Program Official
Christos Patriotis, Ph.D., M.Sc.

Principal Investigator

Christopher I
Amos
Awardee Organization

Baylor College Of Medicine
United States

Fiscal Year
2020
Activity Code
U01
Project End Date
Notice of Funding Opportunity
NIH RePORTER
For more information, see NIH RePORTER Project 3U01CA196386-06S1

Coordinating Center: Molecular and Cellular Findings of Screen-Detected Lesions

The Molecular and Cellular Characterization of Screen‐Detected Lesions ‐ Coordinating Center and Data Management Group will provide support for the participating studies responding to RFA CA14‐10. The coordinating center supports three main domains: network coordination, statistical support and computational analysis and protocol development and database support. Support for communication is provided through an interactive web portal, management of conference calls, and meeting support. The coordinating center also develops protocols and databases for pan network studies. The coordinating center supports analysis of data across the consortium by providing access by researchers to state of the art analytical facilities and software. Cluster computing for next generation analysis, high dimensional analyses and simulations will be supported on the Discovery cluster. Support for bioinformatical analyses will be provided through access to site licenses for user friendly software along with graphical user interfaces that have been and will be built as required by users. Workflows for managing biomarker analysis will be developed using Biodatomics Enterprise software, where possible, because the process is stored and R software support can be directly integrated. Guidelines for the development and application of statistical approaches will be provided by the statistical support through the coordinating center. Database support is provided by the analytical team that has been supporting the Early Detection Research Network in collaboration with the Jet Propulsion Laboratory. Support for the development of protocols will be provided by the Coordinating Center and with additional support from the Dartmouth CTSA.

Publications

  • Bossé Y, Li Z, Xia J, Manem V, Carreras-Torres R, Gabriel A, Gaudreault N, Albanes D, Aldrich MC, Andrew A, Arnold S, Bickeböller H, Bojesen SE, Brennan P, Brunnstrom H, Caporaso N, Chen C, Christiani DC, Field JK, Goodman G, Grankvist K, Houlston R, Johansson M, Johansson M, Kiemeney LA, Lam S, Landi MT, Lazarus P, Le Marchand L, Liu G, Melander O, Rennert G, Risch A, Rosenberg SM, Schabath MB, Shete S, Song Z, Stevens VL, Tardon A, Wichmann HE, Woll P, Zienolddiny S, Obeidat M, Timens W, Hung RJ, Joubert P, Amos CI, McKay JD. Transcriptome-wide association study reveals candidate causal genes for lung cancer. International journal of cancer. 2020 Apr 1;146(7):1862-1878. Epub 2019 Dec 9. PMID: 31696517
  • Demidenko E, Miller TW. Statistical determination of synergy based on Bliss definition of drugs independence. PloS one. 2019 Nov 25;14(11):e0224137. doi: 10.1371/journal.pone.0224137. eCollection 2019. PMID: 31765385
  • Demidenko E. Exact and Approximate Statistical Inference for Nonlinear Regression and the Estimating Equation Approach. Scandinavian journal of statistics, theory and applications. 2017 Sep;44(3):636-665. Epub 2017 Mar 29. PMID: 29033489
  • McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. American journal of epidemiology. 2017 Oct 1;186(7):753-761. PMID: 28978193
  • Cheng C, Zhao Y, Schaafsma E, Weng YL, Amos C. An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. International journal of cancer. 2020 Nov 1;147(9):2621-2633. Epub 2020 Jun 4. PMID: 32406930
  • Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI, Cheng C. Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer research. 2022 Jan 15;82(2):199-209. Epub 2021 Nov 23. PMID: 34815255
  • Zheng X, Amos CI, Frost HR. Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models. BMC bioinformatics. 2020 Oct 20;21(1):467. PMID: 33081688
  • Kamal Y, Dwan D, Hoehn HJ, Sanz-Pamplona R, Alonso MH, Moreno V, Cheng C, Schell MJ, Kim Y, Felder SI, Rennert HS, Melas M, Lazaris C, Bonner JD, Siegel EM, Shibata D, Rennert G, Gruber SB, Frost HR, Amos CI, Schmit SL. Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse. Oncoimmunology. 2021 Mar 9;10(1):1862529. PMID: 33763292
  • Qian DC, Han Y, Byun J, Shin HR, Hung RJ, McLaughlin JR, Landi MT, Seminara D, Amos CI. A Novel Pathway-Based Approach Improves Lung Cancer Risk Prediction Using Germline Genetic Variations. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2016 Aug;25(8):1208-15. Epub 2016 May 24. PMID: 27222311
  • Jiang Y, Chiu CY, Yan Q, Chen W, Gorin MB, Conley YP, Lakhal-Chaieb ML, Cook RJ, Amos CI, Wilson AF, Bailey-Wilson JE, McMahon FJ, Vazquez AI, Yuan A, Zhong X, Xiong M, Weeks DE, Fan R. Gene-Based Association Testing of Dichotomous Traits With Generalized Functional Linear Mixed Models Using Extended Pedigrees: Applications to Age-Related Macular Degeneration. Journal of the American Statistical Association. 2021;116(534):531-545. Epub 2020 Jul 28. PMID: 34321704
  • Jiang X, Finucane HK, Schumacher FR, Schmit SL, Tyrer JP, Han Y, Michailidou K, Lesseur C, Kuchenbaecker KB, Dennis J, Conti DV, Casey G, Gaudet MM, Huyghe JR, Albanes D, Aldrich MC, Andrew AS, Andrulis IL, Anton-Culver H, Antoniou AC, Antonenkova NN, Arnold SM, Aronson KJ, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Batra J, Beckmann MW, Benitez J, Benlloch S, Berchuck A, Berndt SI, Bickeböller H, Bien SA, Blomqvist C, Boccia S, Bogdanova NV, Bojesen SE, Bolla MK, Brauch H, Brenner H, Brenton JD, Brook MN, Brunet J, Brunnström H, Buchanan DD, Burwinkel B, Butzow R, Cadoni G, Caldés T, Caligo MA, Campbell I, Campbell PT, Cancel-Tassin G, Cannon-Albright L, Campa D, Caporaso N, Carvalho AL, Chan AT, Chang-Claude J, Chanock SJ, Chen C, Christiani DC, Claes KBM, Claessens F, Clements J, Collée JM, Correa MC, Couch FJ, Cox A, Cunningham JM, Cybulski C, Czene K, Daly MB, deFazio A, Devilee P, Diez O, Gago-Dominguez M, Donovan JL, Dörk T, Duell EJ, Dunning AM, Dwek M, Eccles DM, Edlund CK, Edwards DRV, Ellberg C, Evans DG, Fasching PA, Ferris RL, Liloglou T, Figueiredo JC, Fletcher O, Fortner RT, Fostira F, Franceschi S, Friedman E, Gallinger SJ, Ganz PA, Garber J, García-Sáenz JA, Gayther SA, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, Goode EL, Goodman MT, Goodman G, Grankvist K, Greene MH, Gronberg H, Gronwald J, Guénel P, Håkansson N, Hall P, Hamann U, Hamdy FC, Hamilton RJ, Hampe J, Haugen A, Heitz F, Herrero R, Hillemanns P, Hoffmeister M, Høgdall E, Hong YC, Hopper JL, Houlston R, Hulick PJ, Hunter DJ, Huntsman DG, Idos G, Imyanitov EN, Ingles SA, Isaacs C, Jakubowska A, James P, Jenkins MA, Johansson M, Johansson M, John EM, Joshi AD, Kaneva R, Karlan BY, Kelemen LE, Kühl T, Khaw KT, Khusnutdinova E, Kibel AS, Kiemeney LA, Kim J, Kjaer SK, Knight JA, Kogevinas M, Kote-Jarai Z, Koutros S, Kristensen VN, Kupryjanczyk J, Lacko M, Lam S, Lambrechts D, Landi MT, Lazarus P, Le ND, Lee E, Lejbkowicz F, Lenz HJ, Leslie G, Lessel D, Lester J, Levine DA, Li L, Li CI, Lindblom A, Lindor NM, Liu G, Loupakis F, Lubiński J, Maehle L, Maier C, Mannermaa A, Marchand LL, Margolin S, May T, McGuffog L, Meindl A, Middha P, Miller A, Milne RL, MacInnis RJ, Modugno F, Montagna M, Moreno V, Moysich KB, Mucci L, Muir K, Mulligan AM, Nathanson KL, Neal DE, Ness AR, Neuhausen SL, Nevanlinna H, Newcomb PA, Newcomb LF, Nielsen FC, Nikitina-Zake L, Nordestgaard BG, Nussbaum RL, Offit K, Olah E, Olama AAA, Olopade OI, Olshan AF, Olsson H, Osorio A, Pandha H, Park JY, Pashayan N, Parsons MT, Pejovic T, Penney KL, Peters WHM, Phelan CM, Phipps AI, Plaseska-Karanfilska D, Pring M, Prokofyeva D, Radice P, Stefansson K, Ramus SJ, Raskin L, Rennert G, Rennert HS, van Rensburg EJ, Riggan MJ, Risch HA, Risch A, Roobol MJ, Rosenstein BS, Rossing MA, De Ruyck K, Saloustros E, Sandler DP, Sawyer EJ, Schabath MB, Schleutker J, Schmidt MK, Setiawan VW, Shen H, Siegel EM, Sieh W, Singer CF, Slattery ML, Sorensen KD, Southey MC, Spurdle AB, Stanford JL, Stevens VL, Stintzing S, Stone J, Sundfeldt K, Sutphen R, Swerdlow AJ, Tajara EH, Tangen CM, Tardon A, Taylor JA, Teare MD, Teixeira MR, Terry MB, Terry KL, Thibodeau SN, Thomassen M, Bjørge L, Tischkowitz M, Toland AE, Torres D, Townsend PA, Travis RC, Tung N, Tworoger SS, Ulrich CM, Usmani N, Vachon CM, Van Nieuwenhuysen E, Vega A, Aguado-Barrera ME, Wang Q, Webb PM, Weinberg CR, Weinstein S, Weissler MC, Weitzel JN, West CML, White E, Whittemore AS, Wichmann HE, Wiklund F, Winqvist R, Wolk A, Woll P, Woods M, Wu AH, Wu X, Yannoukakos D, Zheng W, Zienolddiny S, Ziogas A, Zorn KK, Lane JM, Saxena R, Thomas D, Hung RJ, Diergaarde B, McKay J, Peters U, Hsu L, García-Closas M, Eeles RA, Chenevix-Trench G, Brennan PJ, Haiman CA, Simard J, Easton DF, Gruber SB, Pharoah PDP, Price AL, Pasaniuc B, Amos CI, Kraft P, Lindström S. Shared heritability and functional enrichment across six solid cancers. Nature communications. 2019 Jan 25;10(1):431. PMID: 30683880
  • Kamal Y, Schmit SL, Hoehn HJ, Amos CI, Frost HR. Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes. Cancer research. 2019 Aug 15;79(16):4227-4241. Epub 2019 Jun 25. PMID: 31239274
  • Zheng X, Amos CI, Frost HR. Comparison of pathway and gene-level models for cancer prognosis prediction. BMC bioinformatics. 2020 Feb 28;21(1):76. PMID: 32111152
  • Frost HR, Amos CI. Unsupervised gene set testing based on random matrix theory. BMC bioinformatics. 2016 Nov 4;17(1):442. PMID: 27809777
  • Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PD, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2017 Jan;26(1):126-135. Epub 2016 Oct 3. PMID: 27697780
  • Frost HR, Amos CI. A multi-omics approach for identifying important pathways and genes in human cancer. BMC bioinformatics. 2018 Dec 12;19(1):479. PMID: 30541428
  • Shin SJ, Dodd-Eaton EB, Gao F, Bojadzieva J, Chen J, Kong X, Amos CI, Ning J, Strong LC, Wang W. Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective. Cancer research. 2020 Jan 15;80(2):347-353. Epub 2019 Nov 12. PMID: 31719099
  • Patel CJ, Kerr J, Thomas DC, Mukherjee B, Ritz B, Chatterjee N, Jankowska M, Madan J, Karagas MR, McAllister KA, Mechanic LE, Fallin MD, Ladd-Acosta C, Blair IA, Teitelbaum SL, Amos CI. Opportunities and Challenges for Environmental Exposure Assessment in Population-Based Studies. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2017 Sep;26(9):1370-1380. Epub 2017 Jul 14. PMID: 28710076
  • Shin SJ, Dodd-Eaton EB, Peng G, Bojadzieva J, Chen J, Amos CI, Frone MN, Khincha PP, Mai PL, Savage SA, Ballinger ML, Thomas DM, Yuan Y, Strong LC, Wang W. Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts. Cancer research. 2020 Jan 15;80(2):354-360. Epub 2019 Nov 12. PMID: 31719101