Computational Systems Biology Methods and Protocols.7z

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Systematic large-scale meta-analysis identifies a
panel of two mRNAs as blood biomarkers for
colorectal cancer detection. Oncotarget 7
(21):30295–30306. https://doi.org/10.
18632/oncotarget.8108


  1. Allen-Mersh TG, McCullough TK, Patel H,
    Wharton RQ, Glover C, Jonas SK (2007)
    Role of circulating tumour cells in predicting
    recurrence after excision of primary colorectal
    carcinoma. Br J Surg 94(1):96–105.https://
    doi.org/10.1002/bjs.5526

  2. Katsuno H, Zacharakis E, Aziz O, Rao C,
    Deeba S, Paraskeva P, Ziprin P, Athanasiou T,
    Darzi A (2008) Does the presence of circulat-
    ing tumour cells in the venous drainage of
    curative colorectal cancer resections determine
    prognosis? A meta-analysis. Ann Surg Oncol
    15(11):3083–3091. https://doi.org/10.
    1245/s10434-008-0131-8

  3. El-Hefnawy T, Raja S, Kelly L, Bigbee WL,
    Kirkwood JM, Luketich JD, Godfrey TE
    (2004) Characterization of amplifiable, circu-
    lating RNA in plasma and its potential as a tool
    for cancer diagnostics. Clin Chem 50
    (3):564–573. https://doi.org/10.1373/
    clinchem.2003.028506

  4. Bao Y, Ching B, Mouanoutoua M, Yu W,
    Keys D, Desai S, Stevens J (2012) Cancer bio-
    marker research using castPCR technology.
    AACR

  5. Wilkening S, Hemminki K, Thirumaran RK,
    Bermejo JL, Bonn S, Fo ̈rsti A, Kumar R
    (2005) Determination of allele frequency in
    pooled DNA: comparison of three PCR-based
    methods. BioTechniques 39(6):853–858

  6. Goto K, Ichinose Y, Ohe Y, Yamamoto N,
    Negoro S, Nishio K, Itoh Y, Jiang H,
    Duffield E, McCormack R, Saijo N, Mok T,
    Fukuoka M (2012) Epidermal growth factor
    receptor mutation status in circulating free
    DNA in serum: from IPASS, a phase III study
    of gefitinib or carboplatin/paclitaxel in
    non-small cell lung cancer. J Thorac Oncol 7
    (1):115–121.https://doi.org/10.1097/JTO.
    0b013e3182307f98

  7. Karachaliou N, Mayo-de las Casas C,
    Queralt C, de Aguirre I, Melloni B,
    Cardenal F, Garcia-Gomez R, Massuti B, Sa ́n-
    chez JM, Porta R, Ponce-Aix S, Moran T,
    Carcereny E, Felip E, Bover I, Insa A,
    Reguart N, Isla D, Vergnenegre A, de
    Marinis F, Gervais R, Corre R, Paz-Ares L,
    Morales-Espinosa D, Viteri S,
    Drozdowskyj A, Jordana-Ariza N, Ramirez-
    Serrano JL, Molina-Vila MA, Rosell R, Spanish
    Lung Cancer Group (2015) Association of
    EGFR L858R mutation in circulating free
    DNA with survival in the EURTAC trial.


JAMA Oncol 1(2):149–157.https://doi.org/
10.1001/jamaoncol.2014.257


  1. Hindson BJ, Ness KD, Masquelier DA,
    Belgrader P, Heredia NJ, Makarewicz AJ,
    Bright IJ, Lucero MY, Hiddessen AL, Legler
    TC, Kitano TK, Hodel MR, Petersen JF, Wyatt
    PW, Steenblock ER, Shah PH, Bousse LJ,
    Troup CB, Mellen JC, Wittmann DK, Erndt
    NG, Cauley TH, Koehler RT, So AP, Dube S,
    Rose KA, Montesclaros L, Wang S, Stumbo
    DP, Hodges SP, Romine S, Milanovich FP,
    White HE, Regan JF, Karlin-Neumann GA,
    Hindson CM, Saxonov S, Colston BW (2011)
    High-throughput droplet digital PCR system
    for absolute quantitation of DNA copy num-
    ber. Anal Chem 83(22):8604–8610.https://
    doi.org/10.1021/ac202028g

  2. Taniguchi K, Uchida J, Nishino K, Kumagai T,
    Okuyama T, Okami J, Kato K (2011) Quanti-
    tative detection of EGFR mutations in circulat-
    ing tumour DNA derived from lung
    adenocarcinomas. Clin Cancer Res 17
    (24):7808–7815. https://doi.org/10.1158/
    1078-0432.CCR-11-1712

  3. Taniguchi K, Uchida J, Nishino K, Kumagai T,
    Okuyama T, Okami J, Higashiyama M,
    Kodama K, Imamura F, Kato K (2012) Nonin-
    vasive identification and monitoring of cancer
    mutations by targeted deep sequencing of
    plasma DNA. Sci Transl Med 4
    (136):136ra168-136ra168. https://doi.org/
    10.1158/1078-0432.CCR-11-1712

  4. Kinde I, Wu J, Papadopoulos N, Kinzler KW,
    Vogelstein B (2011) Detection and quantifica-
    tion of rare mutations with massively parallel
    sequencing. Proc Natl Acad Sci 108
    (23):9530–9535. https://doi.org/10.1073/
    pnas.1105422108

  5. Newman AM, Bratman SV, To J, Wynne JF,
    Eclov NC, Modlin LA, Liu CL, Neal JW,
    Wakelee HA, Merritt RE, Shrager JB, Loo
    BW Jr, Alizadeh AA, Diehn M (2014) An ultra-
    sensitive method for quantitating circulating
    tumour DNA with broad patient coverage.
    Nat Med 20(5):548–554. https://doi.org/
    10.1038/nm.3519

  6. Griffin TJ, Smith LM (2000) Single-nucleotide
    polymorphism analysis by MALDI–TOF mass
    spectrometry. Trends Biotechnol 18(2):77–84

  7. Giannini R, Lupi C, Sensi E, Alı`G, Proietti A,
    Boldrini L, Servadio A, Giordano M,
    Macerola E, Bruno R, Borrelli N, Chella A,
    Melfi F, Lucchi M, Ribechini A, Vasile E,
    Cappuzzo F, Mussi A, Fontanini G (2016)
    EGFR and KRAS mutational analysis in a
    large series of Italian non-small cell lung cancer
    patients: 2,387 cases from a single center.


62 Jun Li et al.

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