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National Child Cancer Network Next-Generation Sequencing (NGS) and Targeted Therapy Guideline

This guideline covers the use of Next-Generation Sequencing (NGS) in paediatric malignancies outside the setting of a clinical trial. The NCCN Molecular Therapeutics Symposium held in January 2016 reached consensus that off-study NGS and targeted therapy may be ethically and clinically appropriate in the New Zealand setting. The purpose of this document is to provide clinical guidance, and to promote consistent and equitable clinical care.

The following situations are excluded from this guideline:

  1. NGS performed as part of a clinical trial
  2. Standard of care diagnostic tests, e.g. BCR-ABL in CML and Ph+ ALL, ALK translocations in ALCL
  3. Testing for Ph-like ALL
  4. NGS where the primary intent is to detect or exclude a germline cancer predisposition.

Indications for consideration of NGS

  1. At diagnosis:
    1. NGS can detect druggable mutation missed by other diagnostic techniques such as FISH (and vice versa), e.g. NGS detected ALK and ROS translocations in inflammatory myofibroblastic tumour (IMT) following false negative FISH1.
    2. NGS may clarify indeterminate genetic results obtained by other methodologies, such as karyotypes where FISH is inconclusive2.
    3. If the diagnosis is not secure despite the standard work up2. Several groups have reported that NGS may lead to revision of the original diagnosis, with rates as high as 7% of refractory cases3 leading to successful treatment when the appropriate conventional therapy was used.
  2. Failure of standard therapy
    1. NGS and consideration of results may take weeks to many months. Initiation of 2nd line therapy for refractory or recurrent disease may be an indication to discuss NGS to enable timely initiation of 3rd line therapy.
    2. NGS is reasonable where mutations in that histology are associated with clinical responses to an appropriate targeted therapy, e.g. ALK mutations in neuroblastoma4, ROS translocations in IMT1.
    3. NGS is more sensitive than Sanger sequencing. NGS gene panels may therefore be preferable even if there is a single gene of interest5,6.
    4. If tumour material cannot be safely or reasonably obtained at relapse , NGS of cell free DNA has detected targetable paediatric mutations7, e.g. FoundationACT liquid biopsy.
  3. Consensus following a documented evidence based discussion in a Multi-Disciplinary Meeting (MDM).
  4. Failure of standard therapy or treating with palliative intent is not an automatic indication for NGS. Parent or patients may request NGS to ensure "no options are missed" even when NGS is not supported by an evidenced based discussion in a MDM. In these situations, the cost of NGS should be paid by the family or patient, but the treating centres should take all steps to facilitate the family's wishes.

Note: NGS is not indicated where families or individuals have declined further therapy.

Next-generation sequencing can generate clinical and ethical dilemmas8. NGS requires the documentation of a pre-test discussion in the written medical record. Where the primary goal is somatic sequencing a haematologist and/or oncologist is sufficient for pre-test discussions9. We recommend parents, and where applicable patients, sign the NCCN NGS consent form. The decision to perform NGS and pre-test discussions with the patient should consider:

  • The most likely outcome is that treatment will not be altered3,10-12.
  • Risk of technical failure or incorrect results particularly if the sample is suboptimal.
  • Discovery of variants of unknown significance (VUS), e.g. it may be unclear if mutations predict drug response, or unclear if germline VUS indicate a cancer predisposition.
  • Discovery of a variant that predicts clinical response to a targeted therapy does guarantee treatment with that drug. Reasons include: drug unavailable, no safe paediatric dose, drug contraindicated due to comorbidities, improvement or deterioration in clinical status, imminent death by the time the result or drug are available, response to other therapies, or superior evidence for alternative therapies11.
  • Discovery of variants associated with germline genetic disorders relevant to the patient and wider family that may induce anxiety or distress. With cancer gene panel sequencing the most common germline discovery is cancer predisposition, but other clinically relevant germline disorders or predispositions may be discovered9. A negative family history of premature cancer is arguably unreliable at excluding germline predisposition in paediatric cancer patients12,13. Return of incidental germline findings outside the goal of the NGS testing is controversial in pediatrics14-16 and risks vary based on the exact NGS methodology and reporting9,13. Some families may wish to have additional pre-test discussions with a Genetics service prior to testing if the probability of a germline cancer predisposition is high.
  • At the pre-test discussion families and patients should be given the opportunity to "opt out" from being advised of germline test results9. Parents should be advised that where germline test results significantly influence the treatment offered or other aspects of the care that a result will be disclosed. When such a situation arises, the treating physician should consult with colleagues to confirm disclosure is reasonable and document the discussion in the medical record.

Types of cancer NGS and providers

The ideal paediatric NGS test is not yet known and will certainly evolve. Broadly speaking gene panels are most common, and there are two major approaches:

  1. Tumour NGS sequences tumour material only. It may not be clear if mutations are germline or somatically acquired, e.g. Foundation Medicine.
  2. Tumour-Normal NGS sequences both tumour and normal (peripheral blood DNA). This approach may be more accurate in detecting somatic mutations. Germline NGS may avoid unnecessary anxiety that a mutation is somatically acquired and not inherited, or it may demonstrate that prompt referral to Genetics is appropriate.

All NGS assays, bioinformatics pipelines, and reports have strengths and limitations, and evolve over time so a particular provider may be preferable in specific situations. The ordering clinician must ensure the most appropriate test is ordered and understand the gene panel, analytic and curation pipeline. Pitfalls include absence of relevant regions, and pipelines that may not report therapeutically targetable mutations in the germline, e.g. RET mutations in medullary thyroid cancer. If research studies return NGS results to clinicians and families, consideration should be given to whether validation with a clinical grade assay is required.

Should relapse tissue be obtained for NGS?

Cancer genomes at diagnosis and relapse frequently differ. Therefore, NGS of tumour obtained at diagnosis, may miss targetable mutations that evolved at relapse such as ALK and RAS/MAPK mutations in neuroblastoma17,18. For this reason some precision medicine studies mandate or suggest repeat biopsy at relapse. However, the ultimate effect of repeat biopsy for the sole purpose of NGS and targeted therapy is not yet clear. Invasive procedures incur risks and discomfort, and the odds of NGS influencing treatment decisions and outcome are modest3,10,11 particularly if access to novel agents is limited. Therefore, the decision to obtain relapse tissue for the explicit purpose of NGS and targeted therapies should be made with caution, incorporate knowledge of the diagnostic and relapse genomes, drug availability, and must be endorsed in a multi-disciplinary meeting. Liquid biopsies have detected targetable mutations in paediatric solid tumours but sensitivity varied based on mutation7.

Interpretation of results and identification of a predictive biomarker

A fundamental debate in precision medicine is the level of evidence required to start a targeted therapy in a patient with limited therapeutic options8. While some paediatric groups have adopted relatively stringent criteria requiring robust evidence11, some other groups believe less stringent criteria are reasonable 3,10.

Interpretation of sequencing results should be discussed in a group setting. Where results are relatively straight forward email may be reasonable if all participants agree, but where there is uncertainty teleconference may be preferable. Discussions should be open to health professionals, and the minimum group should constitute 4 members:

  1. Primary oncologist
  2. A physician, pathologist, or scientist familiar with the relevant next-generation sequencing pipeline
  3. At least one member from the other Paediatric Oncology center to assist in providing equitable national practice.
  4. The clinical director at the treating center.

The following framework8 should be considered and discussed:

  1. Is there analytical validity?
  2. Is there clinical validity? Is there bioinformatic or experimental evidence19 that this gene and particular mutation are relevant to this disease?
  3. Is there evidence of clinical validity? Is there published evidence that this exact mutation is associated with a clinically meaningful response to a targeted therapy in this disease?
  4. Is there evidence of a safe dose for the patient age and weight, and adequate evidence of safety and tolerability?

MDM clinical decisions do not require universal agreement, but there should be a majority opinion that a treatment option is reasonable before that treatment is offered to the patient and family. If there is strong difference of opinion it is reasonable to consider broadening the discussion to include other team members.

Discussions and minutes should be recorded and considered educational. All evidence and expert opinion should be reviewed rigorously. An international expert opinion or anecdote is not sufficient evidence of efficacy, or proof that therapy is appropriate. International physicians may be invited to present unpublished data they believe to be compelling.

NCCN Molecular Therapeutics Symposium 2016 - Summary of Consensus

  1. Off-study next generation sequencing and targeted therapy may be an ethically and clinically reasonable option in the New Zealand setting; but on-study sequencing and treatment in New Zealand is preferred where available.
  2. Treating centers will not fund participation in phase 1 trials at international centers.
  3. Treating physicians will not insist patients participate in a clinical trial internationally, where equivalent diagnostic studies and molecular therapy can be prescribed off-study in New Zealand.
  4. No therapy should be prescribed unless a safe paediatric or adult dose is available.
  5. Tumour next-generation sequencing should generally be considered a trigger for involvement of the palliative care service to support Haematology-Oncology in treating the patient and family appropriately.
  6. Adolescents aged 16-18 years treated in adult services at other institutions should be considered for transfer to Christchurch or Auckland paediatric oncology for the express purpose of accessing resources only available at paediatric centers.

Resources for Researching Mutations

  • Gene name: HUGO
  • Variant check: Alamut, UCSC Genome Browser
  • Gene function: KEGG pathway, NCBI gene, UniProt
  • Germline associations: OMIM, GeneReviews
  • Gene and cancer: cBioPortal, COSMIC, Pediatric Cancer Genome Project/explore
  • Google
  • Variant: UniProt (domain), ESP, 1000 genomes, Exome Consortium
  • Variant germline: LOVD, ClinVar
  • Variant cancer: COSMIC, cBioPortal, Genomic Data Commons portal
  • Functional prediction: SIFT, Polyphen-2 (Humvar), etc.
  • My Cancer Genome (Vanderbilt)
  • MD Anderson personalized cancer therapy knowledge base
  • CIViC (U Washington, St. Louis)
  • NCI drug dictionary
  • COG website (study reports)
  • PubMed with record of search strategy to be presented
  • NCI Genomic Data Commons (GDC) is introducing Data Analysis, Visualization, and Exploration Tools, an online, open-access cancer research resource they're calling DAVE

Click here to open a printable pdf version of the NGS Consent Form for families.


  1. Lovly CM, Gupta A, Lipson D, et al. Inflammatory myofibroblastic tumors harbor multiple potentially actionable kinase fusions. Cancer Discov 2014;4:889-95.
  2. Mathias MD, Chou AJ, Meyers P, et al. Osteosarcoma With Apparent Ewing Sarcoma Gene Rearrangement. J Pediatr Hematol Oncol 2016;38:e166-8.
  3. Chang W, Brohl AS, Patidar R, et al. MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research. Clin Cancer Res 2016;22:3810-20.
  4. Mosse YP, Lim MS, Voss SD, 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;14:472-80.
  5. Dong L, Wang W, Li A, et al. Clinical Next Generation Sequencing for Precision Medicine in Cancer. Curr Genomics 2015;16:253-63.
  6. Bellini A, Bernard V, Leroy Q, et al. Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis. Clin Cancer Res 2015;21:4913-21.
  7. Combaret V, Iacono I, Bellini A, et al. Detection of tumor ALK status in neuroblastoma patients using peripheral blood. Cancer Med 2015;4:540-50.
  8. Hunter DJ. Uncertainty in the Era of Precision Medicine. N Engl J Med 2016;375:711-3.
  9. Robson ME, Bradbury AR, Arun B, et al. American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. J Clin Oncol 2015;33:3660-7.
  10. Ortiz MV, Kobos R, Walsh M, et al. Integrating Genomics Into Clinical Pediatric Oncology Using the Molecular Tumor Board at the Memorial Sloan Kettering Cancer Center. Pediatr Blood Cancer 2016;63:1368-74.
  11. Harris MH, DuBois SG, Glade Bender JL, 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.
  12. Parsons DW, Roy A, Yang Y, et al. Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol 2016.
  13. Zhang J, Walsh MF, Wu G, et al. Germline Mutations in Predisposition Genes in Pediatric Cancer. N Engl J Med 2015;373:2336-46.
  14. Ross LF, Rothstein MA, Clayton EW. Mandatory extended searches in all genome sequencing: "incidental findings," patient autonomy, and shared decision making. JAMA 2013;310:367-8.
  15. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-74.
  16. Clayton EW, McCullough LB, Biesecker LG, et al. Addressing the ethical challenges in genetic testing and sequencing of children. Am J Bioeth 2014;14:3-9.
  17. Schleiermacher G, Javanmardi N, Bernard V, et al. Emergence of new ALK mutations at relapse of neuroblastoma. J Clin Oncol 2014;32:2727-34.
  18. Eleveld TF, Oldridge DA, Bernard V, et al. Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations. Nat Genet 2015;47:864-71.
  19. Frohling S, Scholl C, Levine RL, et al. Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles. Cancer Cell 2007;12:501-13.

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Document Control

  • Date last published: 06 April 2018
  • Document type: Clinical Guideline
  • Services responsible: National Child Cancer Network
  • Owner: Andrew Wood
  • Review frequency: 2 years

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