Genomewide bisulfite sequencing reveals the origin and time-dependent fragmentation of urinary cfDNA

Clinical Biochemistry

Volumn 50, Issue 9, 2017, Pages 496-501

  Cheng, Timothy H T ^a,b   Jiang, Peiyong ^a,b   Tam, Jacqueline C W ^a,b   Sun, Xiao ^a,b   Lee, Wing Shan ^a,b   Yu, Stephanie C Y ^a,b   Teoh, Jeremy Y C ^b   Chiu, Peter K F ^b   Ng, Chi Fai ^b   Chow, Kai Ming ^b   Szeto, Cheuk Chun ^b   Chan, K C Allen ^a,b   Chiu, Rossa W K ^a,b   Lo, Y M Dennis ^a,b  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Genomewide bisulfite sequencing; Liquid biopsy; Urinary cell free DNA

Indexed keywords

BISULFITE; CREATININE; DNA;

ALGORITHM; ARTICLE; CELL FREE SYSTEM; CLINICAL ARTICLE; CREATININE BLOOD LEVEL; DNA METHYLATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HALF LIFE TIME; HEMATOPOIETIC STEM CELL; HUMAN; IN VITRO STUDY; KIDNEY GRAFT; PERCUTANEOUS NEPHROSTOMY; PERIODICITY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; URINARY TRACT; URINE LEVEL; URINE SAMPLING; ALLOGRAFT; CLINICAL TRIAL; DNA FRAGMENTATION; DNA SEQUENCE; FEMALE; GENETICS; HEMATOPOIETIC STEM CELL TRANSPLANTATION; KIDNEY TRANSPLANTATION; MALE; URINE;

ALLOGRAFTS; DNA; DNA FRAGMENTATION; DNA METHYLATION; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HUMANS; KIDNEY TRANSPLANTATION; MALE; SEQUENCE ANALYSIS, DNA;

EID: 85013994249     PISSN: 00099120     EISSN: 18732933     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2017.02.017     Document Type: Article

References (33)

1. Stroun, M., Maurice, P., Vasioukhin, V., Lyautey, J., Lederrey, C., Lefort, F., et al. The origin and mechanism of circulating DNA. Ann. N. Y. Acad. Sci. 906 (2000), 161–168.
2. Lo, Y.M., Corbetta, N., Chamberlain, P.F., Rai, V., Sargent, I.L., Redman, C.W., et al. Presence of fetal DNA in maternal plasma and serum. Lancet 350 (1997), 485–487.
3. Chen, X.Q., Stroun, M., Magnenat, J.L., Nicod, L.P., Kurt, A.M., Lyautey, J., et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat. Med. 2 (1996), 1033–1035.
4. Lo, Y.M., Tein, M.S., Pang, C.C., Yeung, C.K., Tong, K.L., Hjelm, N.M., Presence of donor-specific DNA in plasma of kidney and liver-transplant recipients. Lancet 351 (1998), 1329–1330.
5. Chiu, R.W.K., Chan, K.C.A., Gao, Y., Lau, V.Y.M., Zheng, W., Leung, T.Y., et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc. Natl. Acad. Sci. U. S. A. 105 (2008), 20458–20463.
6. Leary, R.J., Sausen, M., Kinde, I., Papadopoulos, N., Carpten, J.D., Craig, D., et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci. Transl. Med., 4, 2012, 162ra154.
7. Chan, K.C.A., Jiang, P., Chan, C.W.M., Sun, K., Wong, J., Hui, E.P., 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. 110 (2013), 18761–18768.
8. De Vlaminck, I., Valantine, H.A., Snyder, T.M., Strehl, C., Cohen, G., Luikart, H., et al. Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci. Transl. Med., 6, 2014, 241ra77.
9. Botezatu, I., Serdyuk, O., Potapova, G., Shelepov, V., Alechina, R., Molyaka, Y., et al. Genetic analysis of DNA excreted in urine: a new approach for detecting specific genomic DNA sequences from cells dying in an organism. Clin. Chem. 46 (2000), 1078–1084.
10. Al-Yatama, M.K., Mustafa, A.S., Ali, S., Abraham, S., Khan, Z., Khaja, N., Detection of Y chromosome-specific DNA in the plasma and urine of pregnant women using nested polymerase chain reaction. Prenat. Diagn. 21 (2001), 399–402.
11. Tsui, N.B.Y., Jiang, P., Chow, K.C.K., Su, X., Leung, T.Y., Sun, H., et al. High resolution size analysis of fetal DNA in the urine of pregnant women by paired-end massively parallel sequencing. PLoS One, 7, 2012, e48319.
12. Hung, E.C.W., Shing, T.K.F., Chim, S.S.C., Yeung, P.C., Chan, R.W.Y., Chik, K.W., et al. Presence of donor-derived DNA and cells in the urine of sex-mismatched hematopoietic stem cell transplant recipients: implication for the transrenal hypothesis. Clin. Chem. 55 (2009), 715–722.
13. Su, Y.-H., Wang, M., Brenner, D.E., Norton, P.A., Block, T.M., Detection of mutated K-ras DNA in urine, plasma, and serum of patients with colorectal carcinoma or adenomatous polyps. Ann. N. Y. Acad. Sci. 1137 (2008), 197–206.
14. Chan, K.C.A., Leung, S.F., Yeung, S.W., Chan, A.T.C., Lo, Y.M.D., Quantitative analysis of the transrenal excretion of circulating EBV DNA in nasopharyngeal carcinoma patients. Clin. Cancer Res. 14 (2008), 4809–4813.
15. Zhang, J., Tong, K.-L., Li, P.K.T., Chan, A.Y.W., Yeung, C.-K., Pang, C.C.P., et al. Presence of donor- and recipient-derived DNA in cell-free urine samples of renal transplantation recipients: urinary DNA chimerism. Clin. Chem. 45 (1999), 1741–1746.
16. Szarvas, T., Kovalszky, I., Bedi, K., Szendroi, A., Majoros, A., Riesz, P., et al. Deletion analysis of tumor and urinary DNA to detect bladder cancer: urine supernatant versus urine sediment. Oncol. Rep. 18 (2007), 405–409.
17. Birkenkamp-Demtröder, K., Nordentoft, I., Christensen, E., Høyer, S., Reinert, T., Vang, S., et al. Genomic alterations in liquid biopsies from patients with bladder cancer. Eur. Urol. 70 (2016), 75–82.
18. Li, Y., Zhong, X.Y., Kang, A., Troeger, C., Holzgreve, W., Hahn, S., Inability to detect cell free fetal DNA in the urine of normal pregnant women nor in those affected by preeclampsia associated HELLP syndrome. J. Soc. Gynecol. Investig. 10 (2003), 503–508.
19. Fernandez, A.F., Assenov, Y., Martin-Subero, J.I., Balint, B., Siebert, R., Taniguchi, H., et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 22 (2012), 407–419.
20. Consortium, R.E., Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., et al. Integrative analysis of 111 reference human epigenomes. Nature 518 (2015), 317–330.
21. Houseman, E.A., Accomando, W.P., Koestler, D.C., Christensen, B.C., Marsit, C.J., Nelson, H.H., et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinf., 13, 2012, 86.
22. Sun, K., Jiang, P., Chan, K.C.A., Wong, J., Cheng, Y.K.Y., Liang, R.H.S., 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. 112 (2015), E5503–E5512.
23. Wong, F.C.K., Sun, K., Jiang, P., Cheng, Y.K.Y., Chan, K.C.A., Leung, T.Y., et al. Cell-free DNA in maternal plasma and serum: a comparison of quantity, quality and tissue origin using genomic and epigenomic approaches. Clin. Biochem. 49:18 (2016), 1379–1386.
24. Yu, S.C.Y., Lee, S.W.Y., Jiang, P., Leung, T.Y., Chan, K.C.A., Chiu, R.W.K., et al. High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing. Clin. Chem. 59 (2013), 1228–1237.
25. Chan, K.C.A., Jiang, P., Zheng, Y.W.L., Liao, G.J.W., 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. 59 (2013), 211–224.
26. Lun, F.M.F., Chiu, R.W.K., Sun, K., Leung, T.Y., Jiang, P., Chan, K.C.A., et al. Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin. Chem. 59 (2013), 1583–1594.
27. Jiang, P., Sun, K., Lun, F.M.F., Guo, A.M., Wang, H., Chan, K.C.A., et al. Methy-pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS One, 9, 2014, e100360.
28. Lui, Y.Y.N., Chik, K.W., Chiu, R.W.K., Ho, C.Y., Lam, C.W.K., Lo, Y.M.D., Predominant hematopoietic origin of cell-free dna in plasma and serum after sex-mismatched bone marrow transplantation. Clin. Chem. 48 (2002), 421–427.
29. Hodges, E., Molaro, A., Dos Santos, C.O., Thekkat, P., Song, Q., Uren, P.J., et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell 44 (2011), 17–28.
30. Ito, K., Minamiura, N., Yamamoto, T., Human urine DNase I: immunological identity with human pancreatic DNase I, and enzymic and proteochemical properties of the enzyme. J. Biochem. 95 (1984), 1399–1406.
31. Nadano, D., Yasuda, T., Kishi, K., Measurement of deoxyribonuclease I activity in human tissues and body fluids by a single radial enzyme-diffusion method. Clin. Chem. 39 (1993), 448–452.
32. Snyder, M.W., Kircher, M., Hill, A.J., Daza, R.M., Shendure, J., Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164 (2016), 57–68.
33. Lo, Y.M.D., Chan, K.C.A., Sun, H., Chen, E.Z., Jiang, P., Lun, F.M.F., et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci. Transl. Med., 2010, 2:61ra91.