Skip to main content

Molecular Testing in Pediatric Oncology Practice

  • Chapter
  • First Online:
Precision Molecular Pathology of Neoplastic Pediatric Diseases

Part of the book series: Molecular Pathology Library ((MPLB))

  • 518 Accesses

Abstract

The goal for the molecular diagnostics workup of pediatric cancer patients is to help uncover as much useful genetic information as possible that can be applied to help guide the care of the patient and his or her family. At a preliminary level, this means making sure the most accurate and refined diagnosis is made, as this is the foundation upon which all subsequent treatment decisions are made. However, assistance in diagnosis is just the tip of the iceberg, and molecular diagnostics are rapidly becoming an essential part of the ongoing management of cancer patients, helping to predict disease progression, providing information regarding actionable targets to support therapeutic choices, and creating new possibilities for monitoring disease status and detecting recurrence at the earliest possible time. With the advent of next-generation sequencing (NGS) and other newer genomics technologies, the complexity of genetic tests and the number of potential testing options continues to increase, placing a premium on proper informed decision-making and integration of results. There are many factors to consider when planning for molecular testing, including the differential diagnosis, the pretest likelihood of the presence of molecular alterations, the performance characteristics and comprehensiveness of potential test options, and the suitability of available specimens. This chapter aims to cover the different facets of formulating and employing a genetic testing strategy for pediatric oncology, including a review of testing indications, descriptions of common specimen types and their relative strengths and weaknesses, factors influencing test selection, and general recommendations for interpretation and integration of results into clinical care. Lastly, ethical considerations for genetic testing in the pediatric oncology population are addressed with the aim of minimizing informational harm and other potentially negative repercussions.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
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

Institutional subscriptions

References

  1. Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360(5):470–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Den Boer ML, Van Slegtenhorst M, De Menezes RX, Cheok MH, Buijs-Gladdines JG, Peters ST, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 2009;10(2):125–34.

    Article  CAS  Google Scholar 

  3. Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol. 2015;12(6):344–57.

    Article  CAS  PubMed  Google Scholar 

  4. Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371(11):1005–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Clifford SC, Lusher ME, Lindsey JC, Langdon JA, Gilbertson RJ, Straughton D, et al. Wnt/wingless pathway activation and chromosome 6 loss characterize a distinct molecular sub-group of medulloblastomas associated with a favorable prognosis. Cell Cycle. 2006;5(22):2666–70.

    Article  CAS  PubMed  Google Scholar 

  6. Ellison DW, Onilude OE, Lindsey JC, Lusher ME, Weston CL, Taylor RE, et al. Beta-catenin status predicts a favorable outcome in childhood medulloblastoma: the United Kingdom children’s cancer study group brain tumour committee. J Clin Oncol. 2005;23(31):7951–7.

    Article  CAS  PubMed  Google Scholar 

  7. Ramaswamy V, Remke M, Bouffet E, Bailey S, Clifford SC, Doz F, et al. Risk stratification of childhood medulloblastoma in the molecular era: the current consensus. Acta Neuropathol. 2016;131(6):821–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Meshinchi S, Arceci RJ, Sanders JE, Smith FO, Woods WB, Radich JP, et al. Role of allogeneic stem cell transplantation in FLT3/ITD-positive AML. Blood. 2006;108(1):400. Author Reply-1.

    Article  CAS  PubMed  Google Scholar 

  9. Schultz KR, Bowman WP, Aledo A, Slayton WB, Sather H, Devidas M, et al. Improved early event-free survival with Imatinib in Philadelphia chromosome-positive acute lymphoblastic leukemia: a children’s oncology group study. J Clin Oncol. 2009;27(31):5175–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mosse YP, Lim MS, Voss SD, Wilner K, Ruffner K, Laliberte J, et al. Safety and activity of crizotinib for paediatric patients with refractory solid tumours or anaplastic large-cell lymphoma: a children’s oncology group phase 1 consortium study. Lancet Oncol. 2013;14(6):472–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Oshima K, Khiabanian H, Da Silva-Almeida AC, Tzoneva G, Abate F, Ambesi-Impiombato A, et al. Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. 2016;113(40):11306–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. O’Hare T, Eide CA, Deininger MW. Bcr-Abl kinase domain mutations, drug resistance, and the road to a cure for chronic myeloid leukemia. Blood. 2007;110(7):2242–9.

    Article  CAS  PubMed  Google Scholar 

  13. Narod SA, Stiller C, Lenoir GM. An estimate of the heritable fraction of childhood Cancer. Br J Cancer. 1991;63(6):993–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, et al. Germline mutations in predisposition genes in pediatric cancer. N Engl J Med. 2015;373(24):2336–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Satsangi J, Jewell DP, Welsh K, Bunce M, Bell JI. Effect of heparin on polymerase chain reaction. Lancet. 1994;343(8911):1509–10.

    Article  CAS  PubMed  Google Scholar 

  16. Scher HI, Lu D, Schreiber NA, Louw J, Graf RP, Vargas HA, et al. Association of AR-V7 on circulating tumor cells as a treatment-specific biomarker with outcomes and survival in castration-resistant prostate cancer. JAMA Oncol. 2016;2(11):1441–9.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Kahlert C, Melo SA, Protopopov A, Tang J, Seth S, Koch M, et al. Identification of double-stranded genomic DNA spanning all chromosomes with mutated KRAS and p53 DNA in the serum exosomes of patients with pancreatic Cancer. J Biol Chem. 2014;289(7):3869–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Best MG, Sol N, Kooi I, Tannous J, Westerman BA, Rustenburg F, et al. RNA-Seq of tumor-educated platelets enables blood-based pan-cancer, multiclass, and molecular pathway cancer diagnostics. Cancer Cell. 2015;28(5):666–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Underhill HR, Kitzman JO, Hellwig S, Welker NC, Daza R, Baker DN, et al. Fragment length of circulating tumor DNA. PLoS Genet. 2016;12(7):E1006162.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Devonshire AS, Whale AS, Gutteridge A, Jones G, Cowen S, Foy CA, et al. Towards standardisation of cell-free DNA measurement in plasma: controls for extraction efficiency, fragment size bias and quantification. Anal Bioanal Chem. 2014;406(26):6499–512.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Remon J, Caramella C, Jovelet C, Lacroix L, Lawson A, Smalley S, et al. Osimertinib benefit in EGFR-mutant NSCLC patients with T790m-mutation detected by circulating tumour DNA. Ann Oncol. 2017;28(4):784–90.

    PubMed  CAS  Google Scholar 

  23. Srinivasan M, Sedmak D, Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol. 2002;161(6):1961–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Singh VM, Salunga RC, Huang VJ, Tran Y, Erlander M, Plumlee P, et al. Analysis of the effect of various decalcification agents on the quantity and quality of nucleic acid (DNA and RNA) recovered from bone biopsies. Ann Diagn Pathol. 2013;17(4):322–6.

    Article  PubMed  Google Scholar 

  25. Blow N. Tissue preparation: tissue issues. Nature. 2007;448(7156):959–63.

    Article  CAS  PubMed  Google Scholar 

  26. Wickham CL, Boyce M, Joyner MV, Sarsfield P, Wilkins BS, Jones DB, et al. Amplification of PCR products in excess of 600 base pairs using DNA extracted from decalcified, paraffin wax embedded bone marrow trephine biopsies. Mol Pathol. 2000;53(1):19–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Misra DN, Dickman PS, Yunis EJ. Fluorescence in situ hybridization (FISH) detection of MYCN oncogene amplification in neuroblastoma using paraffin-embedded tissues. Diagn Mol Pathol. 1995;4(2):128–35.

    Article  CAS  PubMed  Google Scholar 

  28. Fujii T, Barzi A, Sartore-Bianchi A, Cassingena A, Siravegna G, Karp DD, et al. Mutation-enrichment next-generation sequencing for quantitative detection of KRAS mutations in urine cell-free DNA from patients with advanced cancers. Clin Cancer Res. 2017;23(14):3657–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang Y, Springer S, Zhang M, Mcmahon KW, Kinde I, Dobbyn L, et al. Detection of tumor-derived DNA in cerebrospinal fluid of patients with primary tumors of the brain and spinal cord. Proc Natl Acad Sci U S A. 2015;112(31):9704–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. De Mattos-Arruda L, Mayor R, Ng CK, Weigelt B, Martinez-Ricarte F, Torrejon D, et al. Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma. Nat Commun. 2015;6:8839.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Valencia CA, Indugula SR, Mathur A, Wei C, Brown JC, Cole I, et al. Misleading results from saliva samples of patients post-BMT in exome analyses. Blood. 2014;124(4):660–1.

    Article  CAS  PubMed  Google Scholar 

  32. Iacobucci I, Saglio G, Rosti G, Testoni N, Pane F, Amabile M, et al. Achieving a major molecular response at the time of a complete cytogenetic response (CCgR) predicts a better duration of CCgR in imatinib-treated chronic myeloid leukemia patients. Clin Cancer Res. 2006;12(10):3037–42.

    Article  CAS  PubMed  Google Scholar 

  33. Kadri S, Long BC, Mujacic I, Zhen CJ, Wurst MN, Sharma S, et al. Clinical validation of a next-generation sequencing genomic oncology panel via cross-platform benchmarking against established amplicon sequencing assays. J Mol Diagn. 2017;19(1):43–56.

    Article  CAS  PubMed  Google Scholar 

  34. Bardelli A, Pantel K. Liquid biopsies, what we do not know (yet). Cancer Cell. 2017;31(2):172–9.

    Article  CAS  PubMed  Google Scholar 

  35. Basel D, Mccarrier J. Ending a diagnostic odyssey: family education, counseling, and response to eventual diagnosis. Pediatr Clin N Am. 2017;64(1):265–72.

    Article  Google Scholar 

  36. Harris MH, Dubois SG, Glade Bender JL, Kim A, Crompton BD, Parker E, et al. Multicenter feasibility study of tumor molecular profiling to inform therapeutic decisions in advanced pediatric solid tumors: the individualized cancer therapy (iCat) study. JAMA Oncol. 2016. https://doi.org/10.1001/jamaoncol.2015.5689.

  37. Richter S, Haroun I, Graham TC, Eisen A, Kiss A, Warner E. Variants of unknown significance in BRCA testing: impact on risk perception, worry, prevention and counseling. Ann Oncol. 2013;24(Suppl 8):Viii69–74.

    Article  PubMed  Google Scholar 

  38. Ogino S, Wilson RB. Bayesian analysis and risk assessment in genetic counseling and testing. J Mol Diagn. 2004;6(1):1–9.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Knoppers BM. Paediatric research and the communication of not-so incidental findings. Paediatr Child Health. 2012;17(4):190–2.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Frankel LA, Pereira S, Mcguire AL. Potential psychosocial risks of sequencing newborns. Pediatrics. 2016;137(Suppl 1):S24–9.

    Article  PubMed  Google Scholar 

  41. Goedde LN, Stupiansky NW, Lah M, Quaid KA, Cohen S. Cancer genetic counselors’ current practices and attitudes related to the use of tumor profiling. J Genet Couns. 2017;26(4):878–86.

    Article  PubMed  Google Scholar 

  42. Marron JM, Dubois SG, Glade Bender J, Kim A, Crompton BD, Meyer SC, et al. Patient/parent perspectives on genomic tumor profiling of pediatric solid tumors: the individualized cancer therapy (iCat) experience. Pediatr Blood Cancer. 2016;63(11):1974–82.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15(7):565–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kalia SS, Adelman K, Bale SJ, Chung WK, Eng C, Evans JP, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF V2.0): a policy statement of the American college of medical genetics and genomics. Genet Med. 2017;19(2):249–55.

    Article  PubMed  Google Scholar 

  45. Ross LF, Saal HM, David KL, Anderson RR, American Academy of Pediatrics, American College of Medical Genetics and Genomics, et al. Technical report: ethical and policy issues in genetic testing and screening of children. Genet Med. 2013;15(3):234–45.

    Article  PubMed  Google Scholar 

  46. Burke W, Antommaria AH, Bennett R, Botkin J, Clayton EW, Henderson GE, et al. Recommendations for returning genomic incidental findings? We need to talk! Genet Med. 2013;15(11):854–9.

    Article  CAS  PubMed  Google Scholar 

  47. ACMG Board of Directors. ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. Genet Med. 2015;17(1):68–9.

    Article  Google Scholar 

  48. O’Daniel JM, Mclaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, et al. A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories. Genet Med. 2017;19(5):575–82.

    Article  PubMed  Google Scholar 

  49. Allyse M, Michie M. Not-so-incidental findings: the ACMG recommendations on the reporting of incidental findings in clinical whole genome and whole exome sequencing. Trends Biotechnol. 2013;31(8):439–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Green RC, Holm IA, Rehm HL, Mcguire AL, Agrawal PB, Parad RB, et al. The BabySeq Project: preliminary findings from a randomized trial of exome sequencing in newborns. Presented at the American Society of Human Genetics 2016 Annual Meeting; October 18–22; Vancouver, BC; 2016.

    Google Scholar 

  51. Genetti CA, Helm MH, Towne M, Pereira S, Robinson JO, Ceyhan-Birsoy O, et al. Experiences of exome sequencing in newborns: a peek into BabySeq. National Society Of Genetic Counselors, Annual Education Conference; Seattle, WA; 2016.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jeremy P. Segal MD, PhD .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Segal, J.P., Ritterhouse, L. (2018). Molecular Testing in Pediatric Oncology Practice. In: Furtado, L., Husain, A. (eds) Precision Molecular Pathology of Neoplastic Pediatric Diseases . Molecular Pathology Library. Springer, Cham. https://doi.org/10.1007/978-3-319-89626-7_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-89626-7_4

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-89625-0

  • Online ISBN: 978-3-319-89626-7

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics