Clinical trial NCT04273061 - References

Breast Cancer — Investigating the Effects of Atezolizumab in People Whose Tumour DNA or RNA Indicates Possible Sensitivity

Citation(s)

•   Ayers M, Lunceford J, Nebozhyn M, Murphy E, Loboda A, Kaufman DR, Albright A, Cheng JD, Kang SP, Shankaran V, Piha-Paul SA, Yearley J, Seiwert TY, Ribas A, McClanahan TK
  IFN-gamma-related mRNA profile predicts clinical response to PD-1 blockade. J Clin Invest. 2017 Aug 1;127(8):2930-2940. doi: 10.1172/JCI91190. Epub 2017 Jun 26.
•   Balachandran VP, Luksza M, Zhao JN, Makarov V, Moral JA, Remark R, Herbst B, Askan G, Bhanot U, Senbabaoglu Y, Wells DK, Cary CIO, Grbovic-Huezo O, Attiyeh M, Medina B, Zhang J, Loo J, Saglimbeni J, Abu-Akeel M, Zappasodi R, Riaz N, Smoragiewicz M, Kelley ZL, Basturk O; Australian Pancreatic Cancer Genome Initiative; Garvan Institute of Medical Research; Prince of Wales Hospital; Royal North Shore Hospital; University of Glasgow; St Vincent's Hospital; QIMR Berghofer Medical Research Institute; University of Melbourne, Centre for Cancer Research; University of Queensland, Institute for Molecular Bioscience; Bankstown Hospital; Liverpool Hospital; Royal Prince Alfred Hospital, Chris O'Brien Lifehouse; Westmead Hospital; Fremantle Hospital; St John of God Healthcare; Royal Adelaide Hospital; Flinders Medical Centre; Envoi Pathology; Princess Alexandria Hospital; Austin Hospital; Johns Hopkins Medical Institutes; ARC-Net Centre for Applied Research on Cancer; Gonen M, Levine AJ, Allen PJ, Fearon DT, Merad M, Gnjatic S, Iacobuzio-Donahue CA, Wolchok JD, DeMatteo RP, Chan TA, Greenbaum BD, Merghoub T, Leach SD
  Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature. 2017 Nov 23;551(7681):512-516. doi: 10.1038/nature24462. Epub 2017 Nov 8.
•   Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM
  MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364. No abstract available.
•   Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, Britanova OV, Chudakov DM
  MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013 Sep;10(9):813-4. doi: 10.1038/nmeth.2555. Epub 2013 Jul 28. No abstract available.
•   Brown SD, Raeburn LA, Holt RA
  Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Med. 2015 Nov 30;7:125. doi: 10.1186/s13073-015-0248-x.
•   Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, Holt RA
  Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 2014 May;24(5):743-50. doi: 10.1101/gr.165985.113. Epub 2014 Apr 29.
•   Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G
  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013 Mar;31(3):213-9. doi: 10.1038/nbt.2514. Epub 2013 Feb 10.
•   Eisenhauer EA, Therasse P, Bogaerts J, Schwartz LH, Sargent D, Ford R, Dancey J, Arbuck S, Gwyther S, Mooney M, Rubinstein L, Shankar L, Dodd L, Kaplan R, Lacombe D, Verweij J
  New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer. 2009 Jan;45(2):228-47. doi: 10.1016/j.ejca.2008.10.026.
•   Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA
  Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009 Oct;19(10):1817-24. doi: 10.1101/gr.092924.109. Epub 2009 Jun 18.
•   Gogvadze E, Buzdin A
  Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci. 2009 Dec;66(23):3727-42. doi: 10.1007/s00018-009-0107-2. Epub 2009 Aug 2.
•   Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, Berent-Maoz B, Pang J, Chmielowski B, Cherry G, Seja E, Lomeli S, Kong X, Kelley MC, Sosman JA, Johnson DB, Ribas A, Lo RS
  Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell. 2016 Mar 24;165(1):35-44. doi: 10.1016/j.cell.2016.02.065. Epub 2016 Mar 17. Erratum In: Cell. 2017 Jan 26;168(3):542.
•   Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, Berent-Maoz B, Pang J, Chmielowski B, Cherry G, Seja E, Lomeli S, Kong X, Kelley MC, Sosman JA, Johnson DB, Ribas A, Lo RS
  Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell. 2017 Jan 26;168(3):542. doi: 10.1016/j.cell.2017.01.010. No abstract available.
•   Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA
  Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010;11(8):R82. doi: 10.1186/gb-2010-11-8-r82. Epub 2010 Aug 9.
•   Laskin J, Jones S, Aparicio S, Chia S, Ch'ng C, Deyell R, Eirew P, Fok A, Gelmon K, Ho C, Huntsman D, Jones M, Kasaian K, Karsan A, Leelakumari S, Li Y, Lim H, Ma Y, Mar C, Martin M, Moore R, Mungall A, Mungall K, Pleasance E, Rassekh SR, Renouf D, Shen Y, Schein J, Schrader K, Sun S, Tinker A, Zhao E, Yip S, Marra MA
  Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers. Cold Spring Harb Mol Case Stud. 2015 Oct;1(1):a000570. doi: 10.1101/mcs.a000570.
•   Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D, Biedrzycki B, Donehower RC, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Duffy SM, Goldberg RM, de la Chapelle A, Koshiji M, Bhaijee F, Huebner T, Hruban RH, Wood LD, Cuka N, Pardoll DM, Papadopoulos N, Kinzler KW, Zhou S, Cornish TC, Taube JM, Anders RA, Eshleman JR, Vogelstein B, Diaz LA Jr
  PD-1 Blockade in Tumors with Mismatch-Repair Deficiency. N Engl J Med. 2015 Jun 25;372(26):2509-20. doi: 10.1056/NEJMoa1500596. Epub 2015 May 30.
•   Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, Norton C, Bosse D, Wankowicz SM, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder A, Hellmann MD, Ho T, Motzer RJ, Signoretti S, Kaelin WG Jr, Choueiri TK, Van Allen EM
  Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018 Feb 16;359(6377):801-806. doi: 10.1126/science.aan5951. Epub 2018 Jan 4.
•   Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA
  Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.
•   Nielsen M, Andreatta M
  NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med. 2016 Mar 30;8(1):33. doi: 10.1186/s13073-016-0288-x.
•   Ock CY, Hwang JE, Keam B, Kim SB, Shim JJ, Jang HJ, Park S, Sohn BH, Cha M, Ajani JA, Kopetz S, Lee KW, Kim TM, Heo DS, Lee JS
  Genomic landscape associated with potential response to anti-CTLA-4 treatment in cancers. Nat Commun. 2017 Oct 19;8(1):1050. doi: 10.1038/s41467-017-01018-0.
•   Palena C, Polev DE, Tsang KY, Fernando RI, Litzinger M, Krukovskaya LL, Baranova AV, Kozlov AP, Schlom J
  The human T-box mesodermal transcription factor Brachyury is a candidate target for T-cell-mediated cancer immunotherapy. Clin Cancer Res. 2007 Apr 15;13(8):2471-8. doi: 10.1158/1078-0432.CCR-06-2353.
•   Panda A, Betigeri A, Subramanian K, Ross JS, Pavlick DC, Ali S, Markowski P, Silk A, Kaufman HL, Lattime E, Mehnert JM, Sullivan R, Lovly CM, Sosman J, Johnson DB, Bhanot G, Ganesan S
  Identifying a Clinically Applicable Mutational Burden Threshold as a Potential Biomarker of Response to Immune Checkpoint Therapy in Solid Tumors. JCO Precis Oncol. 2017;2017:PO.17.00146. doi: 10.1200/PO.17.00146. Epub 2017 Dec 7.
•   Panda A, de Cubas AA, Stein M, Riedlinger G, Kra J, Mayer T, Smith CC, Vincent BG, Serody JS, Beckermann KE, Ganesan S, Bhanot G, Rathmell WK
  Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma. JCI Insight. 2018 Aug 23;3(16):e121522. doi: 10.1172/jci.insight.121522. eCollection 2018 Aug 23.
•   Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, Xu C, McKenzie JA, Zhang C, Liang X, Williams LJ, Deng W, Chen G, Mbofung R, Lazar AJ, Torres-Cabala CA, Cooper ZA, Chen PL, Tieu TN, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade JL, Glitza IC, Cascone T, Li HS, Kwong LN, Heffernan TP, Hu J, Bassett RL Jr, Bosenberg MW, Woodman SE, Overwijk WW, Lizee G, Roszik J, Gajewski TF, Wargo JA, Gershenwald JE, Radvanyi L, Davies MA, Hwu P
  Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov. 2016 Feb;6(2):202-16. doi: 10.1158/2159-8290.CD-15-0283. Epub 2015 Dec 8.
•   Pereira C, Gimenez-Xavier P, Pros E, Pajares MJ, Moro M, Gomez A, Navarro A, Condom E, Moran S, Gomez-Lopez G, Grana O, Rubio-Camarillo M, Martinez-Marti A, Yokota J, Carretero J, Galbis JM, Nadal E, Pisano D, Sozzi G, Felip E, Montuenga LM, Roz L, Villanueva A, Sanchez-Cespedes M
  Genomic Profiling of Patient-Derived Xenografts for Lung Cancer Identifies B2M Inactivation Impairing Immunorecognition. Clin Cancer Res. 2017 Jun 15;23(12):3203-3213. doi: 10.1158/1078-0432.CCR-16-1946. Epub 2017 Mar 16.
•   Reisle C, Mungall KL, Choo C, Paulino D, Bleile DW, Muhammadzadeh A, Mungall AJ, Moore RA, Shlafman I, Coope R, Pleasance S, Ma Y, Jones SJM
  MAVIS: merging, annotation, validation, and illustration of structural variants. Bioinformatics. 2019 Feb 1;35(3):515-517. doi: 10.1093/bioinformatics/bty621.
•   Roberts CW, Orkin SH
  The SWI/SNF complex--chromatin and cancer. Nat Rev Cancer. 2004 Feb;4(2):133-42. doi: 10.1038/nrc1273. No abstract available.
•   Rowe HM, Trono D
  Dynamic control of endogenous retroviruses during development. Virology. 2011 Mar 15;411(2):273-87. doi: 10.1016/j.virol.2010.12.007. Epub 2011 Jan 20.
•   Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK
  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012 Jul 15;28(14):1811-7. doi: 10.1093/bioinformatics/bts271. Epub 2012 May 10.
•   Seymour L, Bogaerts J, Perrone A, Ford R, Schwartz LH, Mandrekar S, Lin NU, Litiere S, Dancey J, Chen A, Hodi FS, Therasse P, Hoekstra OS, Shankar LK, Wolchok JD, Ballinger M, Caramella C, de Vries EGE; RECIST working group
  iRECIST: guidelines for response criteria for use in trials testing immunotherapeutics. Lancet Oncol. 2017 Mar;18(3):e143-e152. doi: 10.1016/S1470-2045(17)30074-8. Epub 2017 Mar 2. Erratum In: Lancet Oncol. 2019 May;20(5):e242.
•   Shen J, Ju Z, Zhao W, Wang L, Peng Y, Ge Z, Nagel ZD, Zou J, Wang C, Kapoor P, Ma X, Ma D, Liang J, Song S, Liu J, Samson LD, Ajani JA, Li GM, Liang H, Shen X, Mills GB, Peng G
  ARID1A deficiency promotes mutability and potentiates therapeutic antitumor immunity unleashed by immune checkpoint blockade. Nat Med. 2018 May;24(5):556-562. doi: 10.1038/s41591-018-0012-z. Epub 2018 May 7.
•   Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM
  Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 Dec;36(11):1056-1058. doi: 10.1038/nbt.4239. Epub 2018 Aug 16.
•   Solovyov A, Vabret N, Arora KS, Snyder A, Funt SA, Bajorin DF, Rosenberg JE, Bhardwaj N, Ting DT, Greenbaum BD
  Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes. Cell Rep. 2018 Apr 10;23(2):512-521. doi: 10.1016/j.celrep.2018.03.042.
•   Strick R, Strissel PL, Baylin SB, Chiappinelli KB
  Unraveling the molecular pathways of DNA-methylation inhibitors: human endogenous retroviruses induce the innate immune response in tumors. Oncoimmunology. 2015 Dec 29;5(5):e1122160. doi: 10.1080/2162402X.2015.1122160. eCollection 2016 May.
•   Szolek A, Schubert B, Mohr C, Sturm M, Feldhahn M, Kohlbacher O
  OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics. 2014 Dec 1;30(23):3310-6. doi: 10.1093/bioinformatics/btu548. Epub 2014 Aug 20.
•   Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJ, Robert L, Chmielowski B, Spasic M, Henry G, Ciobanu V, West AN, Carmona M, Kivork C, Seja E, Cherry G, Gutierrez AJ, Grogan TR, Mateus C, Tomasic G, Glaspy JA, Emerson RO, Robins H, Pierce RH, Elashoff DA, Robert C, Ribas A
  PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014 Nov 27;515(7528):568-71. doi: 10.1038/nature13954.
•   Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, Sucker A, Hillen U, Foppen MHG, Goldinger SM, Utikal J, Hassel JC, Weide B, Kaehler KC, Loquai C, Mohr P, Gutzmer R, Dummer R, Gabriel S, Wu CJ, Schadendorf D, Garraway LA
  Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015 Oct 9;350(6257):207-211. doi: 10.1126/science.aad0095. Epub 2015 Sep 10. Erratum In: Science. 2015 Nov 13;350(6262):aad8366. Science. 2016 Apr 15;352(6283). pii: aaf8264. doi: 10.1126/science.aaf8264.
•   Vigneron N
  Human Tumor Antigens and Cancer Immunotherapy. Biomed Res Int. 2015;2015:948501. doi: 10.1155/2015/948501. Epub 2015 Jun 16.
•   Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA
  Derivation of HLA types from shotgun sequence datasets. Genome Med. 2012 Dec 10;4(12):95. doi: 10.1186/gm396. eCollection 2012.
•   Yang W, Lee KW, Srivastava RM, Kuo F, Krishna C, Chowell D, Makarov V, Hoen D, Dalin MG, Wexler L, Ghossein R, Katabi N, Nadeem Z, Cohen MA, Tian SK, Robine N, Arora K, Geiger H, Agius P, Bouvier N, Huberman K, Vanness K, Havel JJ, Sims JS, Samstein RM, Mandal R, Tepe J, Ganly I, Ho AL, Riaz N, Wong RJ, Shukla N, Chan TA, Morris LGT
  Immunogenic neoantigens derived from gene fusions stimulate T cell responses. Nat Med. 2019 May;25(5):767-775. doi: 10.1038/s41591-019-0434-2. Epub 2019 Apr 22.

Canadian Atezolizumab Precision Targeting for Immunotherapy Intervention

Details for clinical trial NCT04273061