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Proteogenomic data and resources for pan-cancer analysis.

ABSTRACT: The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

SUBMITTER: Li Y 

PROVIDER: S-EPMC10506762 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Proteogenomic data and resources for pan-cancer analysis.

Li Yize Y   Dou Yongchao Y   Da Veiga Leprevost Felipe F   Geffen Yifat Y   Calinawan Anna P AP   Aguet François F   Akiyama Yo Y   Anand Shankara S   Birger Chet C   Cao Song S   Chaudhary Rekha R   Chilappagari Padmini P   Cieslik Marcin M   Colaprico Antonio A   Zhou Daniel Cui DC   Day Corbin C   Domagalski Marcin J MJ   Esai Selvan Myvizhi M   Fenyö David D   Foltz Steven M SM   Francis Alicia A   Gonzalez-Robles Tania T   Gümüş Zeynep H ZH   Heiman David D   Holck Michael M   Hong Runyu R   Hu Yingwei Y   Jaehnig Eric J EJ   Ji Jiayi J   Jiang Wen W   Katsnelson Lizabeth L   Ketchum Karen A KA   Klein Robert J RJ   Lei Jonathan T JT   Liang Wen-Wei WW   Liao Yuxing Y   Lindgren Caleb M CM   Ma Weiping W   Ma Lei L   MacCoss Michael J MJ   Martins Rodrigues Fernanda F   McKerrow Wilson W   Nguyen Ngoc N   Oldroyd Robert R   Pilozzi Alexander A   Pugliese Pietro P   Reva Boris B   Rudnick Paul P   Ruggles Kelly V KV   Rykunov Dmitry D   Savage Sara R SR   Schnaubelt Michael M   Schraink Tobias T   Shi Zhiao Z   Singhal Deepak D   Song Xiaoyu X   Storrs Erik E   Terekhanova Nadezhda V NV   Thangudu Ratna R RR   Thiagarajan Mathangi M   Wang Liang-Bo LB   Wang Joshua M JM   Wang Ying Y   Wen Bo B   Wu Yige Y   Wyczalkowski Matthew A MA   Xin Yi Y   Yao Lijun L   Yi Xinpei X   Zhang Hui H   Zhang Qing Q   Zuhl Maya M   Getz Gad G   Ding Li L   Nesvizhskii Alexey I AI   Wang Pei P   Robles Ana I AI   Zhang Bing B   Payne Samuel H SH  

Cancer cell 20230801 8

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working  ...[more]

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