2, 100179 (2022).
Olshen, A. B., Venkatraman, E. S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).
Fujikura, K. et al. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut 70, 928–939 (2021).
Zhao, D. et al. Personalized analysis of minimal residual cancer cells in peritoneal lavage fluid predicts peritoneal dissemination of gastric cancer. J. Hematol. Oncol. 14, 164 (2021).
Zhao, L. et al. Integrated analysis of circulating tumour cells and circulating tumour DNA to detect minimal residual disease in hepatocellular carcinoma. Clin. Transl. Med. 12, e793 (2022).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).
Ramos, A. H. et al. Oncotator: cancer variant annotation tool. Hum. Mutat. 36, E2423–E2429 (2015).
[ad_2]
Source link