Proteogenomic data and resources for pan-cancer analysis

Clinical Proteomic Tumor Analysis Consortium; Yize Li; Yongchao Dou; Felipe Da Veiga Leprevost; Yifat Geffen; Anna P. Calinawan; François Aguet; Yo Akiyama; Shankara Anand; Chet Birger; Song Cao; Rekha Chaudhary; Padmini Chilappagari; Marcin Cieslik; Antonio Colaprico; Daniel Cui Zhou; Corbin Day; Marcin J. Domagalski; Myvizhi Esai Selvan; David Fenyö; Steven M. Foltz; Alicia Francis; Tania Gonzalez-Robles; Zeynep H. Gümüş; David Heiman; Michael Holck; Runyu Hong; Yingwei Hu; Eric J. Jaehnig; Jiayi Ji; Wen Jiang; Lizabeth Katsnelson; Karen A. Ketchum; Robert J. Klein; Jonathan T. Lei; Wen Wei Liang; Yuxing Liao; Caleb M. Lindgren; Weiping Ma; Lei Ma; Michael J. MacCoss; Fernanda Martins Rodrigues; Wilson McKerrow; Ngoc Nguyen; Robert Oldroyd; Alexander Pilozzi; Pietro Pugliese; Boris Reva; Paul Rudnick; Kelly V. Ruggles; Dmitry Rykunov; Sara R. Savage; Michael Schnaubelt; Tobias Schraink; Zhiao Shi; Deepak Singhal; Xiaoyu Song; Erik Storrs; Nadezhda V. Terekhanova; Ratna R. Thangudu; Mathangi Thiagarajan; Liang Bo Wang; Joshua M. Wang; Ying Wang; Bo Wen; Yige Wu; Matthew A. Wyczalkowski; Yi Xin; Lijun Yao; Xinpei Yi; Hui Zhang; Qing Zhang; Maya Zuhl; Gad Getz; Li Ding; Alexey I. Nesvizhskii; Pei Wang; Ana I. Robles; Bing Zhang; Samuel H. Payne; Alexander J. Lazar; Amanda G. Paulovich; Antonio Iavarone; Arul M. Chinnaiyan; Brian J. Druker; Chandan Kumar-Sinha; Chelsea J. Newton; Chen Huang; D. R. Mani; Richard D. Smith; Emily Huntsman; Eric E. Schadt; Eunkyung An; Francesca Petralia; Galen Hostetter; Gilbert S. Omenn; Hanbyul Cho; Henry Rodriguez; Iga Kolodziejczak; Jared L. Johnson; Jasmin Bavarva; Jimin Tan; Karin D. Rodland; Karl R. Clauser; Karsten Krug; Lewis C. Cantley; Maciej Wiznerowicz; Matthew J. Ellis; Meenakshi Anurag; Mehdi Mesri; Michael A. Gillette; Michael J. Birrer; Michele Ceccarelli; Saravana M. Dhanasekaran; Nathan Edwards; Nicole Tignor; Özgün Babur; Sara J.C. Gosline; Scott D. Jewell; Shankha Satpathy; Shrabanti Chowdhury; Stephan Schürer; Steven A. Carr; Tao Liu; Tara Hiltke; Tomer M. Yaron; Vasileios Stathias; Wenke Liu; Xu Zhang; Yizhe Song; Zhen Zhang; Daniel W. Chan

doi:10.1016/j.ccell.2023.06.009

Proteogenomic data and resources for pan-cancer analysis

Clinical Proteomic Tumor Analysis Consortium, Yize Li, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P. Calinawan, François Aguet, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieslik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J. Domagalski, Myvizhi Esai Selvan, David FenyöSteven M. Foltz, Alicia Francis, Tania Gonzalez-Robles, Zeynep H. Gümüş, David Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J. Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A. Ketchum, Robert J. Klein, Jonathan T. Lei, Wen Wei Liang, Yuxing Liao, Caleb M. Lindgren, Weiping Ma, Lei Ma, Michael J. MacCoss, Fernanda Martins Rodrigues, Wilson McKerrow, Ngoc Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul Rudnick, Kelly V. Ruggles, Dmitry Rykunov, Sara R. Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V. Terekhanova, Ratna R. Thangudu, Mathangi Thiagarajan, Liang Bo Wang, Joshua M. Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A. Wyczalkowski, Yi Xin, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I. Nesvizhskii, Pei Wang, Ana I. Robles, Bing Zhang, Samuel H. Payne, Alexander J. Lazar, Amanda G. Paulovich, Antonio Iavarone, Arul M. Chinnaiyan, Brian J. Druker, Chandan Kumar-Sinha, Chelsea J. Newton, Chen Huang, D. R. Mani, Richard D. Smith, Emily Huntsman, Eric E. Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S. Omenn, Hanbyul Cho, Henry Rodriguez, Iga Kolodziejczak, Jared L. Johnson, Jasmin Bavarva, Jimin Tan, Karin D. Rodland, Karl R. Clauser, Karsten Krug, Lewis C. Cantley, Maciej Wiznerowicz, Matthew J. Ellis, Meenakshi Anurag, Mehdi Mesri, Michael A. Gillette, Michael J. Birrer, Michele Ceccarelli, Saravana M. Dhanasekaran, Nathan Edwards, Nicole Tignor, Özgün Babur, Sara J.C. Gosline, Scott D. Jewell, Shankha Satpathy, Shrabanti Chowdhury, Stephan Schürer, Steven A. Carr, Tao Liu, Tara Hiltke, Tomer M. Yaron, Vasileios Stathias, Wenke Liu, Xu Zhang, Yizhe Song, Zhen Zhang, Daniel W. Chan

Research output: Contribution to journal › Review article › peer-review

32 Scopus citations

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.

Original language	English
Pages (from-to)	1397-1406
Number of pages	10
Journal	Cancer Cell
Volume	41
Issue number	8
DOIs	https://doi.org/10.1016/j.ccell.2023.06.009
State	Published - Aug 14 2023

Keywords

CPTAC
data harmonization
multi-omics
open data
pan-cancer
proteogenomics

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10.1016/j.ccell.2023.06.009

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Clinical Proteomic Tumor Analysis Consortium, Li, Y., Dou, Y., Da Veiga Leprevost, F., Geffen, Y., Calinawan, A. P., Aguet, F., Akiyama, Y., Anand, S., Birger, C., Cao, S., Chaudhary, R., Chilappagari, P., Cieslik, M., Colaprico, A., Zhou, D. C., Day, C., Domagalski, M. J., Esai Selvan, M., ... Chan, D. W. (2023). Proteogenomic data and resources for pan-cancer analysis. Cancer Cell, 41(8), 1397-1406. https://doi.org/10.1016/j.ccell.2023.06.009

@article{d20f8c148f0242f89015751abba71e15,

title = "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.",

keywords = "CPTAC, data harmonization, multi-omics, open data, pan-cancer, proteogenomics",

author = "{Clinical Proteomic Tumor Analysis Consortium} and Yize Li and Yongchao Dou and {Da Veiga Leprevost}, Felipe and Yifat Geffen and Calinawan, {Anna P.} and Fran{\c c}ois Aguet and Yo Akiyama and Shankara Anand and Chet Birger and Song Cao and Rekha Chaudhary and Padmini Chilappagari and Marcin Cieslik and Antonio Colaprico and Zhou, {Daniel Cui} and Corbin Day and Domagalski, {Marcin J.} and {Esai Selvan}, Myvizhi and David Feny{\"o} and Foltz, {Steven M.} and Alicia Francis and Tania Gonzalez-Robles and G{\"u}m{\"u}{\c s}, {Zeynep H.} and David Heiman and Michael Holck and Runyu Hong and Yingwei Hu and Jaehnig, {Eric J.} and Jiayi Ji and Wen Jiang and Lizabeth Katsnelson and Ketchum, {Karen A.} and Klein, {Robert J.} and Lei, {Jonathan T.} and Liang, {Wen Wei} and Yuxing Liao and Lindgren, {Caleb M.} and Weiping Ma and Lei Ma and MacCoss, {Michael J.} and {Martins Rodrigues}, Fernanda and Wilson McKerrow and Ngoc Nguyen and Robert Oldroyd and Alexander Pilozzi and Pietro Pugliese and Boris Reva and Paul Rudnick and Ruggles, {Kelly V.} and Dmitry Rykunov and Savage, {Sara R.} and Michael Schnaubelt and Tobias Schraink and Zhiao Shi and Deepak Singhal and Xiaoyu Song and Erik Storrs and Terekhanova, {Nadezhda V.} and Thangudu, {Ratna R.} and Mathangi Thiagarajan and Wang, {Liang Bo} and Wang, {Joshua M.} and Ying Wang and Bo Wen and Yige Wu and Wyczalkowski, {Matthew A.} and Yi Xin and Lijun Yao and Xinpei Yi and Hui Zhang and Qing Zhang and Maya Zuhl and Gad Getz and Li Ding and Nesvizhskii, {Alexey I.} and Pei Wang and Robles, {Ana I.} and Bing Zhang and Payne, {Samuel H.} and Lazar, {Alexander J.} and Paulovich, {Amanda G.} and Antonio Iavarone and Chinnaiyan, {Arul M.} and Druker, {Brian J.} and Chandan Kumar-Sinha and Newton, {Chelsea J.} and Chen Huang and Mani, {D. R.} and Smith, {Richard D.} and Emily Huntsman and Schadt, {Eric E.} and Eunkyung An and Francesca Petralia and Galen Hostetter and Omenn, {Gilbert S.} and Hanbyul Cho and Henry Rodriguez and Iga Kolodziejczak and Johnson, {Jared L.} and Jasmin Bavarva and Jimin Tan and Rodland, {Karin D.} and Clauser, {Karl R.} and Karsten Krug and Cantley, {Lewis C.} and Maciej Wiznerowicz and Ellis, {Matthew J.} and Meenakshi Anurag and Mehdi Mesri and Gillette, {Michael A.} and Birrer, {Michael J.} and Michele Ceccarelli and Dhanasekaran, {Saravana M.} and Nathan Edwards and Nicole Tignor and {\"O}zg{\"u}n Babur and Gosline, {Sara J.C.} and Jewell, {Scott D.} and Shankha Satpathy and Shrabanti Chowdhury and Stephan Sch{\"u}rer and Carr, {Steven A.} and Tao Liu and Tara Hiltke and Yaron, {Tomer M.} and Vasileios Stathias and Wenke Liu and Xu Zhang and Yizhe Song and Zhen Zhang and Chan, {Daniel W.}",

note = "Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = aug,

day = "14",

doi = "10.1016/j.ccell.2023.06.009",

language = "English",

volume = "41",

pages = "1397--1406",

journal = "Cancer Cell",

issn = "1535-6108",

number = "8",

}

Clinical Proteomic Tumor Analysis Consortium, Li, Y, Dou, Y, Da Veiga Leprevost, F, Geffen, Y, Calinawan, AP, Aguet, F, Akiyama, Y, Anand, S, Birger, C, Cao, S, Chaudhary, R, Chilappagari, P, Cieslik, M, Colaprico, A, Zhou, DC, Day, C, Domagalski, MJ, Esai Selvan, M, Fenyö, D, Foltz, SM, Francis, A, Gonzalez-Robles, T, Gümüş, ZH, Heiman, D, Holck, M, Hong, R, Hu, Y, Jaehnig, EJ, Ji, J, Jiang, W, Katsnelson, L, Ketchum, KA, Klein, RJ, Lei, JT, Liang, WW, Liao, Y, Lindgren, CM, Ma, W, Ma, L, MacCoss, MJ, Martins Rodrigues, F, McKerrow, W, Nguyen, N, Oldroyd, R, Pilozzi, A, Pugliese, P, Reva, B, Rudnick, P, Ruggles, KV, Rykunov, D, Savage, SR, Schnaubelt, M, Schraink, T, Shi, Z, Singhal, D, Song, X, Storrs, E, Terekhanova, NV, Thangudu, RR, Thiagarajan, M, Wang, LB, Wang, JM, Wang, Y, Wen, B, Wu, Y, Wyczalkowski, MA, Xin, Y, Yao, L, Yi, X, Zhang, H, Zhang, Q, Zuhl, M, Getz, G, Ding, L, Nesvizhskii, AI, Wang, P, Robles, AI, Zhang, B, Payne, SH, Lazar, AJ, Paulovich, AG, Iavarone, A, Chinnaiyan, AM, Druker, BJ, Kumar-Sinha, C, Newton, CJ, Huang, C, Mani, DR, Smith, RD, Huntsman, E, Schadt, EE, An, E, Petralia, F, Hostetter, G, Omenn, GS, Cho, H, Rodriguez, H, Kolodziejczak, I, Johnson, JL, Bavarva, J, Tan, J, Rodland, KD, Clauser, KR, Krug, K, Cantley, LC, Wiznerowicz, M, Ellis, MJ, Anurag, M, Mesri, M, Gillette, MA, Birrer, MJ, Ceccarelli, M, Dhanasekaran, SM, Edwards, N, Tignor, N, Babur, Ö, Gosline, SJC, Jewell, SD, Satpathy, S, Chowdhury, S, Schürer, S, Carr, SA, Liu, T, Hiltke, T, Yaron, TM, Stathias, V, Liu, W, Zhang, X, Song, Y, Zhang, Z & Chan, DW 2023, 'Proteogenomic data and resources for pan-cancer analysis', Cancer Cell, vol. 41, no. 8, pp. 1397-1406. https://doi.org/10.1016/j.ccell.2023.06.009

TY - JOUR

T1 - Proteogenomic data and resources for pan-cancer analysis

AU - Clinical Proteomic Tumor Analysis Consortium

AU - Li, Yize

AU - Dou, Yongchao

AU - Da Veiga Leprevost, Felipe

AU - Geffen, Yifat

AU - Calinawan, Anna P.

AU - Aguet, François

AU - Akiyama, Yo

AU - Anand, Shankara

AU - Birger, Chet

AU - Cao, Song

AU - Chaudhary, Rekha

AU - Chilappagari, Padmini

AU - Cieslik, Marcin

AU - Colaprico, Antonio

AU - Zhou, Daniel Cui

AU - Day, Corbin

AU - Domagalski, Marcin J.

AU - Esai Selvan, Myvizhi

AU - Fenyö, David

AU - Foltz, Steven M.

AU - Francis, Alicia

AU - Gonzalez-Robles, Tania

AU - Gümüş, Zeynep H.

AU - Heiman, David

AU - Holck, Michael

AU - Hong, Runyu

AU - Hu, Yingwei

AU - Jaehnig, Eric J.

AU - Ji, Jiayi

AU - Jiang, Wen

AU - Katsnelson, Lizabeth

AU - Ketchum, Karen A.

AU - Klein, Robert J.

AU - Lei, Jonathan T.

AU - Liang, Wen Wei

AU - Liao, Yuxing

AU - Lindgren, Caleb M.

AU - Ma, Weiping

AU - Ma, Lei

AU - MacCoss, Michael J.

AU - Martins Rodrigues, Fernanda

AU - McKerrow, Wilson

AU - Nguyen, Ngoc

AU - Oldroyd, Robert

AU - Pilozzi, Alexander

AU - Pugliese, Pietro

AU - Reva, Boris

AU - Rudnick, Paul

AU - Ruggles, Kelly V.

AU - Rykunov, Dmitry

AU - Savage, Sara R.

AU - Schnaubelt, Michael

AU - Schraink, Tobias

AU - Shi, Zhiao

AU - Singhal, Deepak

AU - Song, Xiaoyu

AU - Storrs, Erik

AU - Terekhanova, Nadezhda V.

AU - Thangudu, Ratna R.

AU - Thiagarajan, Mathangi

AU - Wang, Liang Bo

AU - Wang, Joshua M.

AU - Wang, Ying

AU - Wen, Bo

AU - Wu, Yige

AU - Wyczalkowski, Matthew A.

AU - Xin, Yi

AU - Yao, Lijun

AU - Yi, Xinpei

AU - Zhang, Hui

AU - Zhang, Qing

AU - Zuhl, Maya

AU - Getz, Gad

AU - Ding, Li

AU - Nesvizhskii, Alexey I.

AU - Wang, Pei

AU - Robles, Ana I.

AU - Zhang, Bing

AU - Payne, Samuel H.

AU - Lazar, Alexander J.

AU - Paulovich, Amanda G.

AU - Iavarone, Antonio

AU - Chinnaiyan, Arul M.

AU - Druker, Brian J.

AU - Kumar-Sinha, Chandan

AU - Newton, Chelsea J.

AU - Huang, Chen

AU - Mani, D. R.

AU - Smith, Richard D.

AU - Huntsman, Emily

AU - Schadt, Eric E.

AU - An, Eunkyung

AU - Petralia, Francesca

AU - Hostetter, Galen

AU - Omenn, Gilbert S.

AU - Cho, Hanbyul

AU - Rodriguez, Henry

AU - Kolodziejczak, Iga

AU - Johnson, Jared L.

AU - Bavarva, Jasmin

AU - Tan, Jimin

AU - Rodland, Karin D.

AU - Clauser, Karl R.

AU - Krug, Karsten

AU - Cantley, Lewis C.

AU - Wiznerowicz, Maciej

AU - Ellis, Matthew J.

AU - Anurag, Meenakshi

AU - Mesri, Mehdi

AU - Gillette, Michael A.

AU - Birrer, Michael J.

AU - Ceccarelli, Michele

AU - Dhanasekaran, Saravana M.

AU - Edwards, Nathan

AU - Tignor, Nicole

AU - Babur, Özgün

AU - Gosline, Sara J.C.

AU - Jewell, Scott D.

AU - Satpathy, Shankha

AU - Chowdhury, Shrabanti

AU - Schürer, Stephan

AU - Carr, Steven A.

AU - Liu, Tao

AU - Hiltke, Tara

AU - Yaron, Tomer M.

AU - Stathias, Vasileios

AU - Liu, Wenke

AU - Zhang, Xu

AU - Song, Yizhe

AU - Zhang, Zhen

AU - Chan, Daniel W.

PY - 2023/8/14

Y1 - 2023/8/14

N2 - 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.

AB - 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.

KW - CPTAC

KW - data harmonization

KW - multi-omics

KW - open data

KW - pan-cancer

KW - proteogenomics

UR - http://www.scopus.com/inward/record.url?scp=85168062422&partnerID=8YFLogxK

U2 - 10.1016/j.ccell.2023.06.009

DO - 10.1016/j.ccell.2023.06.009

M3 - Review article

C2 - 37582339

AN - SCOPUS:85168062422

SN - 1535-6108

VL - 41

SP - 1397

EP - 1406

JO - Cancer Cell

JF - Cancer Cell

IS - 8

ER -

Proteogenomic data and resources for pan-cancer analysis

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Keywords

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