Low-Coverage Sequencing of Urine Sediment DNA for Detection of Copy Number Aberrations in Bladder Cancer

References

• Antoni S, Ferlay J, Soerjomataram I, Znaor A, Jemal A, Bray F. Bladder cancer incidence and mortality: a global overview and recent trends. Eur Urol. 2017;71(1):96–108. doi:10.1016/j.eururo.2016.06.01027370177
   PubMed Web of Science ®Google Scholar
• He YT, Li DJ, Liang D, et al. [Incidence and mortality of bladder cancer in China, 2014]. Zhonghua Zhong Liu Za Zhi. 2018;40(9):647–652. Chinese. doi:10.3760/cma.j.issn.0253-3766.2018.09.00230293387
   PubMedGoogle Scholar
• NCCN Guidelines Version 2.2018 Bladder Cancer.
   Google Scholar
• Cancer Genome Atlas Research N. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507(7492):315–322. doi:10.1038/nature1296524476821
   PubMed Web of Science ®Google Scholar
• Aine M, Eriksson P, Liedberg F, Sjodahl G, Hoglund M. Biological determinants of bladder cancer gene expression subtypes. Sci Rep. 2015;5(1):10957. doi:10.1038/srep1095726051783
   PubMed Web of Science ®Google Scholar
• Lindgren D, Frigyesi A, Gudjonsson S, et al. Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. Cancer Res. 2010;70(9):3463–3472. doi:10.1158/0008-5472.CAN-09-421320406976
   PubMed Web of Science ®Google Scholar
• Wu XR. Urothelial tumorigenesis: a tale of divergent pathways. Nat Rev Cancer. 2005;5(9):713–725. doi:10.1038/nrc169716110317
   PubMed Web of Science ®Google Scholar
• Choi W, Ochoa A, McConkey DJ, et al. Genetic alterations in the molecular subtypes of bladder cancer: illustration in the cancer genome atlas dataset. Eur Urol. 2017;72(3):354–365. doi:10.1016/j.eururo.2017.03.01028365159
   PubMed Web of Science ®Google Scholar
• Sjodahl G, Lauss M, Lovgren K, et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res. 2012;18(12):3377–3386. doi:10.1158/1078-0432.CCR-12-0077-T22553347
   PubMed Web of Science ®Google Scholar
• Cazier JB, Rao SR, McLean CM, et al. Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden. Nat Commun. 2014;5(1):3756. doi:10.1038/ncomms475624777035
   PubMed Web of Science ®Google Scholar
• He H, Han C, Hao L, Zang G. ImmunoCyt test compared to cytology in the diagnosis of bladder cancer: a meta-analysis. Oncol Lett. 2016;12(1):83–88. doi:10.3892/ol.2016.455627347104
   PubMed Web of Science ®Google Scholar
• Patel KM, Tsui DW. The translational potential of circulating tumour DNA in oncology. Clin Biochem. 2015;48(15):957–961. doi:10.1016/j.clinbiochem.2015.04.00525889059
   PubMed Web of Science ®Google Scholar
• Lodewijk I, Dueñas M, Rubio C, et al. Liquid biopsy biomarkers in bladder cancer: a current need for patient diagnosis and monitoring. Int J Mol Sci. 2018;19(9):2514. doi:10.3390/ijms19092514
   PubMed Web of Science ®Google Scholar
• Blick CG, Nazir SA, Mallett S, et al. Evaluation of diagnostic strategies for bladder cancer using computed tomography (CT) urography, flexible cystoscopy and voided urine cytology: results for 778 patients from a hospital haematuria clinic. BJU Int. 2012;110(1):84–94. doi:10.1111/j.1464-410X.2011.10664.x22122739
   PubMed Web of Science ®Google Scholar
• Ge G, Peng D, Guan B, et al. Urothelial carcinoma detection based on copy number profiles of urinary cell-free DNA by shallow whole-genome sequencing. Clin Chem. 2020;66(1):188–198. doi:10.1373/clinchem.2019.30963331811000
   PubMed Web of Science ®Google Scholar
• Tanaka K, Hirota T. Chromosomal instability: a common feature and a therapeutic target of cancer. Biochim Biophys Acta. 2016;1866(1):64–75. doi:10.1016/j.bbcan.2016.06.00227345585
   PubMed Web of Science ®Google Scholar
• Togneri FS, Ward DG, Foster JM, et al. Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA. Eur J Hum Genet. 2016;24(8):1167–1174. doi:10.1038/ejhg.2015.28126757983
   PubMed Web of Science ®Google Scholar
• Ignatiadis M, Lee M, Jeffrey SS. Circulating tumor cells and circulating tumor DNA: challenges and opportunities on the path to clinical utility. Clin Cancer Res. 2015;21(21):4786–4800. doi:10.1158/1078-0432.CCR-14-119026527805
   PubMed Web of Science ®Google Scholar
• Nakabayashi M, Kawashima A, Yasuhara R, et al. Massively parallel sequencing of cell-free DNA in plasma for detecting gynaecological tumour-associated copy number alteration. Sci Rep. 2018;8(1):11205. doi:10.1038/s41598-018-29381-y30046040
   PubMed Web of Science ®Google Scholar
• Cohen PA, Flowers N, Tong S, Hannan N, Pertile MD, Hui L. Abnormal plasma DNA profiles in early ovarian cancer using a non-invasive prenatal testing platform: implications for cancer screening. BMC Med. 2016;14(1):126. doi:10.1186/s12916-016-0667-627558279
   PubMed Web of Science ®Google Scholar
• Vanderstichele A, Busschaert P, Smeets D, et al. Chromosomal instability in cell-free DNA as a highly specific biomarker for detection of ovarian cancer in women with adnexal masses. Clin Cancer Res. 2017;23(9):2223–2231. doi:10.1158/1078-0432.CCR-16-107827852697
   PubMed Web of Science ®Google Scholar
• Mersy E, Smits LJ, van Winden LA, et al. Noninvasive detection of fetal trisomy 21: systematic review and report of quality and outcomes of diagnostic accuracy studies performed between 1997 and 2012. Hum Reprod Update. 2013;19(4):318–329. doi:10.1093/humupd/dmt00123396607
   PubMed Web of Science ®Google Scholar
• Kinnings SL, Geis JA, Almasri E, et al. Factors affecting levels of circulating cell-free fetal DNA in maternal plasma and their implications for noninvasive prenatal testing. Prenat Diagn. 2015;35(8):816–822. doi:10.1002/pd.462526013964
   PubMed Web of Science ®Google Scholar
• Noninvasive Prenatal Testing for Trisomies. 21, 18, and 13, sex chromosome aneuploidies, and microdeletions: a health technology assessment. Ont Health Technol Assess Ser. 2019;19(4):1–166.
   Google Scholar
• Cai YH, Yao GY, Chen LJ, Gan HY, Ye CS, Yang XX. The combining effects of cell-free circulating tumor DNA of breast tumor to the noninvasive prenatal testing results: a simulating investigation. DNA Cell Biol. 2018;37(7):626–633. doi:10.1089/dna.2017.411229957029
   PubMed Web of Science ®Google Scholar
• Zhang S, Wang Y, Bondaruk J, et al. Detection of bladder cancer in urine sediments by a novel multicolor fluorescence in situ hybridization (Quartet) test. Eur Urol Focus. 2018.
   Google Scholar
• Ward DG, Bryan RT. Liquid biopsies for bladder cancer. Transl Androl Urol. 2017;6(2):331–335. doi:10.21037/tau.2017.03.0828540249
   PubMed Web of Science ®Google Scholar
• Salvi S, Casadio V. Urinary cell-free DNA: potential and applications. Methods Mol Biol. 2019;1909:201–209.30580433
   PubMedGoogle Scholar
• Christensen E, Birkenkamp-Demtroder K, Nordentoft I, et al. Liquid biopsy analysis of FGFR3 and PIK3CA hotspot mutations for disease surveillance in bladder cancer. Eur Urol. 2017;71(6):961–969. doi:10.1016/j.eururo.2016.12.01628069289
   PubMed Web of Science ®Google Scholar
• Liu B, Yang L, Huang B, et al. A functional copy-number variation in MAPKAPK2 predicts risk and prognosis of lung cancer. Am J Hum Genet. 2012;91(2):384–390. doi:10.1016/j.ajhg.2012.07.00322883146
   PubMed Web of Science ®Google Scholar
• Li J, Dittmar RL, Xia S, et al. Cell-free DNA copy number variations in plasma from colorectal cancer patients. Mol Oncol. 2017;11(8):1099–1111. doi:10.1002/1878-0261.1207728504856
   PubMed Web of Science ®Google Scholar
• Goodison S, Rosser CJ, Urquidi V. Bladder cancer detection and monitoring: assessment of urine- and blood-based marker tests. Mol Diagn Ther. 2013;17(2):71–84. doi:10.1007/s40291-013-0023-x23479428
   PubMed Web of Science ®Google Scholar
• Zeng S, Ying Y, Xing N, et al. Noninvasive detection of urothelial carcinoma by cost-effective low-coverage whole-genome sequencing from urine-exfoliated cell DNA. Clin Cancer Res. 2020;26(21):5646–5654. doi:10.1158/1078-0432.CCR-20-040133037018
   PubMed Web of Science ®Google Scholar
• Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra224. doi:10.1126/scitranslmed.3007094
   Web of Science ®Google Scholar
• Ma M, Zhu H, Zhang C, Sun X, Gao X, Chen G. “Liquid biopsy”-ctDNA detection with great potential and challenges. Ann Transl Med. 2015;3(16):235. doi:10.3978/j.issn.2305-5839.2015.09.2926539452
   PubMed Web of Science ®Google Scholar
• Lee DH, Yoon H, Park S, et al. Urinary exosomal and cell-free DNA detects somatic mutation and copy number alteration in urothelial carcinoma of bladder. Sci Rep. 2018;8(1):14707. doi:10.1038/s41598-018-32900-630279572
   PubMed Web of Science ®Google Scholar
• Hudecova I. Digital PCR analysis of circulating nucleic acids. Clin Biochem. 2015;48(15):948–956. doi:10.1016/j.clinbiochem.2015.03.01525828047
   PubMed Web of Science ®Google Scholar
• Szarvas T, Kovalszky I, Bedi K, et al. Deletion analysis of tumor and urinary DNA to detect bladder cancer: urine supernatant versus urine sediment. Oncol Rep. 2007;18(2):405–409.17611663
   PubMed Web of Science ®Google Scholar
• Stahlberg A, Krzyzanowski PM, Jackson JB, Egyud M, Stein L, Godfrey TE. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing. Nucleic Acids Res. 2016;44(11):e105. doi:10.1093/nar/gkw22427060140
   PubMed Web of Science ®Google Scholar
• Schmitz-Drager BJ, Droller M, Lokeshwar VB, et al. Molecular markers for bladder cancer screening, early diagnosis, and surveillance: the WHO/ICUD consensus. Urol Int. 2015;94(1):1–24. doi:10.1159/00036935725501325
   PubMed Web of Science ®Google Scholar
• Millholland JM, Li S, Fernandez CA, Shuber AP. Detection of low frequency FGFR3 mutations in the urine of bladder cancer patients using next-generation deep sequencing. Res Rep Urol. 2012;4:33–40. doi:10.2147/RRU.S3273624199178
   PubMedGoogle Scholar
• Cheng THT, Jiang P, Teoh JYC, et al. Noninvasive detection of bladder cancer by shallow-depth genome-wide bisulfite sequencing of urinary cell-free DNA for methylation and copy number profiling. Clin Chem. 2019;65(7):927–936. doi:10.1373/clinchem.2018.30134130988170
   PubMed Web of Science ®Google Scholar
• Xu Z, Ge G, Guan B, et al. Noninvasive detection and localization of genitourinary cancers using urinary sediment DNA methylomes and copy number profiles. Eur Urol. 2020;77(2):288–290. doi:10.1016/j.eururo.2019.11.00631744643
   PubMed Web of Science ®Google Scholar