The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics

Trends in Genetics

Volumn 32, Issue 6, 2016, Pages 360-371

  Jiang, Peiyong ^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

Cell free DNA; Liquid biopsy; Size profile

Indexed keywords

CIRCULATING CELL FREE DNA; DNA; DNA FRAGMENT; MITOCHONDRIAL DNA; UNCLASSIFIED DRUG;

AUTOIMMUNE DISEASE; CANCER PATIENT; CELL FREE SYSTEM; DNA SEQUENCE; ELECTROPHORESIS; FETUS; HUMAN; MICROSCOPY; MOLECULAR DIAGNOSIS; MOLECULAR DIAGNOSTICS; MOLECULE; NEOPLASM; PLASMA; POLYMERASE CHAIN REACTION; PREGNANCY; PREGNANT WOMAN; PRIORITY JOURNAL; REVIEW; TRANSPLANTATION; BLOOD; FEMALE; MOLECULAR PATHOLOGY; PATHOLOGY; PRENATAL DIAGNOSIS;

AUTOIMMUNE DISEASES; DNA; DNA, NEOPLASM; FEMALE; HUMANS; NEOPLASMS; PATHOLOGY, MOLECULAR; PREGNANCY; PRENATAL DIAGNOSIS;

EID: 84964671215     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2016.03.009     Document Type: Review

References (88)

1. Lo Y.M.D., et al. Presence of fetal DNA in maternal plasma and serum. Lancet 1997, 350:485-487.
2. Chen X.Q., et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat. Med. 1996, 2:1033-1035.
3. Finning K., et al. Effect of high throughput RHD typing of fetal DNA in maternal plasma on use of anti-RhD immunoglobulin in RhD negative pregnant women: prospective feasibility study. BMJ 2008, 336:816-818.
4. Lo Y.M.D., et al. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. N. Engl. J. Med. 1998, 339:1734-1738.
5. Costa J.M., et al. New strategy for prenatal diagnosis of X-linked disorders. N. Engl. J. Med. 2002, 346:1502.
6. Lo Y.M.D., et al. Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:13116-13121.
7. Chiu R.W.K., 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. 2008, 105:20458-20463.
8. Fan H.C., et al. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:16266-16271.
9. Chiu R.W.K., et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011, 342:c7401.
10. Bianchi D.W., et al. DNA sequencing versus standard prenatal aneuploidy screening. N. Engl. J. Med. 2014, 370:799-808.
11. Yu S.C.Y., et al. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:8583-8588.
12. Norton M.E., et al. Cell-free DNA analysis for noninvasive examination of trisomy. N. Engl. J. Med. 2015, 372:1589-1597.
13. Lam K.W., et al. Noninvasive prenatal diagnosis of monogenic diseases by targeted massively parallel sequencing of maternal plasma: application to beta thalassemia. Clin. Chem. 2012, 58:1467-1475.
14. Lo Y.M.D., et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci. Transl. Med. 2010, 2:61ra91.
15. Ma D., et al. Haplotype-based approach for noninvasive prenatal diagnosis of congenital adrenal hyperplasia by maternal plasma DNA sequencing. Gene 2014, 544:252-258.
16. New M.I., et al. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J. Clin. Endocrinol. Metab. 2014, 99:E1022-E1030.
17. Tsui N.B., et al. Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood 2011, 117:3684-3691.
18. Yoo S.K., et al. Noninvasive prenatal diagnosis of duchenne muscular dystrophy: comprehensive genetic diagnosis in carrier, proband, and fetus. Clin. Chem. 2015, 61:829-837.
19. Allyse M., et al. Non-invasive prenatal testing: a review of international implementation and challenges. Int. J. Womens Health 2015, 7:113-126.
20. Chandrasekharan S., et al. Noninvasive prenatal testing goes global. Sci. Transl. Med. 2014, 6:231fs215.
21. Chan K.C.A., 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, 110:18761-18768.
22. Chan K.C.A., 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, 59:211-224.
23. Diehl F., et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:16368-16373.
24. Forshew T., et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 2012, 4:136ra168.
25. Heitzer E., et al. Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int. J. Cancer 2013, 133:346-356.
26. Jiang P., et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc. Natl. Acad. Sci. U.S.A. 2015, 112:E1317-E1325.
27. Leary R.J., et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci. Transl. Med. 2010, 2:20ra14.
28. Mouliere F., et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS ONE 2011, 6:e23418.
29. Murtaza M., et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013, 497:108-112.
30. Leary R.J., et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci. Transl. Med. 2012, 4:162ra154.
31. Bettegowda C., et al. Detection of circulating tumor DNA in early and late stage human malignancies. Sci. Transl. Med. 2014, 6:224ra224.
32. Fan H.C., et al. Non-invasive prenatal measurement of the fetal genome. Nature 2012, 487:320-324.
33. Lun F.M.F., et al. Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin. Chem. 2013, 59:1583-1594.
34. Chiu R.W.K., et al. Non-invasive prenatal diagnosis by single molecule counting technologies. Trends Genet. 2009, 25:324-331.
35. Jung K., et al. Cell-free DNA in the blood as a solid tumor biomarker-a critical appraisal of the literature. Clin. Chim. Acta 2010, 411:1611-1624.
36. Lo Y.M.D., Chiu R.W.K. Genomic analysis of fetal nucleic acids in maternal blood. Annu. Rev. Genomics Hum. Genet. 2012, 13:285-306.
37. Schwarzenbach H., et al. Cell-free nucleic acids as biomarkers in cancer patients. Nat. Rev. Cancer 2011, 11:426-437.
38. Wong A.I.C., Lo Y.M.D. Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications. Trends Mol. Med. 2015, 21:98-108.
39. Giacona M.B., et al. Cell-free DNA in human blood plasma: length measurements in patients with pancreatic cancer and healthy controls. Pancreas 1998, 17:89-97.
40. Jahr S., et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001, 61:1659-1665.
41. Rumore P.M., Steinman C.R. Endogenous circulating DNA in systemic lupus erythematosus. Occurrence as multimeric complexes bound to histone. J. Clin. Invest. 1990, 86:69-74.
42. Stroun M., et al. Isolation and characterization of DNA from the plasma of cancer patients. Eur. J. Cancer Clin. Oncol. 1987, 23:707-712.
43. Wyllie A.H., et al. Chromatin cleavage in apoptosis: association with condensed chromatin morphology and dependence on macromolecular synthesis. J. Pathol. 1984, 142:67-77.
44. Chan K.C.A., et al. Size distributions of maternal and fetal DNA in maternal plasma. Clin. Chem. 2004, 50:88-92.
45. Thierry A.R., et al. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res. 2010, 38:6159-6175.
46. Mouliere F., et al. Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer. Mol. Oncol. 2014, 8:927-941.
47. Chan K.C.A., et al. Molecular characterization of circulating EBV DNA in the plasma of nasopharyngeal carcinoma and lymphoma patients. Cancer Res. 2003, 63:2028-2032.
48. Mouliere F., et al. Circulating cell-free DNA from colorectal cancer patients may reveal high KRAS or BRAF mutation load. Transl. Oncol. 2013, 6:319-328.
49. Ellinger J., et al. Noncancerous PTGS2 DNA fragments of apoptotic origin in sera of prostate cancer patients qualify as diagnostic and prognostic indicators. Int. J. Cancer 2008, 122:138-143.
50. Ellinger J., et al. Cell-free circulating DNA: diagnostic value in patients with testicular germ cell cancer. J. Urol. 2009, 181:363-371.
51. Davis R.W., et al. Electron microscope heteroduplex methods for mapping regions of base sequence homology in nucleic acids. Methods Enzymol. 1971, 21:413-418.
52. Binnig G., et al. Atomic force microscope. Phys. Rev. Lett. 1986, 56:930-933.
53. Hansma H.G., et al. Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res. 1996, 24:713-720.
54. Dennin R.H. DNA of free and complexed origin in human plasma: concentration and length distribution. Klin. Wochenschr. 1979, 57:451-456.
55. Zheng Y.W.L., et al. Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. Clin. Chem. 2012, 58:549-558.
56. Fan H.C., et al. Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. Clin. Chem. 2010, 56:1279-1286.
57. Yu S.C.Y., et al. High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing. Clin. Chem. 2013, 59:1228-1237.
58. Mandel P., Metais P. Les acides nucléiques du plasma sanguin chez l'homme. C. R. Seances Soc. Biol. Fil. 1948, 142:241-243.
59. Nagata S. Apoptotic DNA fragmentation. Exp. Cell Res. 2000, 256:12-18.
60. Holdenrieder S., et al. Apoptosis in serum of patients with solid tumours. Anticancer Res. 1999, 19:2721-2724.
61. Chan R.W.Y., et al. Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:E5302-E5311.
62. Suzuki N., et al. Characterization of circulating DNA in healthy human plasma. Clin. Chim. Acta 2008, 387:55-58.
63. Cheng S.H., et al. Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: feasibility assessment. Clin. Chem. 2015, 61:1305-1306.
64. Li Y., et al. Size separation of circulatory DNA in maternal plasma permits ready detection of fetal DNA polymorphisms. Clin. Chem. 2004, 50:1002-1011.
65. Chandrananda D., et al. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med. Genomics 2015, 8:29.
66. Snyder M.W., et al. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 2016, 164:57-68.
67. Sun K., 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:E5503-E5512.
68. Gao Y.J., et al. Increased integrity of circulating cell-free DNA in plasma of patients with acute leukemia. Clin. Chem. Lab. Med. 2010, 48:1651-1656.
69. Umetani N., et al. Prediction of breast tumor progression by integrity of free circulating DNA in serum. J. Clin. Oncol. 2006, 24:4270-4276.
70. Umetani N., et al. Increased integrity of free circulating DNA in sera of patients with colorectal or periampullary cancer: direct quantitative PCR for ALU repeats. Clin. Chem. 2006, 52:1062-1069.
71. Wang B.G., et al. Increased plasma DNA integrity in cancer patients. Cancer Res. 2003, 63:3966-3968.
72. Hanley R., et al. DNA integrity assay: a plasma-based screening tool for the detection of prostate cancer. Clin. Cancer Res. 2006, 12:4569-4574.
73. Jiang W.W., et al. Increased plasma DNA integrity index in head and neck cancer patients. Int. J. Cancer 2006, 119:2673-2676.
74. Kamel A.M., et al. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer. Tumour Biol. 2015, 18. Published online December 18, 2015. 10.1007/s13277-015-4624-3.
75. Chan K.C.A., et al. Persistent aberrations in circulating DNA integrity after radiotherapy are associated with poor prognosis in nasopharyngeal carcinoma patients. Clin. Cancer Res. 2008, 14:4141-4145.
76. Lehner J., et al. Circulating plasma DNA and DNA integrity in breast cancer patients undergoing neoadjuvant chemotherapy. Clin. Chim. Acta 2013, 425:206-211.
77. Schwarzenbach H., et al. Loss of heterozygosity at tumor suppressor genes detectable on fractionated circulating cell-free tumor DNA as indicator of breast cancer progression. Clin. Cancer Res. 2012, 18:5719-5730.
78. Pleasance E.D., et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010, 463:191-196.
79. Totoki Y., et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 2011, 43:464-469.
80. Nakano H., Shinohara K. X-ray-induced cell death: apoptosis and necrosis. Radiat. Res. 1994, 140:1-9.
81. Walker N.I., et al. Patterns of cell death. Methods Achiev. Exp. Pathol. 1988, 13:18-54.
82. Rainer T.H., et al. Prognostic use of circulating plasma nucleic acid concentrations in patients with acute stroke. Clin. Chem. 2003, 49:562-569.
83. Zhong X.Y., et al. Increased concentrations of antibody-bound circulatory cell-free DNA in rheumatoid arthritis. Clin. Chem. 2007, 53:1609-1614.
84. Bartoloni E., et al. Increased levels of circulating DNA in patients with systemic autoimmune diseases: a possible marker of disease activity in Sjogren's syndrome. Lupus 2011, 20:928-935.
85. Antonatos D., et al. Cell-free DNA levels as a prognostic marker in acute myocardial infarction. Ann. N.Y. Acad. Sci. 2006, 1075:278-281.
86. Lo Y.M.D., et al. Plasma DNA as a prognostic marker in trauma patients. Clin. Chem. 2000, 46:319-323.
87. Chen J.A., et al. Sensitive detection of plasma/serum DNA in patients with systemic lupus erythematosus. Autoimmunity 2007, 40:307-310.
88. Raptis L., Menard H.A. Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. J. Clin. Invest. 1980, 66:1391-1399.