1. Nagahashi M, Shimada Y, Ichikawa H, et al. Next generation sequencing- based gene panel tests for the management of solid tumors. Cancer Sci 2019;110:6-15.
2. Tanabe Y, Ichikawa H, Kohno T, et al. Comprehensive screening of target molecules by next-generation sequencing in patients with malignant solid tumors: guiding entry into phase I clinical trials. Mol Cancer 2016;15:73.
3. Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017;23:703-713.
4. Di Nicolantonio F, Martini M, Molinari F, et al. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol 2008;26:5705-5712.
5. Yaeger R, Kotani D, Mondaca S, et al. Response to Anti-EGFR Therapy in Patients with BRAF non-V600-Mutant Metastatic Colorectal Cancer. Clin Cancer Res 2019;25:7089-7097.
6. Barretina J, Caponigro G, Stransky N, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012;483:603-607.
7. Valerie M Weaver SL, Johnathon N Lakins, Micah A Chrenek, Jonathan C R Jones, Filippo Giancotti, Zena Werb, Mina J Bissell. β4 integrin-dependent formation of polarized three-dimensional architecture confers resistance to apoptosis in normal and malignant mammary epithelium. Cancer Cell 2002;2:205-216.
8. Sato T, Vries RG, Snippert HJ, et al. Single Lgr5 stem cells build crypt- villus structures in vitro without a mesenchymal niche. Nature 2009;459:262- 265.
9. Sato T, Stange DE, Ferrante M, et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology 2011;141:1762-1772.
10. Jamieson LE, Harrison DJ, Campbell CJ. Chemical analysis of multicellular tumour spheroids. Analyst 2015;140:3910-3920.
11. Baker BM, Chen CS. Deconstructing the third dimension: how 3D culture microenvironments alter cellular cues. J Cell Sci 2012;125:3015-3024.
12. Fujii M, Shimokawa M, Date S, et al. A Colorectal Tumor Organoid Library Demonstrates Progressive Loss of Niche Factor Requirements during Tumorigenesis. Cell Stem Cell 2016;18:827-838.
13. van de Wetering M, Francies HE, Francis JM, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell 2015;161:933-945.
14. Vlachogiannis G, Hedayat S, Vatsiou A, et al. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 2018;359:920-926.
15. Cargnello M, Roux PP. Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases. Microbiol Mol Biol Rev 2011;75:50-83.
16. Fang JY, Richardson BC. The MAPK signalling pathways and colorectal cancer. The Lancet Oncology 2005;6:322-327.
17. Tol J, Koopman M, Cats A, et al. Chemotherapy, bevacizumab, and cetuximab in metastatic colorectal cancer. N Engl J Med 2009;360:563-572.
18. Kopetz S, Grothey A, Yaeger R, et al. Encorafenib, Binimetinib, and Cetuximab in BRAF V600E-Mutated Colorectal Cancer. N Engl J Med 2019;381:1632-1643.
19. Welsh SJ, Rizos H, Scolyer RA, Long GV. Resistance to combination BRAF and MEK inhibition in metastatic melanoma: Where to next? Eur J Cancer 2016;62:76-85.
20. Liu F, Yang X, Geng M, Huang M. Targeting ERK, an Achilles' Heel of the MAPK pathway, in cancer therapy. Acta Pharm Sin B 2018;8:552-562.
21. Falchook G, Chin H, Lai D. Extracellular signal-regulated kinase (ERK) inhibitors in oncology clinical trials. Journal of Immunotherapy and Precision Oncology 2019;2.
22. Morris EJ, Jha S, Restaino CR, et al. Discovery of a novel ERK inhibitor with activity in models of acquired resistance to BRAF and MEK inhibitors. Cancer Discov 2013;3:742-750.
23. Pal R, Wei N, Song N, et al. Molecular subtypes of colorectal cancer in pre-clinical models show differential response to targeted therapies: Treatment implications beyond KRAS mutations. PLoS One 2018;13:e0200836.
24. Moschos SJ, Sullivan RJ, Hwu WJ, et al. Development of MK-8353, an orally administered ERK1/2 inhibitor, in patients with advanced solid tumors. JCI Insight 2018;3.
25. Corcoran RB, Ebi H, Turke AB, et al. EGFR-mediated re-activation of MAPK signaling contributes to insensitivity of BRAF mutant colorectal cancers to RAF inhibition with vemurafenib. Cancer Discov 2012;2:227-235.
26. Verissimo CS, Overmeer RM, Ponsioen B, et al. Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening. Elife 2016;5.
27. Yamamura A, Miura K, Karasawa H, et al. NDRG2, suppressed expression associates with poor prognosis in pancreatic cancer, is hypermethylated in the second promoter in human gastrointestinal cancers. Biochem Biophys Res Commun 2017;484:138-143.
28. Sato J, Karasawa H, Suzuki T, et al. The Function and Prognostic Significance of Cripto-1 in Colorectal Cancer. Cancer Invest 2020;38:214-227.
29. Sasaki H, Miura K, Horii A, et al. Orthotopic implantation mouse model and cDNA microarray analysis indicates several genes potentially involved in lymph node metastasis of colorectal cancer. Cancer Sci 2008;99:711-719.
30. Medico E, Russo M, Picco G, et al. The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets. Nat Commun 2015;6:7002.
31. Francies HE, Barthorpe A, McLaren-Douglas A, Barendt WJ, Garnett MJ. Drug Sensitivity Assays of Human Cancer Organoid Cultures. Methods Mol Biol 2016.
32. Broutier L, Mastrogiovanni G, Verstegen MM, et al. Human primary liver cancer-derived organoid cultures for disease modeling and drug screening. Nat Med 2017;23:1424-1435.
33. Ikari N, Serizawa A, Mitani S, Yamamoto M, Furukawa T. Near- Comprehensive Resequencing of Cancer-Associated Genes in Surgically Resected Metastatic Liver Tumors of Gastric Cancer. Am J Pathol 2019;189:784-796.
34. Shiihara M, Ishikawa T, Saiki Y, et al. Development of a system combining comprehensive genotyping and organoid cultures for identifying and testing genotype-oriented personalised medicine for pancreatobiliary cancers. European Journal of Cancer 2021;148:239-250.
35. Shibuya Y, Tokunaga H, Saito S, et al. Identification of somatic genetic alterations in ovarian clear cell carcinoma with next generation sequencing. Genes Chromosomes Cancer 2018;57:51-60.
36. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. https://arxiv.org/abs/1303.3997
37. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-1303.
38. Middha S, Zhang L, Nafa K, et al. Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data. JCO Precis Oncol 2017;2017.
39. Niu B, Ye K, Zhang Q, et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics 2014;30:1015-1016.
40. Wong DJ, Robert L, Atefi MS, et al. Antitumor activity of the ERK inhibitor SCH772984 [corrected] against BRAF mutant, NRAS mutant and wild- type melanoma. Mol Cancer 2014;13:194.
41. Schutte M, Risch T, Abdavi-Azar N, et al. Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors. Nat Commun 2017;8:14262.
42. Roerink SF, Sasaki N, Lee-Six H, et al. Intra-tumour diversification in colorectal cancer at the single-cell level. Nature 2018;556:457-+.
43. Porta C, Paglino C, Mosca A. Targeting PI3K/Akt/mTOR Signaling in Cancer. Front Oncol 2014;4:64.
44. Li D, March ME, Gutierrez-Uzquiza A, et al. ARAF recurrent mutation causes central conducting lymphatic anomaly treatable with a MEK inhibitor. Nat Med 2019;25:1116-1122.
45. Kim KO, Park WJ, Jung Y, Lee WS. Chemotherapeutic effects of MEK kinase inhibitor and BRAF kinase inhibitor on KRAS-mutated human colon cancer cell lines with different microsatellite instability. J Chemother 2020;32:437-444.
46. Ooft SN, Weeber F, Schipper L, et al. Prospective experimental treatment of colorectal cancer patients based on organoid drug responses. ESMO Open 2021;6:100103.