Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

Huiwen Che , Kate Stanley , Tatjana Jatsenko , Bernard Thienpont , Joris Robert Vermeesch

Extracellular Vesicles and Circulating Nucleic Acids ›› 2022, Vol. 3 ›› Issue (3) : 216 -34.

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Extracellular Vesicles and Circulating Nucleic Acids ›› 2022, Vol. 3 ›› Issue (3) :216 -34. DOI: 10.20517/evcna.2022.21
review-article

Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

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Abstract

Noninvasive sampling of an individual’s body fluids is an easy means to capture circulating cell-free DNA (cfDNA). These small fragments of DNA carry information on the contributing cell’s genome, epigenome, and nuclease content. Analysis of cfDNA for the assessment of genetic risk has already revolutionized clinical practice, and a compendium of increasingly higher-resolution approaches based on epigenetic and fragmentomic cfDNA signatures continues to expand. Profiling cfDNA has unlocked a wealth of molecular information that can be translated to the clinic. This review covers the biological characteristics of cfDNA, recent advances in liquid biopsy and the clinical utility of cfDNA.

Keywords

Cell-free DNA / liquid biopsy / biomarker

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Huiwen Che, Kate Stanley, Tatjana Jatsenko, Bernard Thienpont, Joris Robert Vermeesch. Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility. Extracellular Vesicles and Circulating Nucleic Acids, 2022, 3(3): 216-34 DOI:10.20517/evcna.2022.21

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References

[1]

Thierry AR,Gahan PB,Stroun M.Origins, structures, and functions of circulating DNA in oncology.Cancer Metastasis Rev2016;35:347-76 PMCID:PMC5035665

[2]

Bronkhorst AJ,Holdenrieder S.The emerging role of cell-free DNA as a molecular marker for cancer management.Biomol Detect Quantif2019;17:100087 PMCID:PMC6425120

[3]

Lui YY,Chiu RW,Lam CW.Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation.Clin Chem2002;48:421-7

[4]

Sun K,Chan KC.Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments.Proc Natl Acad Sci USA2015;112:E5503-12 PMCID:PMC4603482

[5]

Sender R.The distribution of cellular turnover in the human body.Nat Med2021;27:45-8

[6]

Moss J,Neiman D.Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease.Nat Commun2018;9:5068 PMCID:PMC6265251

[7]

Giacona MB,Iczkowski KA,Porter DM.Cell-free DNA in human blood plasma: length measurements in patients with pancreatic cancer and healthy controls.Pancreas1998;17:89-97

[8]

Jiang P.The long and short of circulating cell-free DNA and the ins and outs of molecular diagnostics.Trends Genet2016;32:360-71

[9]

Lo YM,Sun H.Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus.Sci Transl Med2010;2:61ra91

[10]

Jahr S,Englisch S.DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells.Cancer Res2001;61:1659-1665

[11]

Fan HC,Chitkara U,Quake SR.Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing.Clin Chem2010;56:1279-86

[12]

Ivanov M,Butler T,Mileyko V.Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation.BMC Genomics2015;16 Suppl 13:S1 PMCID:PMC4686799

[13]

Sanchez C,Mazard T.Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.JCI Insight2021;6:144561 PMCID:PMC8119211

[14]

Aucamp J,Badenhorst CPS.The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature.Biol Rev Camb Philos Soc2018;93:1649-83

[15]

Kustanovich A,Peretz T.Life and death of circulating cell-free DNA.Cancer Biol Ther2019;20:1057-67 PMCID:PMC6606043

[16]

Elkon KB.Review: cell death, nucleic acids, and immunity: inflammation beyond the grave.Arthritis Rheumatol2018;70:805-16 PMCID:PMC5984680

[17]

Stroun M,Lederrey C,Anker P.About the possible origin and mechanism of circulating DNA.Clinica Chimica Acta2001;313:139-42

[18]

Lau TW,Chan LYS.Fetal DNA clearance from maternal plasma is impaired in preeclampsia.Clin Chem2002;48:2141-2146

[19]

Courtney PA,Williamson K,Kennedy RJ.Increased apoptotic peripheral blood neutrophils in systemic lupus erythematosus: relations with disease activity, antibodies to double stranded DNA, and neutropenia.Ann Rheum Dis1999;58:309-14 PMCID:PMC1752888

[20]

Heitzer E,Speicher MR.Cell-free DNA and apoptosis: how dead cells inform about the living.Trends Mol Med2020;26:519-28

[21]

Han DSC,Chan RWY.The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3, and DFFB.Am J Hum Genet2020;106:202-14 PMCID:PMC7010979

[22]

Duvvuri B.Cell-free DNA as a biomarker in autoimmune rheumatic diseases.Front Immunol2019;10:502 PMCID:PMC6433826

[23]

Al-Mayouf SM,Abdwani R.Loss-of-function variant in DNASE1L3 causes a familial form of systemic lupus erythematosus.Nat Genet2011;43:1186-8

[24]

Leffler J,Gullstrand B,Martin M.A subset of patients with systemic lupus erythematosus fails to degrade DNA from multiple clinically relevant sources.Arthritis Res Ther2015;17:205 PMCID:PMC4535789

[25]

Diehl F,Choti MA.Circulating mutant DNA to assess tumor dynamics.Nat Med2008;14:985-90 PMCID:PMC2820391

[26]

Lo YMD,Chamberlain PF.Presence of fetal DNA in maternal plasma and serum.The Lancet1997;350:485-7

[27]

Alberry M,Jones M.Free fetal DNA in maternal plasma in anembryonic pregnancies: confirmation that the origin is the trophoblast.Prenat Diagn2007;27:415-8

[28]

Karakas B,Al-Hassan S.Noninvasive digital detection of fetal DNA in plasma of 4-week-pregnant women following in vitro fertilization and embryo transfer.PLoS One2015;10:e0126501 PMCID:PMC4430227

[29]

Chim SS,Chiu RW.Detection of the placental epigenetic signature of the maspin gene in maternal plasma.Proc Natl Acad Sci USA2005;102:14753-8 PMCID:PMC1253547

[30]

Chiu RW,Wong IH.Hypermethylation of RASSF1A in human and rhesus placentas.Am J Pathol2007;170:941-50 PMCID:PMC1864885

[31]

Lun FM,Sun K.Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA.Clin Chem2013;59:1583-94

[32]

Masuzaki H,Yoshiura KI,Niikawa N.Detection of cell free placental DNA in maternal plasma: direct evidence from three cases of confined placental mosaicism.J Med Genet2004;41:289-92 PMCID:PMC1735725

[33]

Faas BH,Janssen I.Non-invasive prenatal diagnosis of fetal aneuploidies using massively parallel sequencing-by-ligation and evidence that cell-free fetal DNA in the maternal plasma originates from cytotrophoblastic cells.Expert Opin Biol Ther2012;12 Suppl 1:S19-26

[34]

Villela D,Van Ghelue M.Fetal sex determination in twin pregnancies using non-invasive prenatal testing.NPJ Genom Med2019;4:15 PMCID:PMC6609680

[35]

Levine RJ,Leshane ES.Two-stage elevation of cell-free fetal DNA in maternal sera before onset of preeclampsia.Am J Obstet Gynecol2004;190:707-13

[36]

Hahn S,Hösli I.Cell-free nucleic acids as potential markers for preeclampsia.Placenta2011;32 Suppl:S17-20

[37]

Karapetian АО,Sadekova АА,Sukhikh GT.Cell-free foetal DNA as a useful marker for preeclampsia prediction.Reprod Sci2021;28:1563-9

[38]

Palomaki GE,Lambert-Messerlian GM.DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study.Genet Med2011;13:913-20

[39]

Chiu RWK.Cell-free fetal DNA coming in all sizes and shapes.Prenat Diagn2021;41:1193-201 PMCID:PMC8518878

[40]

Yu SC,Jiang P.High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing.Clin Chem2013;59:1228-37

[41]

Sun K,Wong AIC.Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing.Proc Natl Acad Sci USA2018;115:E5106-14 PMCID:PMC5984542

[42]

Kim SK,Geis J.Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts.Prenat Diagn2015;35:810-5

[43]

Straver R,Sistermans EA.Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles.Prenat Diagn2016;36:614-21 PMCID:PMC5111749

[44]

Stroun M,Maurice P,Lederrey C.Neoplastic characteristics of the DNA found in the plasma of cancer patients.Oncology1989;46:318-22

[45]

Chen XQ,Magnenat JL.Microsatellite alterations in plasma DNA of small cell lung cancer patients.Nat Med1996;2:1033-5

[46]

Nawroz H,Anker P,Sidransky D.Microsatellite alterations in serum DNA of head and neck cancer patients.Nat Med1996;2:1035-7

[47]

Ulz P,Auer M.Inferring expressed genes by whole-genome sequencing of plasma DNA. Nature Genetics. 2016;48:1273.

[48]

De Mattos-Arruda L,Cortes J.Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle.Ann Oncol2014;25:1729-35 PMCID:PMC6276937

[49]

Murtaza M,Pogrebniak K.Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.Nat Commun2015;6:8760 PMCID:PMC4659935

[50]

Snyder MW,Hill AJ,Shendure J.Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin.Cell2016;164:57-68 PMCID:PMC4715266

[51]

Mouliere F.The importance of examining the proportion of circulating DNA originating from tumor, microenvironment and normal cells in colorectal cancer patients.Expert Opin Biol Ther2012;12 Suppl 1:S209-15

[52]

Bettegowda C,Leary RJ.Detection of circulating tumor DNA in early- and late-stage human malignancies.Sci Transl Med2014;6:224ra24 PMCID:PMC4017867

[53]

Tie J,Wang Y.Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer.Ann Oncol2015;26:1715-22 PMCID:PMC4511218

[54]

Gray ES,Reid AL.Circulating tumor DNA to monitor treatment response and detect acquired resistance in patients with metastatic melanoma.Oncotarget2015;6:42008-18 PMCID:PMC4747205

[55]

Vanderstichele A,Smeets D.Chromosomal instability in cell-free DNA as a highly specific biomarker for detection of ovarian cancer in women with adnexal masses.Clin Cancer Res2017;23:2223-31

[56]

Lenaerts L,Brison N.Breast cancer detection and treatment monitoring using a noninvasive prenatal testing platform: utility in pregnant and nonpregnant populations.Clin Chem2020;66:1414-23

[57]

Smith CG,Mouliere F.Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors.Genome Med2020;12:23 PMCID:PMC7048087

[58]

Markus H,Contente-Cuomo T.Analysis of recurrently protected genomic regions in cell-free DNA found in urine.Sci Transl Med2021;13:eaaz3088 PMCID:PMC9258975

[59]

Mouliere F,Arnau Peyrotte E.High fragmentation characterizes tumour-derived circulating DNA.PLoS One2011;6:e23418 PMCID:PMC3167805

[60]

Kerachian MA,Mozaffari-Jovin S.Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clin Epigenetics2021;13:193 PMCID:PMC8525023

[61]

van der Pol Y,Verkuijlen S.The effect of preanalytical and physiological variables on cell-free DNA fragmentation.Clin Chem2022;68:803-13

[62]

Van Paemel R,Caggiano C.Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome.Epigenetics2021;16:797-807 PMCID:PMC8216177

[63]

Kwak DW,Kim HJ,Kim YH.Maternal total cell-free DNA in preeclampsia with and without intrauterine growth restriction.Sci Rep2020;10:11848 PMCID:PMC7367308

[64]

Tug S,Menke J.Correlation between cell free DNA levels and medical evaluation of disease progression in systemic lupus erythematosus patients.Cell Immunol2014;292:32-9

[65]

Chen E,Leong L.Cell-free DNA concentration and fragment size as a biomarker for prostate cancer.Sci Rep2021;11:5040 PMCID:PMC7930042

[66]

Sifakis S,Spandidos DA.Cell-free fetal DNA and pregnancy-related complications (review).Mol Med Rep2015;11:2367-72 PMCID:PMC4337476

[67]

Forshew T,Parkinson C.Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.Sci Transl Med2012;4:136ra68

[68]

Chiu RW,Gao Y.Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma.Proc Natl Acad Sci USA2008;105:20458-63 PMCID:PMC2600580

[69]

Fan HC,Chitkara U,Quake SR.Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.Proc Natl Acad Sci USA2008;105:16266-71 PMCID:PMC2562413

[70]

Ehrich M,Zwiefelhofer T.Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting.Am J Obstet Gynecol2011;204:205.e1-11

[71]

Bianchi DW,Goldberg JD,Sehnert AJ.MatErnal BLood IS Source to Accurately diagnose fetal aneuploidy (MELISSA) Study GroupGenome-wide fetal aneuploidy detection by maternal plasma DNA sequencing.Obstet Gynecol2012;119:890-901

[72]

Chiu RW,Zheng YW.Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study.BMJ2011;342:c7401 PMCID:PMC3019239

[73]

Heitzer E,Belic J.Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing.Genome Med2013;5:30 PMCID:PMC3707016

[74]

Lenaerts L,Brison N.Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors.Ann Oncol2019;30:85-95

[75]

Newman AM,To J.An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.Nat Med2014;20:548-54 PMCID:PMC4016134

[76]

Newman AM,Klass DM.Integrated digital error suppression for improved detection of circulating tumor DNA.Nat Biotechnol2016;34:547-55 PMCID:PMC4907374

[77]

Wan JCM,Gale D.ctDNA monitoring using patient-specific sequencing and integration of variant reads.Sci Transl Med2020;12:eaaz8084

[78]

Zhang J,Saucier JB.Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA.Nat Med2019;25:439-47

[79]

Kurtz DM,Co Ting Keh L.Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA.Nat Biotechnol2021;39:1537-47 PMCID:PMC8678141

[80]

Leary RJ,Diehl F.Development of personalized tumor biomarkers using massively parallel sequencing.Sci Transl Med2010;2:20ra14 PMCID:PMC2858564

[81]

Clark TA,Kennedy M.Analytical validation of a hybrid capture-based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA.J Mol Diagn2018;20:686-702 PMCID:PMC6593250

[82]

Wong IHN,Zhang J.Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients.Cancer Res1999;59:71-73

[83]

Poon LL,Lau TK,Lo YD.Differential DNA methylation between fetus and mother as a strategy for detecting fetal DNA in maternal plasma.Clin Chem2002;48:35-41

[84]

Chan KC,Gerovassili A.Hypermethylated RASSF1A in maternal plasma: a universal fetal DNA marker that improves the reliability of noninvasive prenatal diagnosis.Clin Chem2006;52:2211-8

[85]

Chan KC,Chan CW.Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.Proc Natl Acad Sci USA2013;110:18761-8 PMCID:PMC3839703

[86]

Jensen TJ,Zhu Z.Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.Genome Biol2015;16:78 PMCID:PMC4427941

[87]

Liu MC,Klein EA,Seiden MV.CCGA ConsortiumSensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA.Ann Oncol2020;31:745-59 PMCID:PMC8274402

[88]

Guo S,Plongthongkum N,Zhang K.Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA.Nat Genet2017;49:635-42 PMCID:PMC5374016

[89]

Shen SY,Fehringer G.Sensitive tumour detection and classification using plasma cell-free DNA methylomes.Nature2018;563:579-83

[90]

Erger F,Borchert D.cfNOMe - a single assay for comprehensive epigenetic analyses of cell-free DNA.Genome Med2020;12:54 PMCID:PMC7315486

[91]

Vaisvila R,Sun Z.Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA.Genome Res2021;31:1280-9 PMCID:PMC8256858

[92]

Liu Y,Velikova G.Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.Nat Biotechnol2019;37:424-9

[93]

Yu SCY,Peng W.Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma.Proc Natl Acad Sci USA2021;118:e2114937118 PMCID:PMC8685924

[94]

Sadeh R,Fialkoff G.ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin.Nat Biotechnol2021;39:586-98

[95]

Yu SC,Zheng YW.Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing.Proc Natl Acad Sci USA2014;111:8583-8 PMCID:PMC4060699

[96]

Cristiano S,Phallen J.Genome-wide cell-free DNA fragmentation in patients with cancer.Nature2019;570:385-9 PMCID:PMC6774252

[97]

Mouliere F,Piskorz AM.Enhanced detection of circulating tumor DNA by fragment size analysis.Sci Transl Med2018;10:eaat4921 PMCID:PMC6483061

[98]

Budis J,Radvanszky J.Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing.Bioinformatics2019;35:1284-91

[99]

Liu J,Huang Y.Genome-wide cell-free DNA methylation analyses improve accuracy of non-invasive diagnostic imaging for early-stage breast cancer.Mol Cancer2021;20:36 PMCID:PMC7893735

[100]

Ulz P,Zhou Q.Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection.Nat Commun2019;10:4666 PMCID:PMC6789008

[101]

Sun K,Cheng SH.Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin.Genome Res2019;29:418-27 PMCID:PMC6396422

[102]

Jiang P,Peng W.Plasma DNA end-motif profiling as a fragmentomic marker in cancer, pregnancy, and transplantation.Cancer Discov2020;10:664-73

[103]

Serpas L,Jiang P.Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA.Proc Natl Acad Sci USA2019;116:641-9 PMCID:PMC6329986

[104]

Chan RWY,Ni M.Plasma DNA profile associated with DNASE1L3 gene mutations: clinical observations, relationships to nuclease substrate preference, and in vivo correction.Am J Hum Genet2020;107:882-94 PMCID:PMC7674998

[105]

Jiang P,Ding SC.Detection and characterization of jagged ends of double-stranded DNA in plasma.Genome Res2020;30:1144-53 PMCID:PMC7462074

[106]

Suzuki N,Yamaki J.Characterization of circulating DNA in healthy human plasma.Clin Chim Acta2008;387:55-8

[107]

Han DSC.The nexus of cfDNA and nuclease biology.Trends Genet2021;37:758-70

[108]

Van Den Bogaert K,Brison N.Outcome of publicly funded nationwide first-tier noninvasive prenatal screening.Genet Med2021;23:1137-42

[109]

Ravitsky V,Haidar H.The emergence and global spread of noninvasive prenatal testing.Annu Rev Genomics Hum Genet2021;22:309-38

[110]

Petersen AK,Smith JL.Positive predictive value estimates for cell-free noninvasive prenatal screening from data of a large referral genetic diagnostic laboratory.Am J Obstet Gynecol2017;217:691.e1-6

[111]

Wellesley D,Boyd PA.Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe.Eur J Hum Genet2012;20:521-6 PMCID:PMC3330224

[112]

Pertile MD,Flowers N.Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease.Sci Transl Med2017;9:eaan1240

[113]

Benn P,Grimi B,Simoni G.Rare autosomal trisomies: comparison of detection through cell-free DNA analysis and direct chromosome preparation of chorionic villus samples.Ultrasound Obstet Gynecol2019;54:458-67

[114]

Bianchi DW.Sequencing of circulating cell-free DNA during pregnancy.N Engl J Med2018;379:464-73

[115]

Bianchi DW.Cherchez la femme: maternal incidental findings can explain discordant prenatal cell-free DNA sequencing results.Genet Med2018;20:910-7

[116]

Chitty LS,Barrett AN.Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.Prenat Diagn2015;35:656-62 PMCID:PMC4657458

[117]

Lench N,Fielding S.The clinical implementation of non-invasive prenatal diagnosis for single-gene disorders: challenges and progress made.Prenat Diagn2013;33:555-62

[118]

Chiu EKL,Chiu RWK.cfDNA screening and diagnosis of monogenic disorders - where are we heading?.Prenat Diagn2018;38:52-8 PMCID:PMC5839244

[119]

Scotchman E,Paternoster B,Chitty LS.Non-invasive prenatal diagnosis and screening for monogenic disorders.Eur J Obstet Gynecol Reprod Biol2020;253:320-7

[120]

Che H,Dimitriadou E.Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA.Genet Med2020;22:962-73

[121]

Zill OA,Sebisanovic D.Cell-Free DNA next-generation sequencing in pancreatobiliary carcinomas.Cancer Discov2015;5:1040-8 PMCID:PMC4592417

[122]

Oxnard GR,Alden RS.Association between plasma genotyping and outcomes of treatment with osimertinib (AZD9291) in advanced non-small-cell lung cancer.J Clin Oncol2016;34:3375-82 PMCID:PMC5035123

[123]

Shu Y,Tong X.Circulating tumor DNA mutation profiling by targeted next generation sequencing provides guidance for personalized treatments in multiple cancer types.Sci Rep2017;7:583 PMCID:PMC5428730

[124]

Adalsteinsson VA,Freeman SS.Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.Nat Commun2017;8:1324 PMCID:PMC5673918

[125]

Dawson SJ,Murtaza M.Analysis of circulating tumor DNA to monitor metastatic breast cancer.N Engl J Med2013;368:1199-209

[126]

Siravegna G,Buscarino M.Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients.Nat Med2015;21:795-801

[127]

Chabon JJ,Lovejoy AF.Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients.Nat Commun2016;7:11815

[128]

Corcoran RB.Application of cell-free DNA analysis to cancer treatment.N Engl J Med2018;379:1754-65

[129]

Chaudhuri AA,Lovejoy AF.Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling.Cancer Discov2017;7:1394-403 PMCID:PMC5895851

[130]

McDonald BR,Sammut SJ.Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer.Sci Transl Med2019;11:eaax7392 PMCID:PMC7236617

[131]

Chan DCT,Hui EP.Improved risk stratification of nasopharyngeal cancer by targeted sequencing of Epstein-Barr virus DNA in post-treatment plasma.Ann Oncol2022;33:794-803

[132]

Hanna GJ,Kuang Y.Plasma HPV cell-free DNA monitoring in advanced HPV-associated oropharyngeal cancer.Ann Oncol2018;29:1980-6

[133]

Chan KCA,King A.Analysis of plasma epstein-barr virus DNA to screen for nasopharyngeal cancer.N Engl J Med2017;377:513-22

[134]

Klein EA,Cohn A.Clinical validation of a targeted methylation-based multi-cancer early detection test using an independent validation set.Ann Oncol2021;32:1167-77

[135]

Cohen JD,Wang Y.Detection and localization of surgically resectable cancers with a multi-analyte blood test.Science2018;359:926-30 PMCID:PMC6080308

[136]

Sefrioui D,Toure E.Diagnostic value of CA19.9, circulating tumour DNA and circulating tumour cells in patients with solid pancreatic tumours.Br J Cancer2017;117:1017-25 PMCID:PMC5625666

[137]

Cohen JD,Thoburn C.Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers.Proc Natl Acad Sci USA2017;114:10202-7 PMCID:PMC5617273

[138]

Lennon AM,Kinde I.Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention.Science2020;369:eabb9601 PMCID:PMC7509949

[139]

Vandenberghe P,Tousseyn T.Non-invasive detection of genomic imbalances in Hodgkin/Reed-Sternberg cells in early and advanced stage Hodgkin's lymphoma by sequencing of circulating cell-free DNA: a technical proof-of-principle study.Lancet Haematol2015;2:e55-65

[140]

Amant F,Wlodarska I.Presymptomatic identification of cancers in pregnant women during noninvasive prenatal testing.JAMA Oncol2015;1:814-9

[141]

Lenaerts L,Maggen C.Comprehensive genome-wide analysis of routine non-invasive test data allows cancer prediction: a single-center retrospective analysis of over 85,000 pregnancies.EClinicalMedicine2021;35:100856 PMCID:PMC8138727

[142]

Heesterbeek CJ,Galjaard RH.Dutch NIPT consortiumnoninvasive prenatal test results indicative of maternal malignancies: a nationwide genetic and clinical follow-up study.J Clin Oncol2022;40:2426-35

[143]

Snyder TM,Valantine HA.Universal noninvasive detection of solid organ transplant rejection.Proc Natl Acad Sci USA2011;108:6229-34 PMCID:PMC3076856

[144]

De Vlaminck I,Snyder TM.Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection.Sci Transl Med2014;6:241ra77 PMCID:PMC4326260

[145]

Sharon E,Kharbanda S.Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.PLoS Comput Biol2017;13:e1005629 PMCID:PMC5542400

[146]

Cheng AP,Lee JR.A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection.Proc Natl Acad Sci USA2019;116:18738-44 PMCID:PMC6744880

[147]

Schütz E,Beck J.Time-dependent apparent increase in dd-cfDNA percentage in clinically stable patients between one and five years following kidney transplantation.Clin Chem2020;66:1290-9

[148]

Zhou Y,Liu H.A Noninvasive and donor-independent method simultaneously monitors rejection and infection in patients with organ transplant.Transplant Proc2019;51:1699-705

[149]

Cheng AP,Loy CJ.Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation.Proc Natl Acad Sci USA2022;119:e2113476118 PMCID:PMC8795552

[150]

Long Y,Gong Y.Diagnosis of sepsis with cell-free DNA by next-generation sequencing technology in ICU patients.Arch Med Res2016;47:365-71

[151]

Hong DK,Kertesz M,Truong C.Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease.Diagn Microbiol Infect Dis2018;92:210-3

[152]

Chesnais V,Chaplais E.Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study.Sci Rep2018;8:4321 PMCID:PMC5847603

[153]

Liu S,Chen F.Genomic analyses from non-invasive prenatal testing reveal genetic associations, patterns of viral infections, and Chinese population history.Cell2018;175:347-359.e14

[154]

Linthorst J,Welkers MRA.The cell-free DNA virome of 108,349 Dutch pregnant women.Prenat Diagn2022;

[155]

Blauwkamp TA,Rosen MJ.Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.Nat Microbiol2019;4:663-74

[156]

Kitsios GD,Al-Yousif N.Plasma microbial cell-free DNA load is associated with mortality in patients with COVID-19.Respir Res2021;22:24 PMCID:PMC7816055

[157]

Benamu E,Anderson JN.Plasma microbial cell-free DNA next-generation sequencing in the diagnosis and management of febrile neutropenia.Clin Infect Dis2022;74:1659-68 PMCID:PMC9070798

[158]

Gu W,Chiu CY.Clinical metagenomic next-generation sequencing for pathogen detection.Annu Rev Pathol2019;14:319-38 PMCID:PMC6345613

[159]

Cheng AP,Gu W.Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity.Med2021;2:411-422.e5 PMCID:PMC7836424

[160]

Andargie TE,Seifuddin F.Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury.JCI Insight2021;6:147610 PMCID:PMC8119224

[161]

Montier LL, Deng JJ, Bai Y. Number matters: control of mammalian mitochondrial DNA copy number.J Genet Genomics2009;36:125-31 PMCID:PMC4706993

[162]

Chiu RW,Lam NY.Quantitative analysis of circulating mitochondrial DNA in plasma.Clin Chem2003;49:719-26

[163]

Al Amir Dache Z,Tanos R.Blood contains circulating cell-free respiratory competent mitochondria.FASEB J2020;34:3616-30

[164]

Lindqvist D,Picard M.Circulating cell-free mitochondrial DNA, but not leukocyte mitochondrial DNA copy number, is elevated in major depressive disorder.Neuropsychopharmacology2018;43:1557-64

[165]

Zhang Q,Chen Y.Circulating mitochondrial DAMPs cause inflammatory responses to injury.Nature2010;464:104-7 PMCID:PMC2843437

[166]

Kung CT,Tsai TC.Plasma nuclear and mitochondrial DNA levels as predictors of outcome in severe sepsis patients in the emergency room.J Transl Med2012;10:130 PMCID:PMC3441240

[167]

Gambardella S,Ferese R.ccf-mtDNA as a potential link between the brain and immune system in neuro-immunological disorders.Front Immunol2019;10:1064 PMCID:PMC6520662

[168]

Liu Y,Guo S.NGS-based accurate and efficient detection of circulating cell-free mitochondrial DNA in cancer patients.Mol Ther Nucleic Acids2021;23:657-66 PMCID:PMC7851424

[169]

Ma ML,Jiang P.Topologic analysis of plasma mitochondrial DNA reveals the coexistence of both linear and circular molecules.Clin Chem2019;65:1161-70

[170]

Ma ML,Zhang H.Fetal mitochondrial DNA in maternal plasma in surrogate pregnancies: detection and topology.Prenat Diagn2021;41:368-75 PMCID:PMC7984455

[171]

Shibata Y,Layer R.Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues.Science2012;336:82-6 PMCID:PMC3703515

[172]

Turner KM,Beyter D.Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.Nature2017;543:122-5 PMCID:PMC5334176

[173]

Kumar P,Shibata Y,Jones DR.Normal and cancerous tissues release extrachromosomal circular DNA (eccDNA) into the circulation.Mol Cancer Res2017;15:1197-205 PMCID:PMC5581709

[174]

Zhu J,Du M,Fu S.Molecular characterization of cell-free eccDNAs in human plasma.Sci Rep2017;7:10968 PMCID:PMC5591271

[175]

Sin STK,Deng J.Identification and characterization of extrachromosomal circular DNA in maternal plasma.Proc Natl Acad Sci USA2020;117:1658-65 PMCID:PMC6983429

[176]

Sin STK,Deng J.Characteristics of fetal extrachromosomal circular DNA in maternal plasma: methylation status and clearance.Clin Chem2021;67:788-96

[177]

Sin ST,Ji L.Effects of nucleases on cell-free extrachromosomal circular DNA.JCI Insight2022;7:e156070 PMCID:PMC9089787

[178]

Fernández-Domínguez IJ,Taja-Chayeb L,Pérez-Cárdenas E.The role of extracellular DNA (exDNA) in cellular processes.Cancer Biol Ther2021;22:267-78 PMCID:PMC8183512

[179]

Liang H,Dong C.Cationic nanoparticle as an inhibitor of cell-free DNA-induced inflammation.Nat Commun2018;9:4291 PMCID:PMC6191420

[180]

Napirei M,Zevnik B,Mannherz HG.Features of systemic lupus erythematosus in Dnase1-deficient mice.Nat Genet2000;25:177-81

[181]

Martinez-Valle F,Ordi-Ros J,Sellas-Fernandez A.DNase 1 activity in patients with systemic lupus erythematosus: relationship with epidemiological, clinical, immunological and therapeutical features.Lupus2009;18:418-23

[182]

Thiam HR,Wagner DD.Cellular mechanisms of NETosis.Annu Rev Cell Dev Biol2020;36:191-218 PMCID:PMC8499668

[183]

Leffler J,Gullstrand B.Neutrophil extracellular traps that are not degraded in systemic lupus erythematosus activate complement exacerbating the disease.J Immunol2012;188:3522-31

[184]

Denning NL,Gurien SD.DAMPs and NETs in sepsis.Front Immunol2019;10:2536 PMCID:PMC6831555

[185]

Demers M.Neutrophil extracellular traps: a new link to cancer-associated thrombosis and potential implications for tumor progression.Oncoimmunology2013;2:e22946 PMCID:PMC3601165

[186]

Yang L,Zhang X.DNA of neutrophil extracellular traps promotes cancer metastasis via CCDC25.Nature2020;583:133-8

[187]

Jiménez-Alcázar M,Panda R.Host DNases prevent vascular occlusion by neutrophil extracellular traps.Science2017;358:1202-6.

[188]

Zuo Y,Shi H.Neutrophil extracellular traps in COVID-19.JCI Insight2020;5:138999 PMCID:PMC7308057

[189]

Dholakia S,Khush KK.Adding insult on injury: immunogenic role for donor-derived cell-free DNA?.Transplantation2020;104:2266-71 PMCID:PMC7590963

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