CancerLocator: Non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

Genome Biology

Volumn 18, Issue 1, 2017, Pages

  Kang, Shuli ^a   Li, Qingjiao ^a   Chen, Quan ^a   Zhou, Yonggang ^b,c   Park, Stacy ^b   Lee, Gina ^d   Grimes, Brandon ^b   Krysan, Kostyantyn ^b   Yu, Min ^e   Wang, Wei ^f   Alber, Frank ^a   Sun, Fengzhu ^a   Dubinett, Steven M ^b   Li, Wenyuan ^b   Zhou, Xianghong Jasmine ^b,c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d VA GREATER LOS ANGELES HEALTHCARE SYSTEM   (United States)

^e UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^f Tongde Hospital of Zhejiang Province   (China)

Author keywords

Cancer diagnosis; Cell free DNA; DNA methylation; Liquid biopsy; Next generation sequencing

Indexed keywords

DNA;

ARTICLE; BLOOD SAMPLING; DIAGNOSTIC VALUE; DNA METHYLATION; HUMAN; INTERMETHOD COMPARISON; MALIGNANT NEOPLASM; MATHEMATICAL ANALYSIS; NON INVASIVE MEASUREMENT; PREDICTION; PROBABILITY; RANDOM FOREST; SIMULATION; SOFTWARE; SUPPORT VECTOR MACHINE; TUMOR LOCALIZATION; ALGORITHM; BLOOD; COMPUTER SIMULATION; CPG ISLAND; EPIGENETICS; GENETIC EPIGENESIS; GENETICS; NEOPLASMS; PROCEDURES; REPRODUCIBILITY; STATISTICAL MODEL; WORKFLOW;

ALGORITHMS; COMPUTER SIMULATION; CPG ISLANDS; DNA METHYLATION; DNA, NEOPLASM; EPIGENESIS, GENETIC; EPIGENOMICS; HUMANS; MODELS, STATISTICAL; NEOPLASMS; REPRODUCIBILITY OF RESULTS; WORKFLOW;

EID: 85016166382     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1191-5     Document Type: Article

References (29)

1. Esteller M. Molecular origins of cancer epigenetics in cancer. N Engl J Med. 2008;358:1148-59.
2. Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated DNA sequences in cancer. Epigenomics. 2010;2:245-69.
3. Yang Z, Jones A, Widschwendter M, Teschendorff AE. An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer. Genome Biol. 2015;16:140.
4. Sahnane N, Magnoli F, Bernasconi B, Tibiletti MG, Romualdi C, Pedroni M, et al. Aberrant DNA methylation profiles of inherited and sporadic colorectal cancer. Clin Epigenetics. 2015;7:131.
5. Lee S-T, Wiemels JL. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites. Nucleic Acids Res. 2016;44:1105-17.
6. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13:679-92.
7. Schübeler D. Function and information content of DNA methylation. Nature. 2015;517:321-6.
8. Schwarzenbach H, Hoon DSB, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011;11:426-37.
9. Agostini M, Pucciarelli S, Enzo MV, Del Bianco P, Briarava M, Bedin C, et al. Circulating cell-free DNA: a promising marker of pathologic tumor response in rectal cancer patients receiving preoperative chemoradiotherapy. Ann Surg Oncol. 2011;18:2461-8.
10. Liggett TE, Melnikov A, Yi Q, Replogle C, Hu W, Rotmensch J, et al. Distinctive DNA methylation patterns of cell-free plasma DNA in women with malignant ovarian tumors. Gynecol Oncol. 2011;120:113-20.
11. Radpour R, Barekati Z, Kohler C, Lv Q, Bürki N, Diesch C, et al. Hypermethylation of tumor suppressor genes involved in critical regulatory pathways for developing a blood-based test in breast cancer. PLoS One. 2011;6:e16080.
12. Langevin SM, Koestler DC, Christensen BC, Butler RA, Wiencke JK, Nelson HH, et al. Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: an epigenome-wide association study. Epigenetics. 2012;7:291-9.
13. Danese E, Minicozzi AM, Benati M, Montagnana M, Paviati E, Salvagno GL, et al. Epigenetic alteration: new insights moving from tissue to plasma--the example of PCDH10 promoter methylation in colorectal cancer. Br J Cancer. 2013;109:807-13.
14. Kloten V, Becker B, Winner K, Schrauder MG, Fasching PA, Anzeneder T, et al. Promoter hypermethylation of the tumor-suppressor genes ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening. Breast Cancer Res. 2013;15:R4.
15. Salvianti F, Orlando C, Massi D, De Giorgi V, Grazzini M, Pazzagli M, et al. Tumor-related methylated cell-free DNA and circulating tumor cells in melanoma. Front Mol Biosci. 2015;2:76.
16. Heitzer E, Auer M, Hoffmann EM, Pichler M, Gasch C, Ulz P, et al. Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int J Cancer. 2013;133:346-56.
17. Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012;4:162ra154.
18. Chan KCA, Jiang P, Zheng YWL, Liao GJW, Sun H, Wong J, et al. Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem. 2013;59:211-24.
19. Chan KCA, Jiang P, Chan CWM, Sun K, Wong J, Hui EP, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci U S A. 2013;110:18761-8.
20. Jiang P, Chan CWM, Chan KCA, Cheng SH, Wong J, Wong VW-S, et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc Natl Acad Sci U S A. 2015;112:E1317-25.
21. Sun K, Jiang P, Chan KCA, Wong J, Cheng YKY, Liang RHS, et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci U S A. 2015;112:201508736.
22. Lehmann-Werman R, Neiman D, Zemmour H, Moss J, Magenheim J, Vaknin-Dembinsky A, et al. Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc Natl Acad Sci U S A. 2016;113:201519286.
23. Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164:57-68.
24. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571-2.
25. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, et al. Cell type-specific gene expression differences in complex tissues. Nat Methods. 2010;7:287-9.
26. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86.
27. Joshi AJ, Porikli F, Papanikolopoulos NP. Scalable active learning for multiclass image classification. IEEE Trans Pattern Anal Mach Intell. 2012;34:2259-73.
28. Gupta MR, Bengio S, Weston J. Training highly multiclass classifiers. J Mach Learn Res. 2014;15:1461-92.
29. Kang S, Cho S, Kang P. Constructing a multi-class classifier using one-against-one approach with different binary classifiers. Neurocomputing. 2015;149:677-82.