Computational Systems Biology Methods and Protocols.7z

(nextflipdebug5) #1

  1. Weber B, Meldgaard P, Hager H, Wu L, Wei W,
    Tsai J, Khalil A, Nexo E, Sorensen BS (2014)
    Detection of EGFR mutations in plasma and
    biopsies from non-small cell lung cancer
    patients by allele-specific PCR assays. BMC
    Cancer 14(1):294.https://doi.org/10.1186/
    1471-2407-14-294.

  2. Cross DA, Ashton SE, Ghiorghiu S,
    Eberlein C, Nebhan CA, Spitzler PJ, Orme
    JP, Finlay MR, Ward RA, Mellor MJ,
    Hughes G, Rahi A, Jacobs VN, Red
    Brewer M, Ichihara E, Sun J, Jin H, Ballard P,
    Al-Kadhimi K, Rowlinson R, Klinowska T,
    Richmond GH, Cantarini M, Kim DW, Ranson
    MR, Pao W (2014) AZD9291, an irreversible
    EGFR TKI, overcomes T790M-mediated
    resistance to EGFR inhibitors in lung cancer.
    Cancer Discov 4(9):1046–1061.https://doi.
    org/10.1158/2159-8290.CD-14-0337

  3. Zhou W, Ercan D, Chen L, Yun CH, Li D,
    Capelletti M, Cortot AB, Chirieac L, Iacob
    RE, Padera R, Engen JR, Wong KK, Eck MJ,
    Gray NS, J€anne PA (2009) Novel mutant-
    selective EGFR kinase inhibitors against
    EGFR T790M. Nature 462
    (7276):1070–1074. https://doi.org/10.
    1038/nature08622

  4. Oxnard GR, Thress KS, Alden RS, Lawrance R,
    Paweletz CP, Cantarini M, Yang JC, Barrett
    JC, J€anne PA (2016) Association between
    plasma genotyping and outcomes of treatment
    with osimertinib (AZD9291) in advanced
    non–small-cell lung cancer. J Clin Oncol 34
    (28):3375–3382. https://doi.org/10.1200/
    JCO.2016.66.7162
    54.http://www.fda.gov/ucm/groups/fdagov-
    public/@fdagov-meddev-gen/documents/
    document/ucm510824.pdf

  5. Sequist LV, Yang JC, Yamamoto N,
    O’Byrne K, Hirsh V, Mok T, Geater SL,
    Orlov S, Tsai CM, Boyer M, Su WC,
    Bennouna J, Kato T, Gorbunova V, Lee KH,
    Shah R, Massey D, Zazulina V, Shahidi M,
    Schuler M (2013) Phase III study of afatinib
    or cisplatin plus pemetrexed in patients with
    metastatic lung adenocarcinoma with EGFR
    mutations. J Clin Oncol 31(27):3327–3334.
    https://doi.org/10.1200/JCO.2012.44.
    2806

  6. FDA http://www.accessdata.fda.gov/cdrh_
    docs/pdf12/P120022c.pdf

  7. Douillard J, Ostoros G, Cobo M, Ciuleanu T,
    McCormack R, Webster A, Milenkova T
    (2014) First-line gefitinib in Caucasian EGFR
    mutation-positive NSCLC patients: a phase-
    IV, open-label, single-arm study. Br J Cancer
    110(1):55–62.https://doi.org/10.1038/bjc.
    2013.721


58.http://www.ema.europa.eu/docs/en_GB/
document_library/EPAR_Product_Informa
tion/human/001016/WC500036358.pdf
59.http://www.fda.gov/Drugs/
InformationOnDrugs/ApprovedDrugs/
ucm504540.htm


  1. Jenkins S, Yang J, Ramalingam S, Yu K, Patel S,
    Weston S, Lawrance R, Cantarini M, J€anne P,
    Mitsudomi T (2016) 134O_PR: plasma
    ctDNA analysis for detection of EGFR
    T790M mutation in patients (pts) with EGFR
    mutation-positive advanced non-small cell lung
    cancer (aNSCLC). J Thorac Oncol 11((4):
    S153–S154. https://doi.org/10.1016/
    S1556-0864(16)30327-6

  2. Lanman RB, Mortimer SA, Zill OA,
    Sebisanovic D, Lopez R, Blau S, Collisson
    EA, Divers SG, Hoon DS, Kopetz ES, Lee J,
    Nikolinakos PG, Baca AM, Kermani BG,
    Eltoukhy H, Talasaz A (2015) Analytical and
    clinical validation of a digital sequencing panel
    for quantitative, highly accurate evaluation of
    cell-free circulating tumour DNA. PLoS One
    10(10):e0140712.https://doi.org/10.1371/
    journal.pone.0140712

  3. Zill OA, Mortimer S, Banks K (2016) Somatic
    genomic landscape of over 15,000 patients
    with advanced-stage cancer from clinical next-
    generation sequencing analysis of circulating
    tumour DNA. J Clin Oncol 34(suppl)

  4. Kwak EL, Bang YJ, Camidge DR, Shaw AT,
    Solomon B, Maki RG, Ou SH, Dezube BJ,
    J€anne PA, Costa DB, Varella-Garcia M, Kim
    WH, Lynch TJ, Fidias P, Stubbs H, Engelman
    JA, Sequist LV, Tan W, Gandhi L, Mino-
    Kenudson M, Wei GC, Shreeve SM, Ratain
    MJ, Settleman J, Christensen JG, Haber DA,
    Wilner K, Salgia R, Shapiro GI, Clark JW, Iafrate
    AJ (2010) Anaplastic lymphoma kinase inhibi-
    tion in non–small-cell lung cancer. N Engl J
    Med 363(18):1693–1703. https://doi.org/
    10.1200/JCO.2016.34.15_suppl.LBA11501

  5. Koivunen JP, Kim J, Lee J, Rogers AM, Park
    JO, Zhao X, Naoki K, Okamoto I,
    Nakagawa K, Yeap BY, Meyerson M, Wong
    KK, Richards WG, Sugarbaker DJ, Johnson
    BE, J€anne PA (2008) Mutations in the LKB1
    tumour suppressor are frequently detected in
    tumours from Caucasian but not Asian lung
    cancer patients. Br J Cancer 99(2):245–252.
    https://doi.org/10.1038/sj.bjc.6604469

  6. Shaw AT, Yeap BY, Mino-Kenudson M, Digu-
    marthy SR, Costa DB, Heist RS, Solomon B,
    Stubbs H, Admane S, McDermott U,
    Settleman J, Kobayashi S, Mark EJ, Rodig SJ,
    Chirieac LR, Kwak EL, Lynch TJ, Iafrate AJ
    (2009) Clinical features and outcome of
    patients with non–small-cell lung cancer who


64 Jun Li et al.

Free download pdf