Dissecting single-cell genomes through the clonal organoid technique

키워드

참고문헌 (114)

1. Goodwin, S., "Coming of age : ten years of next-generation sequencing technologies", Nat. Rev. Genet, 17, pp.333~351 (2016)
2. Levy, S. E., "Advancements in next-generation sequencing", Annu. Rev. Genom. Hum. Genet, 17, pp.95~115 (2016)
3. Durbin, R. M., "A map of human genome variation from population-scale sequencing", Nature, 467, pp.1061~1073 (2010)
4. The 1000 Genomes Project Consortium, "A global reference for human genetic variation", Nature, 526, pp.68~74 (2015)
5. Stratton, M. R., "The cancer genome", Nature, 458, pp.719~724 (2009)
6. Alexandrov, L. B., "Signatures of mutational processes in human cancer", Nature, 500, pp.415~421 (2013)
7. Bianconi, E., "An estimation of the number of cells in the human body", Ann. Hum. Biol, 40, pp.463~471 (2013)
8. Schultz, M. B., "When stem cells grow old : phenotypes and mechanisms of stem cell aging", Development, 143, pp.3~14 (2016)
9. Shastry, B. S., "SNP alleles in human disease and evolution", J. Hum. Genet, 47, pp.561~566 (2002)
10. Rahbari, R., "Timing, rates and spectra of human germline mutation", Nat. Genet, 48, pp.126~133 (2016)
11. Veltman, J. A., "De novo mutations in human genetic disease", Nat. Rev. Genet, 13, pp.565~575 (2012)
12. Ju, Y. S., "Somatic mutations reveal asymmetric cellular dynamics in the early human embryo", Nature, 543, pp.714~718 (2017)
13. Szilard, L., "On the nature of the aging process", Proc. Natl Acad. Sci. USA, 45, pp.30~45 (1959)
14. Martincorena, I., "Somatic mutation in cancer and normal cells", Science, 349, pp.1483~1489 (2015)
15. D’Gama, A. M., "Somatic mosaicism and neurodevelopmental disease", Nat. Neurosci, 21, pp.1504~1514 (2018)
16. Lee, J. S., "Germline gain-of-function mutation of STAT1 rescued by somatic mosaicism in immune dysregulation-polyendocrinopathy-enteropathy-X-linkedlike disorder", J. Allergy Clin. Immunol, 145, pp.1017~1021 (2020)
17. Vogelstein, B., "Cancer genome landscapes", Science, 339, pp.1546~1558 (2013)
18. Jaiswal, S., "Clonal hematopoiesis and nonhematologic disorders", Blood, 136, pp.1606~1614 (2020)
19. 이정호, "Somatic mutations in disorders with disrupted brain connectivity", Experimental and Molecular Medicine, 48, pp.1~9 (2016), 생화학분자생물학회
20. Lynch, M., "Rate, molecular spectrum, and consequences of human mutation", Proc. Natl Acad. Sci. USA, 107, pp.961~968 (2010)
21. Tate, J. G., "COSMIC : the catalogue of somatic mutations in cancer", Nucleic Acids Res, 47, pp.D941~D947 (2019)
22. Nowell, P. C., "The clonal evolution of tumor cell populations", Science, 194, pp.23~28 (1976)
23. The ICGC, "TCGA Pan-Cancer Analysis of Whole Genomes Consortium", Pancancer analysis of whole genomes, 2020, pp.578, 82~93
24. Ding, L., "Perspective on oncogenic processes at the end of the beginning of cancer genomics", Cell, 173, pp.305~320 (2018)
25. Fox, E. J., "Accuracy of next generation sequencing platforms", Gener. Seq. Appl, 1, pp.1000106~ (2014)
26. Martincorena, I., "High burden and pervasive positive selection of somatic mutations in normal human skin", Science, 348, pp.880~886 (2015)
27. Schmitt, M. W., "Detection of ultra-rare mutations by next-generation sequencing", Proc. Natl Acad. Sci. USA, 109, pp.14508~14513 (2012)
28. Kennedy, S. R., "Detecting ultralow-frequency mutations by Duplex Sequencing", Nat. Protoc, 9, pp.2586~2606 (2014)
29. Martincorena, I., "Somatic mutant clones colonize the human esophagus with age", Science, 362, pp.911~917 (2018)
30. Yizhak, K., "RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues", Science, 364, pp.eaaw0726~ (2019)
31. Schutgens, F., "Human organoids : tools for understanding biology and treating diseases", Annu. Rev. Pathol, 15, pp.211~234 (2020)
32. Kim, J., "Human organoids : model systems for human biology and medicine", Nat. Rev. Mol. Cell. Biol, 21, pp.571~584 (2020)
33. Ellis, P., "Reliable detection of somatic mutations in solid tissues by lasercapture microdissection and low-input DNA sequencing", Nat. Protoc, 16, pp.841~871 (2020)
34. Aigrain, L., "Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays—a systematic comparison of DNA library preparation kits for Illumina sequencing", BMC Genomics, 17, pp.458~ (2016)
35. Baumer, C., "Exploring DNA quality of single cells for genome analysis with simultaneous whole-genome amplification", Sci. Rep, 8, pp.7476~ (2018)
36. Gawad, C., "Single-cell genome sequencing : current state of the science", Nat. Rev. Genet, 17, pp.175~188 (2016)
37. Troutt, A. B., "Ligationanchored PCR : a simple amplification technique with single-sided specificity", Proc. Natl Acad. Sci. USA, 89, pp.9823~9825 (1992)
38. Blainey, P. C., "The future is now : single-cell genomics of bacteria and archaea", FEMS Microbiol. Rev, 37, pp.407~427 (2013)
39. Telenius, H., "Degenerate oligonucleotide-primed PCR : general amplification of target DNA by a single degenerate primer", Genomics, 13, pp.718~725 (1992)
40. Dean, F. B., "Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification", Genome Res, 11, pp.1095~1099 (2001)
41. Spits, C., "Whole-genome multiple displacement amplification from single cells", Nat. Protoc, 1, pp.1965~1970 (2006)
42. Zong, C., "Genome-wide detection of singlenucleotide and copy-number variations of a single human cell", Science, 338, pp.1622~1626 (2012)
43. Chen, C., "Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion(LIANTI)", Science, 356, pp.189~194 (2017)
44. de Bourcy, C. F. A., "A quantitative comparison of single-cell whole genome amplification methods", PLoS One, 9, pp.e105585~ (2014)
45. Blokzijl, F., "Tissue-specific mutation accumulation in human adult stem cells during life", Nature, 538, pp.260~264 (2016)
46. Dou, Y., "Detecting somatic mutations in normal cells", Trends Genet, 34, pp.545~557 (2018)
47. Huang, L., "Single-Cell whole-genome amplification and sequencing : methodology and applications", Annu. Rev. Genom. Hum. Genet, 16, pp.79~102 (2015)
48. Lodato, M. A., "Aging and neurodegeneration are associated with increased mutations in single human neurons", Science, 359, pp.555~559 (2018)
49. Huang, A. Y., "Parallel RNA and DNA analysis after deep sequencing(PRDDseq)reveals cell type-specific lineage patterns in human brain", Proc. Natl Acad. Sci. USA, 117, pp.13886~ (2020)
50. "Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development" (2020)[URL]
51. Barker, N., "Identification of stem cells in small intestine and colon by marker gene Lgr5", Nature, 449, pp.1003~1007 (2007)
52. Moore, L., "The mutational landscape of normal human endometrial epithelium", Nature, 580, pp.640~646 (2020)
53. Nicholson, A. M., "Fixation and spread of somatic mutations in adult human colonic epithelium", Cell Stem Cell, 22, pp.909~918 (2018)
54. Brunner, S. F., "Somatic mutations and clonal dynamics in healthy and cirrhotic human liver", Nature, 574, pp.538~542 (2019)
55. Coorens, T. H. H., "Inherent mosaicism and extensive mutation of human placentas", Nature, 592, pp.80~85 (2021)
56. Moore, L., "The mutational landscape of human somatic and germline cells", Nature, 597, pp.381~386 (2021)
57. Lee-Six, H., "The landscape of somatic mutation in normal colorectal epithelial cells", Nature, 574, pp.532~537 (2019)
58. Lawson, A. R. J., "Extensive heterogeneity in somatic mutation and selection in the human bladder", Science, 370, pp.75~82 (2020)
59. Li, R., "Macroscopic somatic clonal expansion in morphologically normal human urothelium", Science, 370, pp.82~89 (2020)
60. Brody, Y., "Quantification of somatic mutation flow across individual cell division events by lineage sequencing", Genome Res, 28, pp.1901~1918 (2018)
61. Lee-Six, H., "Population dynamics of normal human blood inferred from somatic mutations", Nature, 561, pp.473~478 (2018)
62. Yoshida, K., "Tobacco smoking and somatic mutations in human bronchial epithelium", Nature, 578, pp.266~272 (2020)
63. Park, S., "Clonal dynamics in early human embryogenesis inferred from somatic mutation", Nature, 597, pp.393~397 (2021)
64. Kucab, J. E., "A Compendium of mutational signatures of environmental agents", Cell, 177, pp.821~836 (2019)
65. Huangfu, D., "Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2", Nat. Biotechnol, 26, pp.1269~1275 (2008)
66. Warren, L., "Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA", Cell Stem Cell, 7, pp.618~630 (2010)
67. Sato, T., "Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche", Nature, 459, pp.262~265 (2009)
68. Sato, T., "Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium", Gastroenterology, 141, pp.1762~1772 (2011)
69. Huch, M., "Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5", R-spondin axis, 2013, pp.32, 2708~2721
70. Huch, M., "In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration", Nature, 494, pp.247~250 (2013)
71. Karthaus, W. R., "Identification of multipotent luminal progenitor cells in human prostate organoid cultures", Cell, 159, pp.163~175 (2014)
72. Bartfeld, S., "In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection", Gastroenterology, 148, pp.126~136 (2015)
73. Kessler, M., "The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids", Nat. Commun, 6, pp.8989~ (2015)
74. Turco, M. Y., "Long-term, hormone-responsive organoid cultures of human endometrium in a chemically defined medium", Nat. Cell Biol, 19, pp.568~577 (2017)
75. Turco, M. Y., "Trophoblast organoids as a model for maternal–fetal interactions during human placentation", Nature, 564, pp.263~267 (2018)
76. Boonekamp, K. E., "Long-term expansion and differentiation of adult murine epidermal stem cells in 3D organoid cultures", Proc. Natl Acad. Sci. USA, 116, pp.14630~14638 (2019)
77. Sachs, N., "Long-term expanding human airway organoids for disease modeling", EMBO J, 38, pp.e100300~ (2019)
78. Youk, J., "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2", Cell Stem Cell, 27, pp.905~919 (2020)
79. Salahudeen, A. A., "Progenitor identification and SARS-CoV-2 infection in human distal lung organoids", Nature, 588, pp.670~675 (2020)
80. Katsura, H., "Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2-mediated interferon responses and pneumocyte dysfunction", Cell Stem Cell, 27, pp.890~904 (2020)
81. Dekkers, J. F., "Modeling breast cancer using CRISPR-Cas9-mediated engineering of human breast organoids", J. Natl Cancer Inst, 112, pp.540~544 (2020)
82. Hu, H., "Long-term expansion of functional mouse and human hepatocytes as 3D organoids", Cell, 175, pp.1591~1606 (2018)
83. Huch, M., "Long-term culture of genome-stable bipotent stem cells from adult human liver", Cell, 160, pp.299~312 (2015)
84. Kim, H., "FIREVAT : finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures", Genome Med, 11, pp.81~ (2019)
85. Jager, M., "Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures", Nat. Protoc, 13, pp.59~ (2017)
86. Kuijk, E., "The mutational impact of culturing human pluripotent and adult stem cells", Nat. Commun, 11, pp.2493~ (2020)
87. Drost, J., "Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer", Science, 358, pp.234~238 (2017)
88. Behjati, S., "Genome sequencing of normal cells reveals developmental lineages and mutational processes", Nature, 513, pp.422~425 (2014)
89. Alexandrov, L. B., "The repertoire of mutational signatures in human cancer", Nature, 578, pp.94~101 (2020)
90. Alexandrov, L. B., "Clock-like mutational processes in human somatic cells", Nat. Genet, 47, pp.1402~1407 (2015)
91. Nanki, K., "Somatic inflammatory gene mutations in human ulcerative colitis epithelium", Nature, 577, pp.254~259 (2020)
92. Olafsson, S., "Somatic evolution in non-neoplastic IBD-affected colon", Cell, 182, pp.672~684 (2020)
93. Roerink, S. F., "Intra-tumour diversification in colorectal cancer at the singlecell level", Nature, 556, pp.457~462 (2018)
94. van de Wetering, M., "Prospective derivation of a living organoid biobank of colorectal cancer patients", Cell, 161, pp.933~945 (2015)
95. Dijkstra, K. K., "Challenges in establishing pure lung cancer organoids limit their utility for personalized medicine", Cell Rep, 31, pp.107588~ (2020)
96. Yokoyama, A., "Age-related remodelling of oesophageal epithelia by mutated cancer drivers", Nature, 565, pp.312~317 (2019)
97. Lynch, H. T., "Hereditary colorectal cancer", N. Engl. J. Med., 348, pp.919~932 (2003)
98. Bullman, S., "Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer", Science, 358, pp.1443~1448 (2017)
99. Gagnaire, A., "Collateral damage:insights into bacterial mechanisms that predispose host cells to cancer", Nat. Rev. Microbiol., 15, pp.109~128 (2017)
100. Pleguezuelos-Manzano, C., "Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli", Nature, 580, pp.269~273 (2020)
101. Christensen, S., "5-Fluorouracil treatment induces characteristic T>G mutations in human cancer", Nat. Commun, 10, pp.4571~ (2019)
102. "Mutational impact and signature of ionizing radiation" (2021)[URL]
103. The Cancer Genome Atlas Research Network, "Comprehensive genomic characterization defines human glioblastoma genes and core pathways", Nature, 455, pp.1061~1068 (2008)
104. The Cancer Genome Atlas Research Network, "Comprehensive molecular profiling of lung adenocarcinoma", Nature, 511, pp.543~550 (2014)
105. Akdemir, K. C., "Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer", Nat. Genet, 52, pp.294~305 (2020)
106. Hasin, Y., "Multi-omics approaches to disease", Genome Biol, 18, pp.83~ (2017)
107. 이기종, "Patterns and mechanisms of structural variations in human cancer", Experimental and Molecular Medicine, 50, pp.1~11 (2018), 생화학분자생물학회
108. Stephens, Z. D., "Big data: astronomical or genomical?", PLoS Biol., 13, pp.e1002195~ (2015)
109. Levy, S., "The diploid genome sequence of an individual human", PLoS Biol, 5, pp.e254~ (2007)
110. Lee, J. -K., "Clonal history and genetic predictors of transformation into smallcell carcinomas from lung adenocarcinomas", J. Clin. Oncol, 35, pp.3065~3074 (2017)
111. Coorens, T. H. H., "Extensive phylogenies of human development inferred from somatic mutations", Nature, 597, pp.387~392 (2021)
112. Koboldt, D. C., "The next-generation sequencing revolution and its impact on genomics", Cell, 155, pp.27~38 (2013)
113. Frésard, L., "Diagnosing rare diseases after the exome", Cold Spring Harb. Mol. Case Stud, 4, pp.a003392~ (2018)
114. Biesecker, L. G., "A genomic view of mosaicism and human disease", Nat. Rev. Genet, 14, pp.307~320 (2013)

관련 논문AI추천