維基百科

全基因組泛癌分析

全基因組泛癌分析（英語：Pan-Cancer Analysis of Whole Genomes，PCAWG）是由國際癌症基因組聯盟（ICGC）組織的一個國際性合作項目，對超過2600組癌細胞基因進行分析。

歷史

編輯

1984年，人類基因組計劃被提出，旨在測定人類染色體的核苷酸序列。[1]這一計劃自1990年啟動開始，於2003年完成。在這一計劃中，有研究者希望藉助同樣的手段，通過對腫瘤基因組的表徵，深入研究腫瘤。[2]因此，癌症基因組圖譜計劃（TCGA）於2006年啟動，對33個癌症類型和2萬個癌症以及正常組織的分子特徵進行測序分析。2008年，ICGC成立，負責系統性分析癌症基因突變。由於TCGA和ICGC的研究範圍重疊，為實現泛癌分析的標準化，提高研究效率，由來自超過700個研究機構的研究者共同形成了PCAWG聯盟，根據癌症基因的不同分析方向分為16個小組共同研究。

概述

編輯

PCAWG項目採納了來自2793名捐獻者的基因數據，數據總量接近800TB。[3]2020年2月，ICGC發表這一項目的研究成果，是目前最全面的癌症基因組分析。[4]

研究成果

編輯

2020年2月5日，PCAWG項目在Nature期刊上首先發表了6篇主要的研究成果。[4]Nature的多個子刊中也刊登了多個項目階段性成果。這6篇文章分別觸及癌症基因組攜帶的驅動突變、非編碼區域的改變、體細胞突變的特徵、結構變異、腫瘤基因進化歷程和RNA突變。

驅動突變

編輯

在對PCAWG數據庫中的38種腫瘤類型所包含的2658個腫瘤全基因組進行整體分析後發現，當統計編碼和非編碼序列時，每一個腫瘤基因組平均攜帶4-5個驅動突變。[5]

已發表研究

編輯
標題 發表刊物 發表時間 備註
Pan-cancer analysis of whole genomes Nature 2020-02-05 [6]
Patterns of somatic structural variation in human cancer genomes Nature 2020-02-05 [6]
The repertoire of mutational signatures in human cancer Nature 2020-02-05 [7]
The evolutionary history of 2,658 cancers Nature 2020-02-05 [8]
Genomic basis for RNA alterations in cancer Nature 2020-02-05 [9]
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Nature 2020-02-05 [10]

參考文獻

編輯
  1. ^ The Alta Summit, December 1984. Human Genome Project Information Archive 1990–2003. [2020-02-26]. （原始內容存檔於2020-02-22）. 
  2. ^ Schmutz, Jeremy; Wheeler, Jeremy; Grimwood, Jane; Dickson, Mark; Yang, Joan; Caoile, Chenier; Bajorek, Eva; Black, Stacey; Chan, Yee Man; Denys, Mirian; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Garcia, Carmen; Gomez, Maria; Gonzales, Eidelyn; Haydu, Lauren; Lopez, Frederick; Ramirez, Lucia; Retterer, James; Rodriguez, Alex; Rogers, Stephanie; Salazar, Angelica; Tsai, Ming; Myers, Richard M. Quality assessment of the human genome sequence. Nature. 2004, 429 (6990): 365–368 [2020-02-26]. ISSN 1476-4687. （原始內容存檔於2022-04-01） （英語）. 
  3. ^ PCAWG - PANCANCER ANALYSIS OF WHOLE GENOMES. ICGC Data Portal. [2020-02-26]. （原始內容存檔於2020-02-26）. 
  4. ^ 4.0 4.1 Pan-Cancer Analysis of Whole Genomes. Nature. [2020-02-26]. （原始內容存檔於2022-05-21）. 
  5. ^ Campbell, Peter J.; Getz, Gad; Korbel, Jan O.; Stuart, Joshua M.; Jennings, Jennifer L.; Stein, Lincoln D.; Perry, Marc D.; Nahal-Bose, Hardeep K.; Ouellette, B. F. Francis; Li, Constance H.; Rheinbay, Esther; Nielsen, G. Petur; Sgroi, Dennis C.; Wu, Chin-Lee; Faquin, William C.; Deshpande, Vikram; Boutros, Paul C.; Lazar, Alexander J.; Hoadley, Katherine A.; Louis, David N.; Dursi, L. Jonathan; Yung, Christina K.; Bailey, Matthew H.; Saksena, Gordon; Raine, Keiran M.; Buchhalter, Ivo; Kleinheinz, Kortine; Schlesner, Matthias; Zhang, Junjun; Wang, Wenyi; Wheeler, David A.; Ding, Li; Simpson, Jared T.; O』Connor, Brian D.; Yakneen, Sergei; Ellrott, Kyle; Miyoshi, Naoki; Butler, Adam P.; Royo, Romina; Shorser, Solomon I.; Vazquez, Miguel; Rausch, Tobias; Tiao, Grace; Waszak, Sebastian M.; Rodriguez-Martin, Bernardo; Shringarpure, Suyash; Wu, Dai-Ying; Demidov, German M.; Delaneau, Olivier; Hayashi, Shuto; Imoto, Seiya; Habermann, Nina; Segre, Ayellet V.; Garrison, Erik; Cafferkey, Andy; Alvarez, Eva G.; Heredia-Genestar, José María; Muyas, Francesc; Drechsel, Oliver; Bruzos, Alicia L.; Temes, Javier; Zamora, Jorge; Baez-Ortega, Adrian; Kim, Hyung-Lae; Mashl, R. Jay; Ye, Kai; DiBiase, Anthony; Huang, Kuan-lin; Letunic, Ivica; McLellan, Michael D.; Newhouse, Steven J.; Shmaya, Tal; Kumar, Sushant; Wedge, David C.; Wright, Mark H.; Yellapantula, Venkata D.; Gerstein, Mark; Khurana, Ekta; Marques-Bonet, Tomas; Navarro, Arcadi; Bustamante, Carlos D.; Siebert, Reiner; Nakagawa, Hidewaki; Easton, Douglas F.; Ossowski, Stephan; Tubio, Jose M. C.; De La Vega, Francisco M.; Estivill, Xavier; Yuen, Denis; Mihaiescu, George L.; Omberg, Larsson; Ferretti, Vincent; Sabarinathan, Radhakrishnan; Pich, Oriol; Gonzalez-Perez, Abel; Taylor-Weiner, Amaro; Fittall, Matthew W.; Demeulemeester, Jonas; Tarabichi, Maxime; Roberts, Nicola D.; Van Loo, Peter; Cortés-Ciriano, Isidro; Urban, Lara; Park, Peter; Zhu, Bin; Pitkänen, Esa; Li, Yilong; Saini, Natalie; Klimczak, Leszek J.; Weischenfeldt, Joachim; Sidiropoulos, Nikos; Alexandrov, Ludmil B.; Rabionet, Raquel; Escaramis, Georgia; Bosio, Mattia; Holik, Aliaksei Z.; Susak, Hana; Prasad, Aparna; Erkek, Serap; Calabrese, Claudia; Raeder, Benjamin; Harrington, Eoghan; Mayes, Simon; Turner, Daniel; Juul, Sissel; Roberts, Steven A.; Song, Lei; Koster, Roelof; Mirabello, Lisa; Hua, Xing; Tanskanen, Tomas J.; Tojo, Marta; Chen, Jieming; Aaltonen, Lauri A.; Rätsch, Gunnar; Schwarz, Roland F.; Butte, Atul J.; Brazma, Alvis; Chanock, Stephen J.; Chatterjee, Nilanjan; Stegle, Oliver; Harismendy, Olivier; Bova, G. Steven; Gordenin, Dmitry A.; Haan, David; Sieverling, Lina; Feuerbach, Lars; Chalmers, Don; Joly, Yann; Knoppers, Bartha; Molnár-Gábor, Fruzsina; Phillips, Mark; Thorogood, Adrian; Townend, David; Goldman, Mary; Fonseca, Nuno A.; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; Muñoz, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John; Huber, Wolfgang; Valencia, Alfonso; Papatheodorou, Irene; Zhu, Jingchun; Fan, Yu; Torrents, David; Bieg, Matthias; Chen, Ken; Chong, Zechen; Cibulskis, Kristian; Eils, Roland; Fulton, Robert S.; Gelpi, Josep L.; Gonzalez, Santiago; Gut, Ivo G.; Hach, Faraz; Heinold, Michael; Hu, Taobo; Huang, Vincent; Hutter, Barbara; Jäger, Natalie; Jung, Jongsun; Kumar, Yogesh; Lalansingh, Christopher; Leshchiner, Ignaty; Livitz, Dimitri; Ma, Eric Z.; Maruvka, Yosef E.; Milovanovic, Ana; Nielsen, Morten Muhlig; Paramasivam, Nagarajan; Pedersen, Jakob Skou; Puiggròs, Montserrat; Sahinalp, S. Cenk; Sarrafi, Iman; Stewart, Chip; Stobbe, Miranda D.; Wala, Jeremiah A.; Wang, Jiayin; Wendl, Michael; Werner, Johannes; Wu, Zhenggang; Xue, Hong; Yamaguchi, Takafumi N.; Yellapantula, Venkata; Davis-Dusenbery, Brandi N.; Grossman, Robert L.; Kim, Youngwook; Heinold, Michael C.; Hinton, Jonathan; Jones, David R.; Menzies, Andrew; Stebbings, Lucy; Hess, Julian M.; Rosenberg, Mara; Dunford, Andrew J.; Gupta, Manaswi; Imielinski, Marcin; Meyerson, Matthew; Beroukhim, Rameen; Reimand, Jüri; Dhingra, Priyanka; Favero, Francesco; Dentro, Stefan; Wintersinger, Jeff; Rudneva, Vasilisa; Park, Ji Wan; Hong, Eun Pyo; Heo, Seong Gu; Kahles, André; Lehmann, Kjong-Van; Soulette, Cameron M.; Shiraishi, Yuichi; Liu, Fenglin; He, Yao; Demircioğlu, Deniz; Davidson, Natalie R.; Greger, Liliana; Li, Siliang; Liu, Dongbing; Stark, Stefan G.; Zhang, Fan; Amin, Samirkumar B.; Bailey, Peter; Chateigner, Aurélien; Frenkel-Morgenstern, Milana; Hou, Yong; Huska, Matthew R.; Kilpinen, Helena; Lamaze, Fabien C.; Li, Chang; Li, Xiaobo; Li, Xinyue; Liu, Xingmin; Marin, Maximillian G.; Markowski, Julia; Nandi, Tannistha; Ojesina, Akinyemi I.; Pan-Hammarström, Qiang; Park, Peter J.; Pedamallu, Chandra Sekhar; Su, Hong; Tan, Patrick; Teh, Bin Tean; Wang, Jian; Xiong, Heng; Ye, Chen; Yung, Christina; Zhang, Xiuqing; Zheng, Liangtao; Zhu, Shida; Awadalla, Philip; Creighton, Chad J.; Wu, Kui; Yang, Huanming; Göke, Jonathan; Zhang, Zemin; Brooks, Angela N.; Fittall, Matthew W.; Martincorena, Iñigo; Rubio-Perez, Carlota; Juul, Malene; Schumacher, Steven; Shapira, Ofer; Tamborero, David; Mularoni, Loris; Hornshøj, Henrik; Deu-Pons, Jordi; Muiños, Ferran; Bertl, Johanna; Guo, Qianyun; Gonzalez-Perez, Abel; Xiang, Qian. Pan-cancer analysis of whole genomes. Nature. 2020, 578 (7793) [2020-03-10]. ISSN 1476-4687. （原始內容存檔於2020-02-09） （英語）. 
  6. ^ 6.0 6.1 Li, Yilong; Roberts, Nicola D.; Wala, Jeremiah A.; Shapira, Ofer; Schumacher, Steven E.; Kumar, Kiran; Khurana, Ekta; Waszak, Sebastian; Korbel, Jan O.; Haber, James E.; Imielinski, Marcin; Weischenfeldt, Joachim; Beroukhim, Rameen; Campbell, Peter J. Patterns of somatic structural variation in human cancer genomes. Nature. 2020, 578 (7793): 112–121. ISSN 1476-4687 （英語）. 
  7. ^ Alexandrov, Ludmil B.; Kim, Jaegil; Haradhvala, Nicholas J.; Huang, Mi Ni; Tian Ng, Alvin Wei; Wu, Yang; Boot, Arnoud; Covington, Kyle R.; Gordenin, Dmitry A.; Bergstrom, Erik N.; Islam, S. M. Ashiqul; Lopez-Bigas, Nuria; Klimczak, Leszek J.; McPherson, John R.; Morganella, Sandro; Sabarinathan, Radhakrishnan; Wheeler, David A.; Mustonen, Ville; Getz, Gad; Rozen, Steven G.; Stratton, Michael R. The repertoire of mutational signatures in human cancer. Nature. 2020, 578 (7793): 94–101. ISSN 1476-4687 （英語）. 
  8. ^ Gerstung, Moritz; Jolly, Clemency; Leshchiner, Ignaty; Dentro, Stefan C.; Gonzalez, Santiago; Rosebrock, Daniel; Mitchell, Thomas J.; Rubanova, Yulia; Anur, Pavana; Yu, Kaixian; Tarabichi, Maxime; Deshwar, Amit; Wintersinger, Jeff; Kleinheinz, Kortine; Vázquez-García, Ignacio; Haase, Kerstin; Jerman, Lara; Sengupta, Subhajit; Macintyre, Geoff; Malikic, Salem; Donmez, Nilgun; Livitz, Dimitri G.; Cmero, Marek; Demeulemeester, Jonas; Schumacher, Steven; Fan, Yu; Yao, Xiaotong; Lee, Juhee; Schlesner, Matthias; Boutros, Paul C.; Bowtell, David D.; Zhu, Hongtu; Getz, Gad; Imielinski, Marcin; Beroukhim, Rameen; Sahinalp, S. Cenk; Ji, Yuan; Peifer, Martin; Markowetz, Florian; Mustonen, Ville; Yuan, Ke; Wang, Wenyi; Morris, Quaid D.; Spellman, Paul T.; Wedge, David C.; Loo, Peter Van. The evolutionary history of 2,658 cancers. Nature. 2020, 578 (7793): 122–128. ISSN 1476-4687 （英語）. 
  9. ^ Calabrese, Claudia; Davidson, Natalie R.; Demircioğlu, Deniz; Fonseca, Nuno A.; He, Yao; Kahles, André; Lehmann, Kjong-Van; Liu, Fenglin; Shiraishi, Yuichi; Soulette, Cameron M.; Urban, Lara; Greger, Liliana; Li, Siliang; Liu, Dongbing; Perry, Marc D.; Xiang, Qian; Zhang, Fan; Zhang, Junjun; Bailey, Peter; Erkek, Serap; Hoadley, Katherine A.; Hou, Yong; Huska, Matthew R.; Kilpinen, Helena; Korbel, Jan O.; Marin, Maximillian G.; Markowski, Julia; Nandi, Tannistha; Pan-Hammarström, Qiang; Pedamallu, Chandra Sekhar; Siebert, Reiner; Stark, Stefan G.; Su, Hong; Tan, Patrick; Waszak, Sebastian M.; Yung, Christina; Zhu, Shida; Awadalla, Philip; Creighton, Chad J.; Meyerson, Matthew; Ouellette, B. F. Francis; Wu, Kui; Yang, Huanming; Brazma, Alvis; Brooks, Angela N.; Göke, Jonathan; Rätsch, Gunnar; Schwarz, Roland F.; Stegle, Oliver; Zhang, Zemin. Genomic basis for RNA alterations in cancer. Nature. 2020, 578 (7793): 129–136. ISSN 1476-4687 （英語）. 
  10. ^ Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A.; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M.; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; Madsen, Tobias; Kim, Jaegil; Mularoni, Loris; Shuai, Shimin; Lanzós, Andrés; Herrmann, Carl; Maruvka, Yosef E.; Shen, Ciyue; Amin, Samirkumar B.; Bandopadhayay, Pratiti; Bertl, Johanna; Boroevich, Keith A.; Busanovich, John; Carlevaro-Fita, Joana; Chakravarty, Dimple; Chan, Calvin Wing Yiu; Craft, David; Dhingra, Priyanka; Diamanti, Klev; Fonseca, Nuno A.; Gonzalez-Perez, Abel; Guo, Qianyun; Hamilton, Mark P.; Haradhvala, Nicholas J.; Hong, Chen; Isaev, Keren; Johnson, Todd A.; Juul, Malene; Kahles, Andre; Kahraman, Abdullah; Kim, Youngwook; Komorowski, Jan; Kumar, Kiran; Kumar, Sushant; Lee, Donghoon; Lehmann, Kjong-Van; Li, Yilong; Liu, Eric Minwei; Lochovsky, Lucas; Park, Keunchil; Pich, Oriol; Roberts, Nicola D.; Saksena, Gordon; Schumacher, Steven E.; Sidiropoulos, Nikos; Sieverling, Lina; Sinnott-Armstrong, Nasa; Stewart, Chip; Tamborero, David; Tubio, Jose M. C.; Umer, Husen M.; Uusküla-Reimand, Liis; Wadelius, Claes; Wadi, Lina; Yao, Xiaotong; Zhang, Cheng-Zhong; Zhang, Jing; Haber, James E.; Hobolth, Asger; Imielinski, Marcin; Kellis, Manolis; Lawrence, Michael S.; von Mering, Christian; Nakagawa, Hidewaki; Raphael, Benjamin J.; Rubin, Mark A.; Sander, Chris; Stein, Lincoln D.; Stuart, Joshua M.; Tsunoda, Tatsuhiko; Wheeler, David A.; Johnson, Rory; Reimand, Jüri; Gerstein, Mark; Khurana, Ekta; Campbell, Peter J.; López-Bigas, Núria; Weischenfeldt, Joachim; Beroukhim, Rameen; Martincorena, Iñigo; Pedersen, Jakob Skou; Getz, Gad. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020, 578 (7793): 102–111. ISSN 1476-4687 （英語）. 
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