Review Article| Volume 42, ISSUE 3, P485-496, September 2022

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When Tissue Is the Issue

Expanding Cell-Free DNA “Liquid Biopsies” to Supernatants and Nonplasma Biofluids
  • Vera Paulson
    Corresponding author.
    Department of Laboratory Medicine and Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA

    Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA
    Search for articles by this author
  • Eric Q. Konnick
    Department of Laboratory Medicine and Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA

    Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA
    Search for articles by this author
  • Christina H. Lockwood
    Department of Laboratory Medicine and Pathology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA

    Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA
    Search for articles by this author
Published:August 22, 2022DOI:


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        • Mandel P.
        • Metais P.
        Nuclear acids in human blood plasma.
        C R Seances Soc Biol Fil. 1948; 142 (Les acides nucleiques du plasma sanguin chez l'homme): 241-243
        • Kustanovich A.
        • Schwartz R.
        • Peretz T.
        • et al.
        Life and death of circulating cell-free DNA.
        Cancer Biol Ther. 2019; 20: 1057-1067
        • Leon S.A.
        • Shapiro B.
        • Sklaroff D.M.
        • et al.
        Free DNA in the serum of cancer patients and the effect of therapy.
        Cancer Res. 1977; 37: 646-650
        • Stroun M.
        • Anker P.
        • Lyautey J.
        • et al.
        Isolation and characterization of DNA from the plasma of cancer patients.
        Eur J Cancer Clin Oncol. 1987; 23: 707-712
        • Sorenson G.D.
        • Pribish D.M.
        • Valone F.H.
        • et al.
        Soluble normal and mutated DNA sequences from single-copy genes in human blood.
        Cancer Epidemiol Biomarkers Prev. 1994; 3: 67-71
        • Volckmar A.L.
        • Sultmann H.
        • Riediger A.
        • et al.
        A field guide for cancer diagnostics using cell-free DNA: from principles to practice and clinical applications.
        Genes Chromosomes Cancer. 2018; 57: 123-139
        • Perrone M.E.
        • Alvarez R.
        • Vo T.T.
        • et al.
        Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens.
        Cancer Cytopathol. 2021; 129: 956-965
        • McEwen A.E.
        • Leary S.E.S.
        • Lockwood C.M.
        Beyond the blood: CSF-derived cfDNA for diagnosis and characterization of CNS tumors.
        Front Cell Dev Biol. 2020; 8: 45
        • Roy-Chowdhuri S.
        • Mehrotra M.
        • Bolivar A.M.
        • et al.
        Salvaging the supernatant: next generation cytopathology for solid tumor mutation profiling.
        Mod Pathol. 2018; 31: 1036-1045
        • Merker J.D.
        • Oxnard G.R.
        • Compton C.
        • et al.
        Circulating tumor DNA analysis in patients with cancer: american society of clinical oncology and college of american pathologists joint review.
        J Clin Oncol. 2018; 36: 1631-1641
        • Russo A.
        • Incorvaia L.
        • Del Re M.
        • et al.
        The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM-SIAPEC-IAP-SIBioC-SIC-SIF Italian Scientific Societies.
        ESMO Open. 2021; 6: 100164
        • Giacona M.B.
        • Ruben G.C.
        • Iczkowski K.A.
        • et al.
        Cell-free DNA in human blood plasma: length measurements in patients with pancreatic cancer and healthy controls.
        Pancreas. 1998; 17: 89-97
        • Wan J.C.M.
        • Massie C.
        • Garcia-Corbacho J.
        • et al.
        Liquid biopsies come of age: towards implementation of circulating tumour DNA.
        Nat Rev Cancer. 2017; 17: 223-238
        • Snyder M.W.
        • Kircher M.
        • Hill A.J.
        • et al.
        Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin.
        Cell. 2016; 164: 57-68
        • Mouliere F.
        • Chandrananda D.
        • Piskorz A.M.
        • et al.
        Enhanced detection of circulating tumor DNA by fragment size analysis.
        Sci Transl Med. 2018; 10: eaat4921
        • Zheng Y.W.
        • Chan K.C.
        • Sun H.
        • et al.
        Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model.
        Clin Chem. 2012; 58: 549-558
        • Patel A.
        • Hissong E.
        • Rosado L.
        • et al.
        Next-generation sequencing of cell-free DNA extracted from pleural effusion supernatant: applications and challenges.
        Front Med (Lausanne). 2021; 8: 662312
        • Yu Y.
        • Qian J.
        • Shen L.
        • et al.
        Distinct profile of cell-free DNA in malignant pleural effusion of non-small cell lung cancer and its impact on clinical genetic testing.
        Int J Med Sci. 2021; 18: 1510-1518
        • Pos Z.
        • Pos O.
        • Styk J.
        • et al.
        Technical and methodological aspects of cell-free nucleic acids analyzes.
        Int J Mol Sci. 2020; 21: 8634
        • Oshi M.
        • Murthy V.
        • Takahashi H.
        • et al.
        Urine as a source of liquid biopsy for cancer.
        Cancers (Basel). 2021; 13: 2652
        • Geeurickx E.
        • Hendrix A.
        Targets, pitfalls and reference materials for liquid biopsy tests in cancer diagnostics.
        Mol Aspects. 2020; 72: 100828
        • Dressman D.
        • Yan H.
        • Traverso G.
        • et al.
        Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.
        Proc Natl Acad Sci U S A. 2003; 100: 8817-8822
        • De Luca G.
        • Dono M.
        The opportunities and challenges of molecular tagging next-generation sequencing in liquid biopsy.
        Mol Diagn Ther. 2021; 25: 537-547
        • Narayan A.
        • Carriero N.J.
        • Gettinger S.N.
        • et al.
        Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing.
        Cancer Res. 2012; 72: 3492-3498
        • Newman A.M.
        • Lovejoy A.F.
        • Klass D.M.
        • et al.
        Integrated digital error suppression for improved detection of circulating tumor DNA.
        Nat Biotechnol. 2016; 34: 547-555
        • Dudley J.C.
        • Diehn M.
        Detection and diagnostic utilization of cellular and cell-free tumor DNA.
        Annu Rev Pathol. 2021; 16: 199-222
        • Martinez-Ricarte F.
        • Mayor R.
        • Martinez-Saez E.
        • et al.
        Molecular diagnosis of diffuse gliomas through sequencing of cell-free circulating tumor DNA from cerebrospinal fluid.
        Clin Cancer Res. 2018; 24: 2812-2819
        • Pan C.
        • Diplas B.H.
        • Chen X.
        • et al.
        Molecular profiling of tumors of the brainstem by sequencing of CSF-derived circulating tumor DNA.
        Acta Neuropathol. 2019; 137: 297-306
        • Liu A.P.Y.
        • Smith K.S.
        • Kumar R.
        • et al.
        Serial assessment of measurable residual disease in medulloblastoma liquid biopsies.
        Cancer Cell. 2021; 39: 1519-1530.e4
        • Kawahara A.
        • Abe H.
        • Murata K.
        • et al.
        Screening system for epidermal growth factor receptor mutation detection in cytology cell-free DNA of cerebrospinal fluid based on assured sample quality.
        Cytopathology. 2019; 30: 144-149
        • Li Y.S.
        • Jiang B.Y.
        • Yang J.J.
        • et al.
        Unique genetic profiles from cerebrospinal fluid cell-free DNA in leptomeningeal metastases of EGFR-mutant non-small-cell lung cancer: a new medium of liquid biopsy.
        Ann Oncol. 2018; 29: 945-952
        • Swinkels D.W.
        • de Kok J.B.
        • Hanselaar A.
        • et al.
        Early detection of leptomeningeal metastasis by PCR examination of tumor-derived K-ras DNA in cerebrospinal fluid.
        Clin Chem. 2000; 46: 132-133
        • Zhao Y.
        • He J.Y.
        • Zou Y.L.
        • et al.
        Evaluating the cerebrospinal fluid ctDNA detection by next-generation sequencing in the diagnosis of meningeal Carcinomatosis.
        BMC Neurol. 2019; 19: 331
        • Wang Y.
        • Springer S.
        • Mulvey C.L.
        • et al.
        Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas.
        Sci Transl Med. 2015; 7: 293ra104
        • Boyle J.O.
        • Mao L.
        • Brennan J.A.
        • et al.
        Gene mutations in saliva as molecular markers for head and neck squamous cell carcinomas.
        Am J Surg. 1994; 168: 429-432
        • Hubers A.J.
        • Prinsen C.F.
        • Sozzi G.
        • et al.
        Molecular sputum analysis for the diagnosis of lung cancer.
        Br J Cancer. 2013; 109: 530-537
        • Wang Z.
        • Li X.
        • Zhang L.
        • et al.
        Sputum cell-free DNA: valued surrogate sample for the detection of EGFR exon 20 p.T790M mutation in patients with advanced lung adenocarcinoma and acquired resistance to EGFR-TKIs.
        Cancer Med. 2021; 10: 3323-3331
        • Yanev N.
        • Mekov E.
        • Valev D.
        • et al.
        EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy.
        PeerJ. 2021; 9: e11448
        • Park S.
        • Hur J.Y.
        • Lee K.Y.
        • et al.
        Assessment of EGFR mutation status using cell-free DNA from bronchoalveolar lavage fluid.
        Clin Chem Lab Med. 2017; 55: 1489-1495
        • Ryu J.S.
        • Lim J.H.
        • Lee M.K.
        • et al.
        Feasibility of bronchial washing fluid-based approach to early-stage lung cancer diagnosis.
        Oncologist. 2019; 24: e603-e606
        • Kinde I.
        • Bettegowda C.
        • Wang Y.
        • et al.
        Evaluation of DNA from the Papanicolaou test to detect ovarian and endometrial cancers.
        Sci Transl Med. 2013; 5: 167ra4
        • Wang Y.
        • Li L.
        • Douville C.
        • et al.
        Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers.
        Sci Transl Med. 2018; 10: eaap8793
        • Nair N.
        • Camacho-Vanegas O.
        • Rykunov D.
        • et al.
        Genomic analysis of uterine lavage fluid detects early endometrial cancers and reveals a prevalent landscape of driver mutations in women without histopathologic evidence of cancer: a prospective cross-sectional study.
        PLoS Med. 2016; 13: e1002206
        • Maritschnegg E.
        • Wang Y.
        • Pecha N.
        • et al.
        Lavage of the uterine cavity for molecular detection of mullerian duct carcinomas: a proof-of-concept study.
        J Clin Oncol. 2015; 33: 4293-4300
        • Diehl F.
        • Schmidt K.
        • Durkee K.H.
        • et al.
        Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients.
        Gastroenterology. 2008; 135: 489-498
        • Ou Z.
        • Li K.
        • Yang T.
        • et al.
        Detection of bladder cancer using urinary cell-free DNA and cellular DNA.
        Clin Transl Med. 2020; 9: 4
        • Zhang R.
        • Zang J.
        • Xie F.
        • et al.
        Urinary molecular pathology for patients with newly diagnosed urothelial bladder cancer.
        J Urol. 2021; 206: 873-884
        • Dudley J.C.
        • Schroers-Martin J.
        • Lazzareschi D.V.
        • et al.
        Detection and surveillance of bladder cancer using urine tumor DNA.
        Cancer Discov. 2019; 9: 500-509
        • Jain S.
        • Lin S.Y.
        • Song W.
        • et al.
        Urine-based liquid biopsy for nonurological cancers.
        Genet Test Mol Biomarkers. 2019; 23: 277-283
        • Durin L.
        • Pradines A.
        • Basset C.
        • et al.
        Liquid biopsy of non-plasma body fluids in non-small cell lung cancer: look closer to the tumor!.
        Cells. 2020; 9: 2486