Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

被引：202

作者：

Nuzzo, Pier Vitale ^{[1
,2
,3
]}

Berchuck, Jacob E. ^{[1
,2
]}

Korthauer, Keegan ^{[4
,5
]}

Spisak, Sandor ^{[2
]}

Nassar, Amin H. ^{[1
,2
]}

Abou Alaiwi, Sarah ^{[1
,2
]}

Chakravarthy, Ankur ^{[6
]}

Shen, Shu Yi ^{[6
]}

Bakouny, Ziad ^{[1
]}

Boccardo, Francesco ^{[3
,7
]}

Steinharter, John ^{[1
]}

Bouchard, Gabrielle ^{[1
]}

Curran, Catherine R. ^{[1
]}

Pan, Wenting ^{[1
]}

Baca, Sylvan C. ^{[1
,2
,8
]}

Seo, Ji-Heui ^{[1
,2
]}

Lee, Gwo-Shu Mary ^{[1
,2
]}

Michaelson, M. Dror ^{[9
]}

Chang, Steven L. ^{[10
]}

Waikar, Sushrut S. ^{[11
,12
]}

Sonpavde, Guru ^{[1
]}

Irizarry, Rafael A. ^{[13
,14
]}

Pomerantz, Mark ^{[1
,2
]}

De Carvalho, Daniel D. ^{[6
,15
]}

Choueiri, Toni K. ^{[1
,8
]}

Freedman, Matthew L. ^{[1
,2
,8
]}

机构：

[1] Harvard Med Sch, Dana Farber Canc Inst, Lank Ctr Genitourinary Oncol, Dept Med Oncol, Boston, MA 02115 USA

[2] Harvard Med Sch, Dana Farber Canc Inst, Ctr Funct Canc Epigenet, Boston, MA 02115 USA

[3] Univ Genoa, Sch Med, Dept Internal Med & Med Specialties, Genoa, Italy

[4] Univ British Columbia, Dept Stat, Vancouver, BC, Canada

[5] BC Childrens Hosp, Res Inst, Vancouver, BC, Canada

[6] Univ Hlth Network, Princess Margaret Canc Ctr, Toronto, ON, Canada

[7] IRCCS San Martino Polyclin Hosp, Acad Unit Med Oncol, Genoa, Italy

[8] Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA

[9] Massachusetts Gen Hosp, Canc Ctr, Hematol Oncol, Boston, MA 02114 USA

[10] Brigham & Womens Hosp, Div Urol, 75 Francis St, Boston, MA 02115 USA

[11] Brigham & Womens Hosp, Div Renal Med, 75 Francis St, Boston, MA 02115 USA

[12] Boston Univ, Med Ctr, Sect Nephrol, Boston, MA USA

[13] Harvard Univ, Dept Biostat, Cambridge, MA 02138 USA

[14] Harvard Med Sch, Dana Farber Canc Inst, Dept Data Sci, Boston, MA 02115 USA

[15] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada

来源：

NATURE MEDICINE | 2020年 / 26卷 / 07期

基金：

加拿大健康研究院;

关键词：

D O I：

10.1038/s41591-020-0933-1

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A cell-free DNA-methylation sequencing assay accurately identifies renal cell carcinoma using plasma and urine samples. Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all stages of renal cell carcinoma (RCC) in plasma (area under the receiver operating characteristic (AUROC) curve of 0.99) and demonstrate the validity of this assay to identify patients with RCC using urine cell-free DNA (cfDNA; AUROC of 0.86).

引用

页码：1041 / +

页数：11

共 26 条

[1] Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays [J].

Aryee, Martin J. ;

Jaffe, Andrew E. ;

Corrada-Bravo, Hector ;

Ladd-Acosta, Christine ;

Feinberg, Andrew P. ;

Hansen, Kasper D. ;

Irizarry, Rafael A. .

BIOINFORMATICS, 2014, 30 (10) :1363-1369

[2] Detection and localization of surgically resectable cancers with a multi-analyte blood test [J].

Cohen, Joshua D. ;

Li, Lu ;

Wang, Yuxuan ;

Thoburn, Christopher ;

Afsari, Bahman ;

Danilova, Ludmila ;

Douville, Christopher ;

Javed, Ammar A. ;

Wong, Fay ;

Mattox, Austin ;

Hruban, Ralph. H. ;

Wolfgang, Christopher L. ;

Goggins, Michael G. ;

Dal Molin, Marco ;

Wang, Tian-Li ;

Roden, Richard ;

Klein, Alison P. ;

Ptak, Janine ;

Dobbyn, Lisa ;

Schaefer, Joy ;

Silliman, Natalie ;

Popoli, Maria ;

Vogelstein, Joshua T. ;

Browne, James D. ;

Schoen, Robert E. ;

Brand, Randall E. ;

Tie, Jeanne ;

Gibbs, Peter ;

Wong, Hui-Li ;

Mansfield, Aaron S. ;

Jen, Jin ;

Hanash, Samir M. ;

Falconi, Massimo ;

Allen, Peter J. ;

Zhou, Shibin ;

Bettegowda, Chetan ;

Diaz, Luis A., Jr. ;

Tomasetti, Cristian ;

Kinzler, Kenneth W. ;

Vogelstein, Bert ;

Lennon, Anne Marie ;

Papadopoulos, Nickolas .

SCIENCE, 2018, 359 (6378) :926-+

[3] TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data [J].

Colaprico, Antonio ;

Silva, Tiago C. ;

Olsen, Catharina ;

Garofano, Luciano ;

Cava, Claudia ;

Garolini, Davide ;

Sabedot, Thais S. ;

Malta, Tathiane M. ;

Pagnotta, Stefano M. ;

Castiglioni, Isabella ;

Ceccarelli, Michele ;

Bontempi, Gianluca ;

Noushmehr, Houtan .

NUCLEIC ACIDS RESEARCH, 2016, 44 (08) :e71

[4] Comprehensivemolecular characterization of clear cell renal cell carcinoma [J].

Creighton, Chad J. ;

Morgan, Margaret ;

Gunaratne, Preethi H. ;

Wheeler, David A. ;

Gibbs, Richard A. ;

Robertson, A. Gordon ;

Chu, Andy ;

Beroukhim, Rameen ;

Cibulskis, Kristian ;

Signoretti, Sabina ;

Vandin, Fabio ;

Wu, Hsin-Ta ;

Raphael, Benjamin J. ;

Verhaak, Roel G. W. ;

Tamboli, Pheroze ;

Torres-Garcia, Wandaliz ;

Akbani, Rehan ;

Weinstein, John N. ;

Reuter, Victor ;

Hsieh, James J. ;

Brannon, A. Rose ;

Hakimi, A. Ari ;

Jacobsen, Anders ;

Ciriello, Giovanni ;

Reva, Boris ;

Ricketts, Christopher J. ;

Linehan, W. Marston ;

Stuart, Joshua M. ;

Rathmell, W. Kimryn ;

Shen, Hui ;

Laird, Peter W. ;

Muzny, Donna ;

Davis, Caleb ;

Morgan, Margaret ;

Xi, Liu ;

Chang, Kyle ;

Kakkar, Nipun ;

Trevino, Lisa R. ;

Benton, Susan ;

Reid, Jeffrey G. ;

Morton, Donna ;

Doddapaneni, Harsha ;

Han, Yi ;

Lewis, Lora ;

Dinh, Huyen ;

Kovar, Christie ;

Zhu, Yiming ;

Santibanez, Jireh ;

Wang, Min ;

Hale, Walker .

NATURE, 2013, 499 (7456) :43-+

[5] Detection and Surveillance of Bladder Cancer Using Urine Tumor DNA [J].

Dudley, Jonathan C. ;

Schroers-Martin, Joseph ;

Lazzareschi, Daniel, V ;

Shi, William, V ;

Chen, Simon B. ;

Esfahani, Mohammad S. ;

Trivedi, Dharati ;

Chabon, Jacob J. ;

Chaudhuri, Aadel A. ;

Stehr, Henning ;

Liu, Chih Long ;

Lim, Harumi ;

Costa, Helio A. ;

Nabet, Barzin Y. ;

Sin, Mandy L. Y. ;

Liao, Joseph C. ;

Alizadeh, Ash A. ;

Diehn, Maximilian .

CANCER DISCOVERY, 2019, 9 (04) :500-509

[6] MultiQC: summarize analysis results for multiple tools and samples in a single report [J].

Ewels, Philip ;

Magnusson, Mans ;

Lundin, Sverker ;

Kaller, Max .

BIOINFORMATICS, 2016, 32 (19) :3047-3048

[7] Regularization Paths for Generalized Linear Models via Coordinate Descent [J].

Friedman, Jerome ;

Hastie, Trevor ;

Tibshirani, Rob .

JOURNAL OF STATISTICAL SOFTWARE, 2010, 33 (01) :1-22

[8] Small Renal Mass [J].

Gill, Inderbir S. ;

Aron, Monish ;

Gervais, Debra A. ;

Jewett, Michael A. S. .

NEW ENGLAND JOURNAL OF MEDICINE, 2010, 362 (07) :624-634

[9]

Hauser S, 2013, ANTICANCER RES, V33, P4651

[10] Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker [J].

Ibn Sina, Abu Ali ;

Carrascosa, Laura G. ;

Liang, Ziyu ;

Grewal, Yadveer S. ;

Wardiana, Andri ;

Shiddiky, Muhammad J. A. ;

Gardiner, Robert A. ;

Samaratunga, Hemamali ;

Gandhi, Maher K. ;

Scott, Rodney J. ;

Korbie, Darren ;

Trau, Matt .

NATURE COMMUNICATIONS, 2018, 9

← 1 2 3 →