19. Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, et al. Tissue-specific mutation
accumulation in human adult stem cells during life. Nature. 2016;538(7624):260–4.
20. Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, et al. Genomic data analysis
workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. BMC
Med Genomics. 2019;12(1):92.
21. Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet. 2019;20(5):257–72.
22. Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, et al. Toward minimal
residual disease-directed therapy in melanoma. Cell. 2018;174(4):843–855.e19.
23. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su M-J, Melms JC, et al. a cancer cell program
promotes T cell exclusion and resistance to checkpoint blockade. Cell. 2018;175(4):984–997.e24.
24. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat
Rev Genet. 2016;17(3):175–88.
25. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, et al. The human cell atlas.
eLife. 2017;05(6)
26. Ben-David U, Beroukhim R, Golub TR. Genomic evolution of cancer models: perils and
opportunities. Nat Rev Cancer. 2019;19(2):97–109.
27. Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, et al. The life
history of 21 breast cancers. Cell. 2012;149(5):994–1007.
28. Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating
immune cells with CIBERSORT. Methods Mol Biol Clifton NJ. 2018;1711:243–59.
29. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang T-H, et al. The immune
landscape of cancer. Immunity. 2018;48(4):812–830.e14.
30. Cobos FA, Alquicira-Hernandez J, Powell J, Mestdagh P, Preter KD. Comprehensive
benchmarking of computational deconvolution of transcriptomics data. bioRxiv. 2020;
2020.01.10.897116.
31. Suvà ML, Tirosh I. Single-cell RNA sequencing in cancer: lessons learned and emerging
challenges. Mol Cell. 2019;75(1):7–12.
32. Hurst CD, Alder O, Platt FM, Droop A, Stead LF, Burns JE, et al. Genomic subtypes of
non-invasive bladder cancer with distinct metabolic profile, clinical outcome and female gender
bias in KDM6A mutation frequency. Cancer Cell. 2017;32(5):701–715.e7.
33. Echevarría-Vargas IM, Reyes-Uribe PI, Guterres AN, Yin X, Kossenkov AV, Liu Q, et al.
Co-targeting BET and MEK as salvage therapy for MAPK and checkpoint inhibitor-resistant
melanoma. EMBO Mol Med. 2018;10:5.
34. Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J. Consensus molecular
subtypes and the evolution of precision medicine in colorectal cancer. Nat Rev Cancer. 2017;17
(2):79–92.
35. Fragomeni SM, Sciallis A, Jeruss JS. Molecular subtypes and local-regional control of breast
cancer. Surg Oncol Clin N Am. 2018;27(1):95–120.
36. Jiang Y-Z, Ma D, Suo C, Shi J, Xue M, Hu X, et al. Genomic and transcriptomic landscape of
triple-negative breast cancers: subtypes and treatment strategies. Cancer Cell. 2019;35
(3):428–440.e5.
37. Jönsson G, Busch C, Knappskog S, Geisler J, Miletic H, Ringnér M, et al. Gene expression
profiling-based identification of molecular subtypes in stage IV melanomas with different clinical
outcome. Clin Cancer Res Off J Am Assoc Cancer Res. 2010;16(13):3356–67.
38. Goodman AM, Kato S, Bazhenova L, Patel SP, Frampton GM, Miller V, et al. Tumor mutational
burden as an independent predictor of response to immunotherapy in diverse cancers. Mol Cancer
Ther. 2017;16(11):2598–608.
39. Ott PA, Dotti G, Yee C, Goff SL. An update on adoptive T-cell therapy and neoantigen vaccines.
Am Soc Clin Oncol Educ Book Am Soc Clin Oncol Annu Meet. 2019;(39):e70–8.
2 Opportunities and Perspectives of NGS Applications in Cancer Research
37
accumulation in human adult stem cells during life. Nature. 2016;538(7624):260–4.
20. Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, et al. Genomic data analysis
workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. BMC
Med Genomics. 2019;12(1):92.
21. Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet. 2019;20(5):257–72.
22. Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, et al. Toward minimal
residual disease-directed therapy in melanoma. Cell. 2018;174(4):843–855.e19.
23. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su M-J, Melms JC, et al. a cancer cell program
promotes T cell exclusion and resistance to checkpoint blockade. Cell. 2018;175(4):984–997.e24.
24. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat
Rev Genet. 2016;17(3):175–88.
25. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, et al. The human cell atlas.
eLife. 2017;05(6)
26. Ben-David U, Beroukhim R, Golub TR. Genomic evolution of cancer models: perils and
opportunities. Nat Rev Cancer. 2019;19(2):97–109.
27. Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, et al. The life
history of 21 breast cancers. Cell. 2012;149(5):994–1007.
28. Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating
immune cells with CIBERSORT. Methods Mol Biol Clifton NJ. 2018;1711:243–59.
29. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang T-H, et al. The immune
landscape of cancer. Immunity. 2018;48(4):812–830.e14.
30. Cobos FA, Alquicira-Hernandez J, Powell J, Mestdagh P, Preter KD. Comprehensive
benchmarking of computational deconvolution of transcriptomics data. bioRxiv. 2020;
2020.01.10.897116.
31. Suvà ML, Tirosh I. Single-cell RNA sequencing in cancer: lessons learned and emerging
challenges. Mol Cell. 2019;75(1):7–12.
32. Hurst CD, Alder O, Platt FM, Droop A, Stead LF, Burns JE, et al. Genomic subtypes of
non-invasive bladder cancer with distinct metabolic profile, clinical outcome and female gender
bias in KDM6A mutation frequency. Cancer Cell. 2017;32(5):701–715.e7.
33. Echevarría-Vargas IM, Reyes-Uribe PI, Guterres AN, Yin X, Kossenkov AV, Liu Q, et al.
Co-targeting BET and MEK as salvage therapy for MAPK and checkpoint inhibitor-resistant
melanoma. EMBO Mol Med. 2018;10:5.
34. Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J. Consensus molecular
subtypes and the evolution of precision medicine in colorectal cancer. Nat Rev Cancer. 2017;17
(2):79–92.
35. Fragomeni SM, Sciallis A, Jeruss JS. Molecular subtypes and local-regional control of breast
cancer. Surg Oncol Clin N Am. 2018;27(1):95–120.
36. Jiang Y-Z, Ma D, Suo C, Shi J, Xue M, Hu X, et al. Genomic and transcriptomic landscape of
triple-negative breast cancers: subtypes and treatment strategies. Cancer Cell. 2019;35
(3):428–440.e5.
37. Jönsson G, Busch C, Knappskog S, Geisler J, Miletic H, Ringnér M, et al. Gene expression
profiling-based identification of molecular subtypes in stage IV melanomas with different clinical
outcome. Clin Cancer Res Off J Am Assoc Cancer Res. 2010;16(13):3356–67.
38. Goodman AM, Kato S, Bazhenova L, Patel SP, Frampton GM, Miller V, et al. Tumor mutational
burden as an independent predictor of response to immunotherapy in diverse cancers. Mol Cancer
Ther. 2017;16(11):2598–608.
39. Ott PA, Dotti G, Yee C, Goff SL. An update on adoptive T-cell therapy and neoantigen vaccines.
Am Soc Clin Oncol Educ Book Am Soc Clin Oncol Annu Meet. 2019;(39):e70–8.
2 Opportunities and Perspectives of NGS Applications in Cancer Research
37