ABDEL-WAHAB R, CAO LIU,S, MERIC-BERNSTAM JHU,J, XU F, LI J, FENG QYAN,M, ZHAO YLIN,J, JAVLE SWANG,JWANG,KBORAD,MJ, M. & ZHAO H. AB045. P-13. Genomic heterogeneity between Asian and Western intrahepatic cholangiocarcinoma. Hepatobiliary Surgery Nutrition. 2019;8:AB045.
CHAKRAVARTY D, PHILLIPS GAO,J, ZHANG SM,KUNDRA,R, YAEGER HWANG,JRUDOLPH,JE, SOUMERAI R, NISSAN T, CHANG MH, CHANDARLAPATY MT, TRAINA S, PAIK TA, CALLAHAN PK,HO,AL,HANTASH,FM,GRUPE,ABAXI,SS, SNYDER MK, CHI A, DANILA P, GOUNDER D, HELLMANN MHARDING,JJ, IYER MD, JANJIGIAN G, LOWERY YKALEY,TLEVINE,DA, MOMURO,A, POSTOW, M. A., RATHKOPF, D., SHOUSHTARI, A. N., SHUKLA, N., VOSS, MPARAISO,EZEHIR,A, BERGER, M. F., TAYLOR, B. S., SALTZ, L. B., RIELY, G. J., LADANYI, M., HYMAN, D. M., BASELGA, J., SABBATINI, P., SOLIT, D. B. & SCHULTZ, N. (2017). OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol, 2017.
CIBULSKIS K, CARTER LAWRENCE,MS, SIVACHENKO SL, JAFFE A, MEYERSON DSOUGNEZ,CGABRIEL,S, M., LANDER, E. S. & GETZ G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–9.
DEES ND, KANDOTH ZHANG,Q, WENDL C, SCHIERDING MC, MOONEY WKOBOLDT,DC, CALLAWAY TB, DOOLING MB, D., MARDIS, E. R., WILSON, R. K. & DING L. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 2012;22:1589–98.
DHANASEKARAN R, ZENDEJAS HEMMING,AW, GEORGE I, SOLDEVILA-PICO TNELSON,DR, MORELLI CFIRPI,RJ, CLARK G, V. & CABRERA R. Treatment outcomes and prognostic factors of intrahepatic cholangiocarcinoma. Oncol Rep. 2013;29:1259–67.
GAO J, DOGRUSOZ AKSOY,BA, DRESDNER U, GROSS G, SUN BSUMER,SO, SINHA YJACOBSEN,A, SANDER RLARSSON,ECERAMI,E, C. & SCHULTZ, N. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal, 6, pl1.
GBOLAHAN O, HASHEMI-SADRAEI N, O'NEIL B. Prolonged Response to Anti-PD-1 Antibody Therapy in Chemotherapy-Refractory Cholangiocarcinoma With High Tumor Mutational Burden. J Natl Compr Canc Netw. 2019;17:644–8.
GENOMES PROJECT C, ABECASIS GR, ALTSHULER D, BROOKS AUTON,A, L. D., DURBIN, R. M., GIBBS, R. A., HURLES, M. E. & MCVEAN GA. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–73.
HOGDALL D, LINNEMANN LARSEN,OF, SVENSTRUP D, POULSEN T, HOGDALL EV. Exome sequencing of 22 genes using tissue from patients with biliary tract cancer. APMIS. 2020;128:3–9.
HUANG DA W, SHERMAN, B. T. & LEMPICKI RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
KANEHISA M, GOTO S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
KARCZEWSKI KJ, SOLOMONSON WEISBURD,BTHOMAS,B, RUDERFER M, KAVANAGH DM, LEK DHAMAMSY,T, BIRNBAUM MSAMOCHA,KE,CUMMINGS,BB, THE EXOME AGGREGATION D, C., DALY, M. J. & MACARTHUR DG. The ExAC browser: displaying reference data information from over 60 000 exomes. Nucleic Acids Res. 2017;45:D840–5.
KOBOLDT DC, CHEN K, WYLIE T, LARSON DE, MCLELLAN MD, WEINSTOCK MARDIS,ER, G. M., WILSON, R. K. & DING L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25:2283–5.
LAWRENCE MS, STOJANOV P, POLAK P, KRYUKOV GV, CIBULSKIS K, CARTER SIVACHENKO,A, STEWART SL, KIEZUN CMERMEL,CH,ROBERTS,SA, HAMMERMAN A, MCKENNA PS, DRIER A, ZOU Y, RAMOS L, A. H., PUGH TJ, SHEFLER STRANSKY,NHELMAN,EKIM,JSOUGNEZ,CAMBROGIO,LNICKERSON,E, CORTES E, AUCLAIR ML, SAKSENA D, VOET G, NOBLE D, LIN MDICARA,D, LICHTENSTEIN P, HEIMAN L, D. I., FENNELL T, IMIELINSKI M, HERNANDEZ B, MELENDEZ-ZAJGLA HODIS,EBACA,SDULAK,AM,LOHR,JLANDAU,DA,WU,CJ, HIDALGO-MIRANDA J, MORA AKOREN,AMCCARROLL,SA, J., CROMPTON, B., ONOFRIO, R., PARKIN, M., WINCKLER, W., ARDLIE, K., GABRIEL, S. B., ROBERTS, C. W. M., BIEGEL, J. A., STEGMAIER, K., BASS, A. J., GARRAWAY, L. A., MEYERSON, M., GOLUB, T. R., GORDENIN, D. A., SUNYAEV, S., LANDER, E. S. & GETZ, G. (2013). Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature, 499, 214–218.
LEK M, FENNELL KARCZEWSKI,KJ,MINIKEL,EV,SAMOCHA,KE,BANKS,E, O’DONNELL-LURIA T, HILL AH,WARE,JS, TUKIAINEN AJ,CUMMINGS,BB, BIRNBAUM T, DUNCAN DP,KOSMICKI,JA, ESTRADA LE, ZHAO K, ZOU F, PIERCE-HOFFMAN J, BERGHOUT E, COOPER J, KIEZUN DN,DEFLAUX,NDEPRISTO,MDO,RFLANNICK,JFROMER,MGAUTHIER,LGOLDSTEIN,JGUPTA,NHOWRIGAN,D, KURKI A, NATARAJAN MI,MOONSHINE,AL, OROZCO P, PELOSO L, RUANO-RUBIO GM,POPLIN,RRIVAS,MA, RUDERFER VROSE,SA, SHAKIR DM, STENSON K, STEVENS PD, TUSIE-LUNA CTHOMAS,BP,TIAO,G, WEISBURD MT, YU BWON,H-H, ARDISSINO DALTSHULER,DM, BOEHNKE D, DONNELLY MDANESH,J, ELOSUA S, GABRIEL RFLOREZ,JC, MCGOVERN SB,GETZ,GGLATT,SJ,HULTMAN,CM,KATHIRESAN,SLAAKSO,MMCCARROLL,SMCCARTHY,MI, D., MCPHERSON, R., NEALE, B. M., PALOTIE, A., PURCELL, S. M., SALEHEEN, D., SCHARF, J. M., SKLAR, P., SULLIVAN, P. F., TUOMILEHTO, J., TSUANG, M. T., WATKINS, H. C., WILSON, J. G., DALY, M. J., MACARTHUR, D. G. & EXOME AGGREGATION, C. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536, 285.
LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
LI X, ZHANG PASCHE,B, W. & CHEN K. Association of MUC16 Mutation With Tumor Mutation Load and Outcomes in Patients With Gastric Cancer. JAMA Oncol. 2018;4:1691–8.
LOWERY MA, PTASHKIN R, JORDAN E, BERGER MF, CAPANU ZEHIR,A, KEMENY M, O'REILLY NE, EL-DIKA EM, D'ANGELICA IJARNAGIN,WR,HARDING,JJ, CERCEK MI, SCHULTZ AHECHTMAN,JF,SOLIT,DB, N., HYMAN, D. M., KLIMSTRA, D. S., SALTZ, L. B. & ABOU-ALFA GK. Comprehensive Molecular Profiling of Intrahepatic and Extrahepatic Cholangiocarcinomas: Potential Targets for Intervention. Clin Cancer Res. 2018;24:4154–61.
MCKENNA A, HANNA M, SIVACHENKO BANKS,E, CIBULSKIS A, GARIMELLA KKERNYTSKY,A, ALTSHULER K, GABRIEL D, DALY S, M. & DEPRISTO MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
MOU H, HOU YU,LLIAO,Q, WU X, CUI Y, YAO QYAN,NMA,RWANG,L, M. & WANG K. Successful response to the combination of immunotherapy and chemotherapy in cholangiocarcinoma with high tumour mutational burden and PD-L1 expression: a case report. BMC Cancer. 2018;18:1105.
REICH M, LIEFELD T, TAMAYO GOULD,JLERNER,J, P. & MESIROV JP. GenePattern 2.0. Nat Genet. 2006;38:500–1.
SINGAL AK, VAUTHEY, J. N., GRADY, J. J. & STROEHLEIN JR. Intra-hepatic cholangiocarcinoma–frequency and demographic patterns: thirty-year data from the M.D. Anderson Cancer Center. J Cancer Res Clin Oncol. 2011;137:1071–8.
WANG K, LI M, HAKONARSON H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
XIE D, REN Z, FAN, J. & GAO Q. Genetic profiling of intrahepatic cholangiocarcinoma and its clinical implication in targeted therapy. Am J Cancer Res. 2016;6:577–86.
ZEHIR A, MIDDHA BENAYED,RSHAH,RH,SYED,A, KIM S, SRINIVASAN HR, CHAKRAVARTY PGAO,J, HELLMANN DDEVLIN,SM, SCHRAM MD,BARRON,DA, HAMEED AM, DOGAN M, ROSS S, HECHTMAN DS, DELAIR JF, YAO DF, MANDELKER J, CHENG DL, CHANDRAMOHAN DT, MOHANTY R, PTASHKIN AS, JAYAKUMARAN RN, PRASAD G, SYED M, STEWART MH,REMA,AB,LIU,ZY,NAFA,KBORSU,LSADOWSKA,JCASANOVA,JBACARES,RKIECKA,IJ,RAZUMOVA,ASON,JB, BALDI L, AL-AHMADIE TMULLANEY,KA, PENSON HVAKIANI,EABESHOUSE,AA, JONSSON AV, CAMACHO P, GROSS NCHANG,MT,WON,HH, KUNDRA BE, HEINS R, CHEN ZJ, PHILLIPS HW, ZHANG S, EUBANK HWANG,JOCHOA,AWILLS,J, DURANY MTHOMAS,SB,GARDOS,SM,REALES,DN,GALLE,J, ABIDA RCAMBRIA,R, FELDMAN WCERCEK,A, GOUNDER DR, IYER MM,HAKIMI,AA,HARDING,JJ, G., JANJIGIAN, Y. Y., JORDAN, E. J., KELLY, C. M., LOWERY, M. A., MORRIS, L. G. T., OMURO, A. M., RAJ, N., RAZAVI, P., SHOUSHTARI, A. N., SHUKLA, N., SOUMERAI, T. E., VARGHESE, A. M., YAEGER, R., COLEMAN, J., BOCHNER, B., RIELY, G. J., SALTZ, L. B., SCHER, H. I., SABBATINI, P. J., ROBSON, M. E., KLIMSTRA, D. S., TAYLOR, B. S., BASELGA, J., SCHULTZ, N., HYMAN, D. M., ARCILA, M. E., SOLIT, D. B., LADANYI, M. & BERGER, M. F. (2017). Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med, 23, 703–713.
ZOU S, LI J, JIANG ZHOU,HFRECH,C, ZHAO XCHU,JS, LI X, LI Y, WANG Q, WU HHU,JKONG,G, M., DING, C., CHEN, N. & HU H. (2014). Mutational landscape of intrahepatic cholangiocarcinoma. Nat Commun, 5, 5696.