Page 34 - GTM-3-3
P. 34

Global Translational Medicine                                  Computational advances in cancer liquid biopsy



            14.  Van Wezel EM, Zwijnenburg D, Zappeij-Kannegieter L,   25.  Franken B, De Groot MR, Mastboom WJ, et al. Circulating
               et  al. Whole-genome sequencing identifies patient-specific   tumor cells, disease recurrence and survival in newly
               DNA minimal residual disease markers in neuroblastoma.   diagnosed breast cancer. Breast Cancer Res. 2012;14(5):R133.
               J Mol Diagn. 2015;17(1):43-52.                     doi: 10.1186/bcr3333
               doi: 10.1016/j.jmoldx.2014.09.005               26.  Poruk KE, Valero V, He J, et al. Circulating epithelial cells
            15.  Wang Y, Li L, Cohen JD,  et al. Prognostic potential of   in intraductal papillary mucinous neoplasms and cystic
               circulating tumor DNA measurement in postoperative   pancreatic lesions. Pancreas. 2017;46(7):943-947.
               surveillance of nonmetastatic colorectal cancer.  JAMA      doi: 10.1097/MPA.0000000000000869
               Oncol. 2019;5(8):1118-1123.
                                                               27.  Franses JW, Basar O, Kadayifci A, et al. Improved detection of
               doi: 10.1001/jamaoncol.2019.0512                   circulating epithelial cells in patients with intraductal papillary
            16.  Newman AM, Bratman SV, To J,  et al. An ultrasensitive   mucinous neoplasms. Oncologist. 2018;23(1):121-127.
               method for quantitating circulating tumor DNA with broad      doi: 10.1634/theoncologist.2017-0234
               patient coverage. Nat Med. 2014;20(5):548-554.
                                                               28.  Man  Y,  Wang Q,  Kemmner  W.  Currently  used  markers
               doi: 10.1038/nm.3519                               for CTC isolation - advantages, limitations and impact on
                                                                  cancer prognosis. J Clin Exp Pathol. 2011;1(1):102.
            17.  Phallen J, Sausen M, Adleff V, et al. Direct detection of early-
               stage cancers using circulating tumor DNA. Sci Transl Med.      doi: 10.4172/2161-0681.1000102
               2017;9(403):eaan2415.
                                                               29.  Alix-Panabières C, Pantel K. Liquid biopsy: From discovery
               doi: 10.1126/scitranslmed.aan2415                  to clinical application. Cancer Discov. 2021;11(4):858-873.
            18.  Abbosh C, Birkbak NJ, Wilson GA,  et al. Phylogenetic      doi: 10.1158/2159-8290.CD-20-1311
               ctDNA analysis depicts early-stage lung cancer evolution.   30.  Ni X, Zhuo M, Su Z, et al. Reproducible copy number variation
               Nature. 2017;545(7655):446-451.                    patterns among single circulating tumor cells of lung cancer
               doi: 10.1038/nature22364                           patients. Proc Natl Acad Sci. 2013;110(52):21083-21088.
            19.  Adalsteinsson VA, Ha G, Freeman SS, et al. Scalable whole-     doi: 10.1073/pnas.1320659110
               exome sequencing of cell-free DNA reveals high concordance   31.  Court CM, Hou S, Liu L,  et al. Somatic copy number
               with metastatic tumors. Nat Commun. 2017;8(1):1324.  profiling from hepatocellular carcinoma circulating tumor
               doi: 10.1038/s41467-017-00965-y                    cells. NPJ Precis Oncol. 2020;4(1):16.
            20.  Zviran A, Schulman RC, Shah M, et al. Genome-wide cell-     doi: 10.1038/s41698-020-0123-0
               free DNA mutational integration enables ultra-sensitive   32.  Silvestri M, Dugo M, Vismara M,  et al. Copy number
               cancer monitoring. Nat Med. 2020;26(7):1114-1124.  alterations analysis of primary tumor tissue and circulating
                                                                  tumor cells from patients with early-stage triple negative
               doi: 10.1038/s41591-020-0915-3
                                                                  breast cancer. Sci Rep. 2022;12(1):1470.
            21.  Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-
               free DNA comprises an in vivo nucleosome footprint that      doi: 10.1038/s41598-022-05502-6
               informs its tissues-of-origin. Cell. 2016;164(1-2):57-68.  33.  Baslan T, Kendall J, Rodgers L, et al. Genome-wide copy number
                                                                  analysis of single cells. Nat Protoc. 2012;7(6):1024-1041.
               doi: 10.1016/j.cell.2015.11.050
                                                                  doi: 10.1038/nprot.2012.039
            22.  Mouliere F, Chandrananda D, Piskorz AM, et al. Enhanced
               detection of circulating tumor DNA by fragment size   34.  Ross MG, Russ C, Costello M,  et al. Characterizing and
               analysis. Sci Transl Med. 2018;10(466):eaat4921.   measuring bias in sequence data. Genome Biol. 2013;14(5):R51.
               doi: 10.1126/scitranslmed.aat4921                  doi: 10.1186/gb-2013-14-5-r51
            23.  Widman AJ, Shah M, Frydendahl A,  et al. Ultrasensitive   35.  Lasken RS, Stockwell TB. Mechanism of chimera formation
               plasma-based monitoring of tumor burden using      during the Multiple Displacement Amplification reaction.
               machine-learning-guided signal enrichment.  Nat Med.   BMC Biotechnol. 2007;7(1):19.
               2024;30(6):1655-1666.                              doi: 10.1186/1472-6750-7-19
               doi: 10.1038/s41591-024-03040-4                 36.  Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory
            24.  Kidess E, Jeffrey SS. Circulating tumor cells versus tumor-  contamination can critically impact sequence-based
               derived cell-free DNA: Rivals or partners in cancer care in   microbiome analyses. BMC Biol. 2014;12(1):87.
               the era of single-cell analysis? Genome Med. 2013;5(8):70.     doi: 10.1186/s12915-014-0087-z
               doi: 10.1186/gm474                              37.  Merchant S, Wood DE, Salzberg SL. Unexpected cross-

            Volume 3 Issue 3 (2024)                         11                              doi: 10.36922/gtm.3063
   29   30   31   32   33   34   35   36   37   38   39