Skip to main content
SpringerLink
Log in
Book cover

Biomarkers for Endometriosis pp 1–25Cite as

Building Translational Research Infrastructure and Access to Expertise for Biomarker Discovery in Cancer

  • Chapter
  • First Online:

Abstract

The way that biomarker research is being conducted in oncology is changing. We are moving away from institutional and expertise specific silos to multicentre studies, networks of institutions and integrated multidisciplinary workflows. These changes are influencing the way that researchers operate and present a host of new challenges, both scientific and operational. Investing in translational research infrastructure represents both an investment in a technical platform and access to expertise to promote high-quality, streamlined procedures under appropriate governance. Key elements that should be addressed to facilitate the translational of biomarkers to clinical practice include sample collection, laboratory analysis, molecular and clinical data collection analysis and interpretation. Building these elements to create a supportive research environment is therefore becoming increasingly important.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Mirnezami R, Nicholson J, Darzi A. Preparing for precision medicine. New England Consensus Expert Group Report. J Med. 2012;366:489–91.

    Google Scholar 

  2. Kern SE. Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures. Cancer Res. 2012;72(23):6097–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Baggerly KA, Coombes KR. What information should be required to support clinical -omics publications? Clin Chem. 2011;57:688–90.

    Article  CAS  PubMed  Google Scholar 

  4. Simon RM, Paik S, Hayes DF. Use of human archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst. 2009;101:1446–52.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Schilsky RL, Doroshow JH, Leblanc M, Conley BA. Development and use integral assays in clinical trials. Clin Cancer Res. 2012;18:1540–6.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Barker AD, Sigman CC, Kelloff GJ, Hylton NM, Berry DA, Esserman LJ. I-SPY 2: an adaptive breast cancer trial design in the setting of neoadjuvant chemotherapy. Clin Pharmacol Ther. 2009;86:97–100.

    Article  CAS  PubMed  Google Scholar 

  7. Kim ES, Herbst RS, Wistuba II, Lee JJ, Blumenschein GR Jr, Tsao A, Stewart DJ, Hicks ME, Erasmus J Jr, Gupta S, Alden CM, Liu S, Tang X, Khuri FR, Tran HT, Johnson BE, Heymach JV, Mao L, Fossella F, Kies MS, Papadimitrakopoulou V, Davis SE, Lippman SM, Hong WK. The BATTLE trial: personalizing therapy for lung cancer. Cancer Discov. 2012;1:44–53.

    Article  Google Scholar 

  8. Cummings J, Raynaud F, Jones L, Sugar R, Dive C. Fit-for-purpose biomarker method validation for application in clinical trials of anticancer drugs. Br J Cancer. 2010;103:1313–131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Yap AT, Workman P. Exploiting the clinical development of targeted molecular therapeutics. Annu Rev Pharmacol Toxicol. 2013;52:549–573.

    Google Scholar 

  10. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM, Statistics Subcommittee of NCI-EORTC Working Group on Cancer Diagnostics. Reporting recommendations for tumour marker prognostic studies (REMARK). J Natl Cancer Inst. 2005;97:416–22.

    Article  Google Scholar 

  11. International Society for Biological and Environmental Repositories. ISBER Best Practices for Repositories: collection, storage, retrieval, and distribution of biological materials for research. Biopreserv Biobank. 2012;10(2):79–161.

    Article  Google Scholar 

  12. P3G Consortium. http://www.p3g.org/biobank-toolkit/comparison-chart-guidelines. Accessed 22 Dec 2016.

  13. Moore HM, Kelly AB, Jewell SD, McShane LM, Clark DP, Greenspan R, Hayes DF, Hainaut P, Kim P, Mansfield EA, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J. Biospecimen reporting for improved study quality (BRISQ). Cancer Cytopathol. 2011;119(2):92–101.

    Article  PubMed  Google Scholar 

  14. Caboux E, Plymoth A, Hainaut P. International Network of Biological Resource Centres for Cancer Research: recommendations on common minimal technical standards. Lyon: IARC/WHO; 2007.

    Google Scholar 

  15. Lièvre A, Bachet JB, Le Corre D, Boige V, Landi B, Emile JF, Côté JF, Tomasic G, Penna C, Ducreux M, Rougier P, Penault-Llorca F, Laurent-Puig P. KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res. 2006;66:3992–5.

    Article  PubMed  Google Scholar 

  16. Hall JA, Daidone MG, Peters GJ, Harbeck N, Lacombe D, Sleijfer S. Integrating collection of biospecimens in clinical trials: the approach of the European organization for research and treatment of cancer. Biopreserv Biobank. 2011;9:181–6.

    Article  PubMed  Google Scholar 

  17. Mager SR, Oomen MH, Morente MM, Ratcliffe C, Knox K, Kerr DJ, Pezzella F, Riegman PH. Standard operating procedure for the collection of fresh frozen tissue samples. Eur J Cancer. 2007;43:828–34.

    Article  CAS  PubMed  Google Scholar 

  18. Bogaerts J, Cardoso F, Buyse M, Braga S, Loi S, Harrison JA, Bines J, Mook S, Decker N, Ravdin P, Therasse P, Rutgers E, van’t Veer LJ, Piccart M, TRANSBIG consortium. Gene signature evaluation a prognostic tool: challenges in the design of the MINDACT trial. Nat Clin Pract Oncol. 2006;3:540–51.

    Article  CAS  PubMed  Google Scholar 

  19. Betsou F, Gunter E, Clements J, DeSouza Y, Goddard KA, Guadagni F, Yan W, Skubitz A, Somiari S, Yeadon T, Chuaqui R. Identification of evidence-based biosample quality-control tools: a report of the International Society for Biological Environmental Repositories (ISBER) biospecimen and reference laboratories in specimens from the science working group. J Mol Diagn. 2012;15:3–16.

    Article  PubMed  Google Scholar 

  20. Heitzer E, Ulz P, Geigl JB. Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem. 2015;61(1):112–23.

    Article  CAS  PubMed  Google Scholar 

  21. Ignatiadis M, Dawson SJ. Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality? Ann Oncol. 2014;25(12):2304–13.

    Article  CAS  PubMed  Google Scholar 

  22. Baker M. Biorepositories: building better biobanks. Nature. 2012;486:141–6.

    Article  CAS  PubMed  Google Scholar 

  23. The International Health Terminology Standards Development Organisation (IHTSDO): Systematised Nomenclature of Medicine Clinical Terms (SNOMED CT) http://www.ihtsdo.org/snomed-ct. Accessed 22 Dec 2016.

  24. Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol. 2014;4:78.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Hayes DF. From genome to bedside: are we lost in translation? Breast. 2013;22(Suppl 2):S22–6.

    Article  PubMed  Google Scholar 

  26. Abeel T, Helleputte T, Van de Peer Y, Dupont P, Saeys Y. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics. 2010;26(3):392–8.

    Article  CAS  PubMed  Google Scholar 

  27. European Medicines Agency. Reflection paper for laboratories that perform the analysis or evaluation of clinical trial samples. GCP Inspectors Working Group. 2012. http://www.ema.europa.eu/docs/en_GB/document_library/Regulatory_and_procedural_guideline/2012/05/WC500127124.pdf. Accessed 22 Dec 2016.

  28. Paik S, Tang G, Shak S, Kim C, Baker J, Kim W, Cronin M, Baehner FL, Watson D, Bryant J, Costantino JP, Geyer CE Jr, Wickerham DL, Wolmark N. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol. 2006;24(23):3726–34.

    Article  CAS  PubMed  Google Scholar 

  29. Albain KS, Barlow WE, Shak S, Hortobagyi GN, Livingston RB, Yeh IT, Ravdin P, Bugarini R, Baehner FL, Davidson NE, Sledge GW, Winer EP, Hudis C, Ingle JN, Perez EA, Pritchard KI, Shepherd L, Gralow JR, Yoshizawa C, Allred DC, Osborne CK, Hayes DF, Breast Cancer Intergroup of North America. Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial. Lancet Oncol. 2010;11(1):55–65.

    Article  CAS  PubMed  Google Scholar 

  30. Teutsch SM, Bradley LA, Palomaki GE, Haddow JE, Piper M, Calonge N, Dotson WD, Douglas MP, Berg AO, on behalf of the EGAPP Working Group. The evaluation of genomic applications in practice and prevention (EGAPP) initiative: methods of the EGAPP Working Group. Genet Med. 2009;11:1.

    Article  Google Scholar 

  31. Cancer Research UK (CRUK). Prognostic/predictive biomarker (BM) roadmap. http://www.cancerresearchuk.org/prod_consump/groups/cr_common/@fre/@fun/documents/generalcontent/cr_027486.pdf. Accessed 22 Dec 2016.

  32. Biomarker, Imaging and Quality of Life Studies Funding Program (BIQSFP). Study checklist for large randomized phase 2 and phase 3 with biomarker assays/imaging tests. https://www.cancer.gov/about-nci/organization/ccct/funding/biqsfp/concept-checklists. Accessed 22 Dec 2016.

  33. Ohmann C, Kuchinke W, Canham S, et al. Standard requirements for GCP-compliant data management in multinational clinical trials. Trials. 2011;12:85.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Norlin L, Fransson MN, Eriksson M, Merino-Martinez R, Anderberg M, Kurtovic S, Litton JE. A minimum data set for sharing biobank samples, information, and data: MIABIS. Biopreserv Biobank. 2012;10(4):343–8.

    Article  PubMed  Google Scholar 

  35. Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt KD, Resenchuk S, Tatusova T, Yaschenko E, Ostell J. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 2011;40:53–63.

    Google Scholar 

  36. Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H. The BioSample database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res. 2011;40:64–70.

    Article  Google Scholar 

  37. Voegele C, Alteyrac L, Caboux E, Smans M, Lesueur F, Le Calvez-Kelm F, Hainaut P. A sample storage management system for biobanks. Bioinformatics. 2010;26:2798–800.

    Article  CAS  PubMed  Google Scholar 

  38. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet. 2010;11:647–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. European Genome-Phenome Archive (EGA). https://ega-archive.org. Accessed 30 Jan 2015.

  40. ELIXIR: a distributed infrastructure for life-science information. http://www.elixir-europe.org. Accessed 30 Jan 2015.

  41. Clinical Data Interchange Standards Consortium (CDISC) open data standards. http://www.cdisc.org/standards-and-implementations. Accessed 30 Jan 2015.

  42. Critical Path Institute (C-Path). http://c-path.org. Accessed 22 Dec 2016.

  43. Miriovsky BJ, Shulman LN, Abernethy AP. Importance of health information technology, electronic health records, and continuously aggregating data to comparative effectiveness research and learning health care. J Clin Oncol. 2012;30:4243–8.

    Article  PubMed  Google Scholar 

  44. Tian Q, Price ND, Hood L. Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med. 2012;271(2):111–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol. 2005;23(29):7332–41.

    Article  CAS  PubMed  Google Scholar 

  46. Teschendorff AE, Zhuang J, Widschwendter M. Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics. 2011;27(11):1496–505.

    Article  CAS  PubMed  Google Scholar 

  47. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, Polley MY, Kim KY, Tricoli JV, Taylor JM, Shuman DJ, Simon RM, Doroshow JH, Conley BA. Criteria for the use of omics-based predictors in clinical trials. Nature. 2013;502(7471):317–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Leisch F. Sweave: dynamic generation of reengineering clinical translational science. Science statistical reports using literate data analysis. Heidelberg: Physika Verlag; 2002.

    Google Scholar 

  49. International Organization for Standardization (ISO). http://www.iso.org. Accessed 22 Dec 2016.

  50. International Society for Biological and Environmental Biorepositories (ISBER): ISBER Self-Assessment Tool (SAT). 2011. http://www.isber.org/?page=SAT. Accessed 30 Jan 2015.

  51. Quinlan PR, Mistry G, Bullbeck H, Carter A. Confederation of Cancer Biobanks (CCB) Working Group 3. A data standard for sourcing fit-for-purpose biological samples in an integrated virtual network of biobanks. Biopreserv Biobank. 2014;12(3):184–91.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Carter A, Betsou F, Clark BJ. Quality management and accreditation of research tissue banks. Virchows Arch. 2011;458:247–8.

    Article  PubMed  Google Scholar 

  53. Carter A, Betsou F. Quality assurance in cancer biobanking. Biopreserv Biobanking. 2011;9:157–63.

    Article  Google Scholar 

  54. Cancer Research UK. Stratified medicine programme. http://www.cancerresearchuk.org/funding-for-researchers/how-we-deliver-research/our-research-partnerships/stratified-medicine-programme. Accessed 22 Dec 2016.

  55. Hall JA, Salgado R, Lively T, Sweep F, Schuh A. A risk-management approach for effective integration of biomarkers in clinical trials: perspectives of an NCI, NCRI and EORTC working group. Lancet Oncol. 2014;15(4):e184.

    Article  PubMed  Google Scholar 

  56. Yassin R, Lockhart N, González del Riego M, Pitt K, Thomas JW, Weiss L, Compton C. Custodianship as an ethical framework for biospecimen-based research. Cancer Epidemiol Biomark Prev. 2010;19:1012–5.

    Article  Google Scholar 

  57. Kaye J. The tension between data sharing and the protection of privacy in genomics research. Annu Rev Genomics Hum Genet. 2012;13:415–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wolfson M, Wallace SE, Masca N, Rowe G, Sheehan NA, Ferretti V, LaFlamme P, Tobin MD, Macleod J, Little J, Fortier I, Knoppers BM, Burton PR. DataSHIELD: resolving a conflict in contemporary bioscience–performing a pooled analysis of individual-level data without sharing the data. Int J Epidemiol. 2010;39:1372–82.

    Article  PubMed  PubMed Central  Google Scholar 

  59. The database of Genotypes and Phenotypes (dbGaP). The National Center for Biotechnology Information (NCBI), Bethesda. http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/about.cgi. Accessed 22 Dec 2016.

  60. Kaye J, Whitley EA, Lund D, Morrison M, Teare H, Melham K. Dynamic consent: a patient interface for twenty-first century research networks. Eur J Hum Genet. 2015;23:141–6.

    Article  PubMed  Google Scholar 

  61. Eck SL, Paul SM. Biomarker qualification via public-private partnerships. Clin Pharmacol Ther. 2009;87:21–3.

    Article  Google Scholar 

  62. Dutch Biomarker Development Center (BDC). http://www.biomarkerdevelopmentcenter.nl. Accessed 22 Dec 2016.

  63. Innovative Medicines Initiative (IMI). http://www.imi.europa.eu. Accessed 22 Dec 2016.

  64. Margolin AA, Huang EBE, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HKM, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci Transl Med. 2013;5(181):181re1.

    Article  PubMed  PubMed Central  Google Scholar 

  65. Seven Bridges Genomics Biomedical Data Analysis Platform. https://www.sbgenomics.com. Accessed 22 Dec 2016.

Download references

Author information

Authors and Affiliations

  1. Vivactiv Ltd, Buckinghamshire, UK

    Jacqueline A. Hall Ph.D.

Authors
  1. Jacqueline A. Hall Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jacqueline A. Hall Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Development and Regeneration Organ Systems, Group Biomedical Sciences, KU Leuven (University of Leuven), Leuven, Belgium

    Thomas D'Hooghe

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Hall, J.A. (2017). Building Translational Research Infrastructure and Access to Expertise for Biomarker Discovery in Cancer. In: D'Hooghe, T. (eds) Biomarkers for Endometriosis. Springer, Cham. https://doi.org/10.1007/978-3-319-59856-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-59856-7_1

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-59854-3

  • Online ISBN: 978-3-319-59856-7

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation