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Childhood Cancer Genomics (PDQ®) 1/8 –Health Professional Version - National Cancer Institute

Childhood Cancer Genomics (PDQ®)–Health Professional Version - National Cancer Institute

National Cancer Institute

Childhood Cancer Genomics (PDQ®)–Health Professional Version







General Information About Childhood Cancer Genomics

Research teams from around the world have made remarkable progress in the past decade in elucidating the genomic landscape of most types of childhood cancer. A decade ago it was possible to hope that targetable oncogenes, such as activated tyrosine kinases, might be identified in a high percentage of childhood cancers. However, it is now clear that the genomic landscape of childhood cancer is highly varied, and in many cases is quite distinctive from that of the common adult cancers.
There are examples of genomic lesions that have provided immediate therapeutic direction, including the following:
  • NPM-ALK fusion genes associated with anaplastic large cell lymphoma cases.
  • ALK point mutations associated with a subset of neuroblastoma cases.
  • BRAF and other kinase genomic alterations associated with subsets of pediatric glioma cases.
  • Hedgehog pathway mutations associated with a subset of medulloblastoma cases.
  • ABL family genes activated by translocation in a subset of acute lymphoblastic leukemia (ALL) cases.
For some cancers, the genomic findings have been highly illuminating in the identification of genomically defined subsets of patients within histologies that have distinctive biological features and distinctive clinical characteristics (particularly in terms of prognosis). In some instances, identification of these subtypes has resulted in early clinical translation as exemplified by the WNT subgroup of medulloblastoma. Because of its excellent outcome, the WNT subgroup will be studied separately in future medulloblastoma clinical trials so that reductions in therapy can be evaluated with the goal of maintaining favorable outcome while reducing long-term morbidity. However, the prognostic significance of the recurring genomic lesions for some other cancers remains to be defined.
A key finding from genomic studies is the extent to which the molecular characteristics of childhood cancers correlate with their tissue (cell) of origin. As with most adult cancers, mutations in childhood cancers do not arise at random, but rather are linked in specific constellations to disease categories. A few examples include the following:
  • The presence of H3.3 and H3.1 K27M mutations almost exclusively among pediatric midline high-grade gliomas.
  • The loss of SMARCB1 in rhabdoid tumors.
  • The presence of RELA translocations in supratentorial ependymomas.
  • The presence of specific fusion proteins in different pediatric sarcomas.
Another theme across multiple childhood cancers is the contribution of mutations of genes involved in normal development of the tissue of origin of the cancer and the contribution of genes involved in epigenomic regulation.
Structural variations play an important role for many childhood cancers. Translocations resulting in oncogenic fusion genes or overexpression of oncogenes play a central role, particularly for the leukemias and sarcomas. However, for other childhood cancers that are primarily characterized by structural variations, functional fusion genes are not produced. Mechanisms by which these recurring structural variations have oncogenic effects have been identified for osteosarcoma (translocations confined to the first intron of TP53) and medulloblastoma (structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements leading to transcriptional activation [enhancer hijacking]).[1,2] However, the oncogenic mechanisms of action for recurring structural variations of other childhood cancers (e.g., the segmental chromosomal alterations in neuroblastoma) need to be elucidated.
Understanding of the contribution of germline mutations to childhood cancer etiology is being advanced by the application of whole-genome and exome sequencing to cohorts of children with cancer. Estimates for rates of pathogenic germline mutations approaching 10% have emerged from studies applying these sequencing methods to childhood cancer cohorts.[3-5] In some cases, the pathogenic germline mutations are clearly contributory to the patient’s cancer (e.g., TP53 mutations arising in the context of Li-Fraumeni syndrome), whereas in other cases the contribution of the germline mutation to the patient’s cancer is less clear (e.g., mutations in adult cancer predisposition genes such as BRCA1 and BRCA2 that have an undefined role in childhood cancer predisposition).[4,5] The frequency of germline mutations varies by tumor type (e.g., lower for neuroblastoma and higher for osteosarcoma),[5] and many of the identified germline mutations fit into known predisposition syndromes (e.g., DICER1 for pleuropulmonary blastoma, SMARCB1 and SMARCA4 for rhabdoid tumor and small cell ovarian cancer, TP53 for adrenocortical carcinoma and Li-Fraumeni syndrome cancers, RB1 for retinoblastoma, etc.). The germline contribution to the development of specific cancers is discussed in the disease-specific sections that follow.
Each section of this document is meant to provide readers with a brief summary of current knowledge about the genomic landscape of specific childhood cancers, an understanding that is critical in considering how to apply precision medicine concepts to childhood cancers.
References
  1. Northcott PA, Lee C, Zichner T, et al.: Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511 (7510): 428-34, 2014. [PUBMED Abstract]
  2. Chen X, Bahrami A, Pappo A, et al.: Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep 7 (1): 104-12, 2014. [PUBMED Abstract]
  3. Mody RJ, Wu YM, Lonigro RJ, et al.: Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth. JAMA 314 (9): 913-25, 2015. [PUBMED Abstract]
  4. 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 2 (5): 616-624, 2016. [PUBMED Abstract]
  5. Zhang J, Walsh MF, Wu G, et al.: Germline Mutations in Predisposition Genes in Pediatric Cancer. N Engl J Med 373 (24): 2336-46, 2015. [PUBMED Abstract]

Leukemias



Acute Lymphoblastic Leukemia (ALL)

The genomics of childhood ALL has been extensively investigated, and multiple distinctive subtypes have been defined on the basis of cytogenetic and molecular characterizations, each with its own pattern of clinical and prognostic characteristics.[1] Figure 1 illustrates the distribution of ALL cases by cytogenetic/molecular subtype.[1]
ENLARGEPie chart showing subclassification of childhood ALL.
Figure 1. Subclassification of childhood ALL. Blue wedges refer to B-progenitor ALL, yellow to recently identified subtypes of B-ALL, and red wedges to T-lineage ALL. Reprinted from Seminars in HematologyExit Disclaimer, Volume 50, Charles G. Mullighan, Genomic Characterization of Childhood Acute Lymphoblastic Leukemia, Pages 314–324, Copyright (2013), with permission from Elsevier.
The genomic landscape of B-ALL is typified by a range of genomic alterations that disrupt normal B-cell development and, in some cases, by mutations in genes that provide a proliferation signal (e.g., activating mutations in RAS family genes or mutations/translocations leading to kinase pathway signaling). Genomic alterations leading to blockage of B-cell development include translocations (e.g., TCF3-PBX1 and ETV6-RUNX1), point mutations (e.g., IKZF1 and PAX5), and intragenic/intergenic deletions (e.g., IKZF1, PAX5, EBF, and ERG).[2]
The genomic alterations in B-ALL tend not to occur at random, but rather to cluster within subtypes that can be delineated by biological characteristics such as their gene expression profiles. Cases with recurring chromosomal translocations (e.g., TCF3-PBX1 and ETV6-RUNX1, and KMT2A [MLL]-rearranged ALL) have distinctive biological features and illustrate this point, as do the examples below of specific genomic alterations within distinctive biological subtypes:
  • IKZF1 deletions and mutations are most commonly observed within cases of Philadelphia (Ph) chromosome–positive (Ph+) ALL and Ph-like (BCR-ABL1-like) ALL.[3,4]
  • Intragenic ERG deletions occur within a distinctive subtype characterized by gene rearrangements involving DUX4.[5,6]
  • TP53 mutations occur at high frequency in patients with low hypodiploid ALL with 32 to 39 chromosomes, and the TP53 mutations in these patients are often germline.[7] TP53 mutations are uncommon in other patients with B-ALL.
Activating point mutations in kinase genes are uncommon in high-risk B-ALL, and JAK genes are the primary kinases that are found to be mutated. These mutations are generally observed in patients with Ph-like ALL that have CRLF2 abnormalities, although JAK2 mutations are also observed in approximately 15% of children with Down syndrome ALL.[4,8,9] Several kinase genes and cytokine receptor genes are activated by translocations, as described below in the discussion of Ph+ ALL and Ph-like ALL. FLT3 mutations occur in a minority of cases (approximately 10%) of hyperdiploid ALL and KMT2A-rearranged ALL, and are rare in other subtypes.[10]
Understanding of the genomics of B-ALL at relapse is less advanced than understanding of ALL genomics at diagnosis. Childhood ALL is often polyclonal at diagnosis and under the selective influence of therapy, some clones may be extinguished and new clones with distinctive genomic profiles may arise.[11] Of particular importance are new mutations that arise at relapse that may be selected by specific components of therapy. As an example, mutations in NT5C2 are not found at diagnosis, whereas specific mutations in NT5C2 were observed in 7 of 44 (16%) and 9 of 20 (45%) cases of B-ALL with early relapse that were evaluated for this mutation.[11,12] NT5C2 mutations are uncommon in patients with late relapse, and they appear to induce resistance to mercaptopurine (6-MP) and thioguanine.[12] Another gene that is found mutated only at relapse is PRSP1, a gene involved in purine biosynthesis.[13] Mutations were observed in 13.0% of a Chinese cohort and 2.7% of a German cohort, and were observed in patients with on-treatment relapses. The PRSP1 mutations observed in relapsed cases induce resistance to thiopurines in leukemia cell lines. CREBBP mutations are also enriched at relapse and appear to be associated with increased resistance to glucocorticoids.[11,14] With increased understanding of the genomics of relapse, it may be possible to tailor upfront therapy to avoid relapse or detect resistance-inducing mutations early and intervene before a frank relapse.
Specific genomic and chromosomal alterations are described below, with a focus on their prognostic significance.
T-cell ALL is characterized by genomic alterations leading to activation of transcriptional programs related to T-cell development and by a high frequency of cases (approximately 60%) with mutations in NOTCH1 and/or FBXW7 that result in activation of the NOTCH1 pathway.[15] In contrast to B-ALL, the prognostic significance of T-cell ALL genomic alterations is less well-defined. Cytogenetic abnormalities common in B-lineage ALL (e.g., hyperdiploidy, 51–65 chromosomes) are rare in T-cell ALL.[16,17]

B-ALL cytogenetics/genomics

A number of recurrent chromosomal abnormalities have been shown to have prognostic significance, especially in B-ALL. Some chromosomal alterations are associated with more favorable outcomes, such as high hyperdiploidy (51–65 chromosomes) and the ETV6-RUNX1 fusion. Other alterations historically have been associated with a poorer prognosis, including the Ph chromosome (t(9;22)(q34;q11.2)), rearrangements of the KMT2A gene, hypodiploidy, and intrachromosomal amplification of the AML1 gene (iAMP21).[18]
In recognition of the clinical significance of many of these genomic alterations, the 2016 revision of the World Health Organization classification of tumors of the hematopoietic and lymphoid tissues lists the following entities for B-ALL:[19]
  • B-lymphoblastic leukemia/lymphoma, not otherwise specified (NOS).
  • B-lymphoblastic leukemia/lymphoma with recurrent genetic abnormalities.
  • B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2); BCR-ABL1.
  • B-lymphoblastic leukemia/lymphoma with t(v;11q23.3); KMT2A rearranged.
  • B-lymphoblastic leukemia/lymphoma with t(12;21)(p13.2;q22.1); ETV6-RUNX1.
  • B-lymphoblastic leukemia/lymphoma with hyperdiploidy.
  • B-lymphoblastic leukemia/lymphoma with hypodiploidy.
  • B-lymphoblastic leukemia/lymphoma with t(5;14)(q31.1;q32.3); IL3-IGH.
  • B-lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3); TCF3-PBX1.
  • Provisional entity: B-lymphoblastic leukemia/lymphoma, BCR-ABL1–like.
  • Provisional entity: B-lymphoblastic leukemia/lymphoma with iAMP21.
These and other chromosomal and genomic abnormalities for childhood ALL are described below.
  1. Chromosome number
    • High hyperdiploidy (51–65 chromosomes)
      High hyperdiploidy, defined as 51 to 65 chromosomes per cell or a DNA index greater than 1.16, occurs in 20% to 25% of cases of B-ALL, but very rarely in cases of T-cell ALL.[20] Hyperdiploidy can be evaluated by measuring the DNA content of cells (DNA index) or by karyotyping. In cases with a normal karyotype or in which standard cytogenetic analysis was unsuccessful, interphase fluorescence in situ hybridization (FISH) may detect hidden hyperdiploidy. High hyperdiploidy generally occurs in cases with clinically favorable prognostic factors (patients aged 1 to <10 years with a low white blood cell [WBC] count) and is an independent favorable prognostic factor.[20-22] Within the hyperdiploid range of 51 to 65 chromosomes, patients with higher modal numbers (58–66) appeared to have a better prognosis in one study.[22] Hyperdiploid leukemia cells are particularly susceptible to undergoing apoptosis and accumulate higher levels of methotrexate and its active polyglutamate metabolites,[23] which may explain the favorable outcome commonly observed in these cases.
      While the overall outcome of patients with high hyperdiploidy is considered to be favorable, factors such as age, WBC count, specific trisomies, and early response to treatment have been shown to modify its prognostic significance.[24,25]
      Patients with trisomies of chromosomes 4, 10, and 17 (triple trisomies) have been shown to have a particularly favorable outcome, as demonstrated by both Pediatric Oncology Group (POG) and Children's Cancer Group analyses of National Cancer Institute (NCI) standard-risk ALL.[26] POG data suggest that NCI standard-risk patients with trisomies of 4 and 10, without regard to chromosome 17 status, have an excellent prognosis.[27]
      Chromosomal translocations may be seen with high hyperdiploidy, and in those cases, patients are more appropriately risk-classified on the basis of the prognostic significance of the translocation. For instance, in one study, 8% of patients with the Ph chromosome (t(9;22)(q34;q11.2)) also had high hyperdiploidy,[28] and the outcome of these patients (treated without tyrosine kinase inhibitors) was inferior to that observed in non-Ph+ high hyperdiploid patients.
      Certain patients with hyperdiploid ALL may have a hypodiploid clone that has doubled (masked hypodiploidy).[29] These cases may be interpretable based on the pattern of gains and losses of specific chromosomes (hyperdiploidy with two and four copies of chromosomes rather than three copies). These patients have an unfavorable outcome, similar to those with hypodiploidy.[30]
      Near triploidy (68–80 chromosomes) and near tetraploidy (>80 chromosomes) are much less common and appear to be biologically distinct from high hyperdiploidy.[31] Unlike high hyperdiploidy, a high proportion of near tetraploid cases harbor a cryptic ETV6-RUNX1 fusion.[31-33] Near triploidy and tetraploidy were previously thought to be associated with an unfavorable prognosis, but later studies suggest that this may not be the case.[31,33]
      The genomic landscape of hyperdiploid ALL is characterized by mutations in genes of the receptor tyrosine kinase (RTK)/RAS pathway in approximately one-half of cases. Genes encoding histone modifiers are also present in a recurring manner in a minority of cases. Analysis of mutation profiles demonstrates that chromosomal gains are early events in the pathogenesis of hyperdiploid ALL.[34]
    • Hypodiploidy (<44 chromosomes)
      B-ALL cases with fewer than the normal number of chromosomes have been subdivided in various ways, with one report stratifying on the basis of modal chromosome number into the following four groups:[30]
      • Near-haploid: 24 to 29 chromosomes (n = 46).
      • Low-hypodiploid: 33 to 39 chromosomes (n = 26).
      • High-hypodiploid: 40 to 43 chromosomes (n = 13).
      • Near-diploid: 44 chromosomes (n = 54).
      Most patients with hypodiploidy are in the near-haploid and low-hypodiploid groups, and both of these groups have an elevated risk of treatment failure compared with nonhypodiploid cases.[30,35] Patients with fewer than 44 chromosomes have a worse outcome than do patients with 44 or 45 chromosomes in their leukemic cells.[30] A number of studies have shown that patients with high minimal residual disease (MRD) (≥0.01%) after induction do very poorly, with 5-year event-free survival (EFS) rates ranging from 25% to 47%. Although hypodiploid patients with low MRD after induction fare better (5-year EFS, 64%–75%), their outcomes are still inferior to most children with other types of ALL.[36-38]
      The recurring genomic alterations of near-haploid and low-hypodiploid ALL appear to be distinctive from each other and from other types of ALL.[7] In near-haploid ALL, alterations targeting RTK signaling, RAS signaling, and IKZF3 are common.[39] In low-hypodiploid ALL, genetic alterations involving TP53, RB1, and IKZF2 are common. Importantly, the TP53 alterations observed in low-hypodiploid ALL are also present in nontumor cells in approximately 40% of cases, suggesting that these mutations are germline and that low-hypodiploid ALL represents, in some cases, a manifestation of Li-Fraumeni syndrome.[7]
      Approximately two-thirds of patients with ALL and germline pathogenic TP53 variants have hypodiploid ALL.[40]
  2. Chromosomal translocations and gains/deletions of chromosomal segments
    • t(12;21)(p13.2;q22.1); ETV6-RUNX1 (formerly known as TEL-AML1)
      Fusion of the ETV6 gene on chromosome 12 to the RUNX1 gene on chromosome 21 is present in 20% to 25% of cases of B-ALL but is rarely observed in T-cell ALL.[32] The t(12;21)(p13;q22) produces a cryptic translocation that is detected by methods such as FISH, rather than conventional cytogenetics, and it occurs most commonly in children aged 2 to 9 years.[41,42] Hispanic children with ALL have a lower incidence of t(12;21)(p13;q22) than do white children.[43]
      Reports generally indicate favorable EFS and overall survival (OS) in children with the ETV6-RUNX1 fusion; however, the prognostic impact of this genetic feature is modified by the following factors:[44-48]
      • Early response to treatment.
      • NCI risk category (age and WBC count at diagnosis).
      • Treatment regimen.
      In one study of the treatment of newly diagnosed children with ALL, multivariate analysis of prognostic factors found age and leukocyte count, but not ETV6-RUNX1, to be independent prognostic factors.[44] It does not appear that the presence of secondary cytogenetic abnormalities, such as deletion of ETV6 (12p) or CDKN2A/B (9p), impacts the outcome of patients with the ETV6-RUNX1 fusion.[48,49] There is a higher frequency of late relapses in patients with ETV6-RUNX1 fusions compared with other B-ALL.[44,50] Patients with the ETV6-RUNX1 fusion who relapse seem to have a better outcome than other relapse patients,[51] with an especially favorable prognosis for patients who relapse more than 36 months from diagnosis.[52] Some relapses in patients with t(12;21)(p13;q22) may represent a new independent second hit in a persistent preleukemic clone (with the first hit being the ETV6-RUNX1 translocation).[53,54]
    • t(9;22)(q34.1;q11.2); BCR-ABL1 (Ph+)
      The Ph chromosome t(9;22)(q34.1;q11.2) is present in approximately 3% of children with ALL and leads to production of a BCR-ABL1 fusion protein with tyrosine kinase activity (refer to Figure 2).
      ENLARGEPhiladelphia chromosome; three-panel drawing shows a piece of chromosome 9 and a piece of chromosome 22 breaking off and trading places, creating a changed chromosome 22 called the Philadelphia chromosome. In the left panel, the drawing shows a normal chromosome 9 with the ABL gene and a normal chromosome 22 with the BCR gene. In the center panel, the drawing shows chromosome 9 breaking apart in the ABL gene and chromosome 22 breaking apart below the BCR gene. In the right panel, the drawing shows chromosome 9 with the piece from chromosome 22 attached and chromosome 22 with the piece from chromosome 9 containing part of the ABL gene attached. The changed chromosome 22 with the BCR-ABLgene is called the Philadelphia chromosome.
      Figure 2. The Philadelphia chromosome is a translocation between the ABL-1 oncogene (on the long arm of chromosome 9) and the BCR gene (on the long arm of chromosome 22), resulting in the fusion gene BCR-ABL1. BCR-ABL1 encodes an oncogenic protein with tyrosine kinase activity.
      This subtype of ALL is more common in older children with B-ALL and high WBC count, with the incidence of the t(9;22)(q34.1;q11.2) increasing to about 25% in young adults with ALL.
      Historically, the Ph chromosome t(9;22)(q34.1;q11.2) was associated with an extremely poor prognosis (especially in those who presented with a high WBC count or had a slow early response to initial therapy), and its presence had been considered an indication for allogeneic hematopoietic stem cell transplantation (HSCT) in patients in first remission.[28,55-57] Inhibitors of the BCR-ABL1 tyrosine kinase, such as imatinib mesylate, are effective in patients with Ph+ ALL.[58] A study by the Children's Oncology Group (COG), which used intensive chemotherapy and concurrent imatinib mesylate given daily, demonstrated a 5-year EFS rate of 70% (± 12%), which was superior to the EFS rate of historical controls in the pre-tyrosine kinase inhibitor (imatinib mesylate) era.[59,60]
    • t(v;11q23.3); KMT2A-rearranged
      Rearrangements involving the KMT2A gene occur in approximately 5% of childhood ALL cases overall, but in up to 80% of infants with ALL. These rearrangements are generally associated with an increased risk of treatment failure.[61-64] The t(4;11)(q21;q23) is the most common rearrangement involving the KMT2A gene in children with ALL and occurs in approximately 1% to 2% of childhood ALL.[62,65]
      Patients with the t(4;11)(q21;q23) are usually infants with high WBC counts; they are more likely than other children with ALL to have central nervous system (CNS) disease and to have a poor response to initial therapy.[66] While both infants and adults with the t(4;11)(q21;q23) are at high risk of treatment failure, children with the t(4;11)(q21;q23) appear to have a better outcome than either infants or adults.[61,62] Irrespective of the type of KMT2A gene rearrangement, infants with leukemia cells that have KMT2A gene rearrangements have a worse treatment outcome than older patients whose leukemia cells have a KMT2A gene rearrangement.[61,62] Whole-genome sequencing has determined that cases of infant ALL with KMT2A gene rearrangements have few additional genomic alterations, none of which have clear clinical significance.[10] Deletion of the KMT2A gene has not been associated with an adverse prognosis.[67]
      Of interest, the t(11;19)(q23;p13.3) involving KMT2A and MLLT1/ENL occurs in approximately 1% of ALL cases and occurs in both early B-lineage and T-cell ALL.[68] Outcome for infants with the t(11;19) is poor, but outcome appears relatively favorable in older children with T-cell ALL and the t(11;19).[68]
    • t(1;19)(q23;p13.3); TCF3-PBX1 and t(17;19)(q22;p13); TCF3-HLF
      The t(1;19) occurs in approximately 5% of childhood ALL cases and involves fusion of the TCF3 gene on chromosome 19 to the PBX1 gene on chromosome 1.[69,70] The t(1;19) may occur as either a balanced translocation or as an unbalanced translocation and is the primary recurring genomic alteration of the pre-B–ALL immunophenotype (cytoplasmic immunoglobulin positive).[71] Black children are relatively more likely than white children to have pre-B–ALL with the t(1;19).[72]
      The t(1;19) had been associated with inferior outcome in the context of antimetabolite-based therapy,[73] but the adverse prognostic significance was largely negated by more aggressive multiagent therapies.[70,74] However, in a trial conducted by St. Jude Children's Research Hospital (SJCRH) on which all patients were treated without cranial radiation, patients with the t(1;19) had an overall outcome comparable to children lacking this translocation, with a higher risk of CNS relapse and a lower rate of bone marrow relapse, suggesting that more intensive CNS therapy may be needed for these patients.[75,76]
      The t(17;19) resulting in the TCF3-HLF fusion occurs in less than 1% of pediatric ALL cases. ALL with the TCF3-HLF fusion is associated with disseminated intravascular coagulation and hypercalcemia at diagnosis. Outcome is very poor for children with the t(17;19), with a literature review noting mortality for 20 of 21 cases reported.[77] In addition to the TCF3-HLF fusion, the genomic landscape of this ALL subtype was characterized by deletions in genes involved in B-cell development (PAX5, BTG1, and VPREB1) and by mutations in RAS pathway genes (NRAS, KRAS, and PTPN11).[71]
    • DUX4-rearranged ALL with frequent ERG deletions
      Approximately 5% of standard-risk and 10% of high-risk pediatric B-ALL patients have a rearrangement involving DUX4 that leads to its overexpression.[5,6] The frequency in older adolescents (aged >15 years) is approximately 10%. The most common rearrangement produces IGH-DUX4 fusions, with ERG-DUX4 fusions also observed.[78] DUX4-rearranged cases show a distinctive gene expression pattern that was initially identified as being associated with focal deletions in ERG,[78-81] and one-half to more than two-thirds of DUX4-rearranged cases have focal intragenic deletions involving ERG that are not observed in other ALL subtypes.[5,78] ERG deletions often appear to be clonal, but using sensitive detection methodology, it appears that most cases are polyclonal.[78] IKZF1 alterations are observed in 20% to 40% of DUX4-rearranged ALL.[5,6]
      ERG deletion connotes an excellent prognosis, with OS rates exceeding 90%; even when the IZKF1 deletion is present, prognosis remains highly favorable.[79-81] While DUX4-rearranged ALL has an overall favorable prognosis, there is uncertainty as to whether this applies to both ERG-deleted and ERG-intact cases. In a study of 50 patients with DUX4-rearranged ALL, patients with ERG deletion detected by genomic polymerase chain reaction (PCR) (n = 33) had a more favorable EFS rate of approximately 90% than did patients with intact ERG (n = 17), with an EFS rate of approximately 70%.
    • MEF2D-rearranged ALL
      Gene fusions involving MEF2D, a transcription factor that is expressed during B-cell development, are observed in approximately 4% of childhood ALL cases.[82,83] Although multiple fusion partners may occur, most cases involve BCL9, which is located on chromosome 1q21, as is MEF2D.[82,84] The interstitial deletion producing the MEF2D-BCL9 fusion is too small to be detected by conventional cytogenetic methods. Cases with MEF2D gene fusions show a distinctive gene expression profile, except for rare cases with MEF2D-CSFR1 that have a Ph-like gene expression profile.[82,85] The median age at diagnosis for cases of MEF2D-rearranged ALL in studies that included both adult and pediatric patients was 12 to 14 years.[82,83] For 22 children with MEF2D-rearranged ALL enrolled in a high-risk ALL clinical trial, the 5-year EFS rate was 72% (standard error, ±10%), which was inferior to that for other patients.[82]
    • ZNF384-rearranged ALL
      ZNF384 is a transcription factor that is rearranged in approximately 4% to 5% of pediatric B-ALL cases.[82,86,87] Multiple fusion partners for ZNF384 have been reported, including ARID1B, CREBBP, EP300, SMARCA2, TAF15, and TCF3. Regardless of the fusion partner, ZNF384-rearranged ALL cases show a distinctive gene expression profile.[82,86,87] ZNF384 rearrangement does not appear to confer independent prognostic significance.[82,86,87] The immunophenotype of B-ALL with ZNF384 rearrangement is characterized by weak or negative CD10 expression, with expression of CD13 and/or CD33 commonly observed.[86,87] Cases of mixed phenotype acute leukemia (MPAL) (B/myeloid) that have ZNF384 gene fusions have been reported, [88,89] and a genomic evaluation of MPAL found that ZNF384 gene fusions were present in approximately one-half of B/myeloid cases.[90]
    • t(5;14)(q31.1;q32.3); IL3-IGH
      This entity is included in the 2016 revision of the WHO classification of tumors of the hematopoietic and lymphoid tissues.[19] The finding of t(5;14)(q31.1;q32.3) in patients with ALL and hypereosinophilia in the 1980s was followed by the identification of the IL3-IGH fusion as the underlying genetic basis for the condition.[91,92] The joining of the IGH locus to the promoter region of the IL3 gene leads to dysregulation of IL3 expression.[93] Cytogenetic abnormalities in children with ALL and eosinophilia are variable, with only a subset resulting from the IL3-IGH fusion.[94]
      The number of cases of IL3-IGH ALL described in the published literature is too small to assess the prognostic significance of the IL3-IGH fusion. Diagnosis of cases of IL3-IGH ALL may be delayed because it can present with hypereosinophilia in the absence of cytopenias and circulating blasts.[19]
    • Intrachromosomal amplification of chromosome 21 (iAMP21)
      iAMP21 is generally diagnosed using FISH and is defined by the presence of greater than or equal to five RUNX1 signals per cell (or ≥3 extra copies of RUNX1 on a single abnormal chromosome).[19] It occurs in approximately 2% of B-ALL cases and is associated with older age (median, approximately 10 years), presenting WBC of less than 50 × 109/L, a slight female preponderance, and high end-induction MRD.[95-97]
      The United Kingdom Acute Lymphoblastic Leukaemia (UKALL) clinical trials group initially reported that the presence of iAMP21 conferred a poor prognosis in patients treated in the MRC ALL 97/99 trial (5-year EFS, 29%).[18] In their subsequent trial (UKALL2003 [NCT00222612]), patients with iAMP21 were assigned to a more intensive chemotherapy regimen and had a markedly better outcome (5-year EFS, 78%).[96] Similarly, the COG has reported that iAMP21 was associated with a significantly inferior outcome in NCI standard-risk patients (4-year EFS, 73% for iAMP21 vs. 92% in others), but not in NCI high-risk patients (4-year EFS, 73% vs. 80%).[95] On multivariate analysis, iAMP21 was an independent predictor of inferior outcome only in NCI standard-risk patients.[95] The results of the UKALL2003 and COG studies suggest that treatment of iAMP21 patients with high-risk chemotherapy regimens abrogates its adverse prognostic significance and obviates the need for SCT in first remission.[97]
    • PAX5 alterations
      Gene expression analysis identified two distinctive ALL subsets with PAX5 genomic alterations, termed PAXalt and PAX p.Pro80Arg.[98] The alterations in the PAX5alt subtype included rearrangements, sequence mutations, and focal intragenic amplifications.
      PAX5 rearrangements have been reported to represent 2% to 3% of pediatric ALL.[99] More than 20 partner genes for PAX5 have been described,[98] with PAX5-ETV6, the primary genomic alteration in dic(9;12)(p13;p13),[100] being the most common gene fusion.[98]
      Intragenic amplification of PAX5 was identified in approximately 1% of B-ALL cases, and it was usually detected in cases lacking known leukemia-driver genomic alterations.[101] Cases with PAX5 amplification show male predominance (66%), with most (55%) having NCI high-risk status. For a cohort of patients with PAX5 amplification diagnosed between 1993 and 2015, the 5-year EFS rate was 49% (95% confidence interval [CI], 36%–61%), and the OS rate was 67% (95% CI, 54%–77%), suggesting a relatively poor prognosis for this B-ALL subtype.
      PAX5 with a p.Pro80Arg mutation shows a gene expression profile distinctive from that of other cases with PAX5 alterations.[98] Cases with PAX5 p.Pro80Arg appear to be more common in the adolescent and young adult (AYA) and adult populations (3%–4% frequency) than in children with NCI standard-risk or high-risk ALL (0.4% and 1.9% frequency, respectively). Outcome for the pediatric patients with PAX5 p.Pro80Arg and PAX5alt treated on a COG clinical trial appears to be intermediate (5-year EFS, approximately 75%).[98]
    • Ph-like (BCR-ABL1-like)
      BCR-ABL1–negative patients with a gene expression profile similar to BCR-ABL1–positive patients have been referred to as Ph-like.[102-104] This occurs in 10% to 20% of pediatric ALL patients, increasing in frequency with age, and has been associated with an IKZF1 deletion or mutation.[8,102,103,105,106]
      Retrospective analyses have indicated that patients with Ph-like ALL have a poor prognosis.[4,102] In one series, the 5-year EFS for NCI high-risk children and adolescents with Ph-like ALL was 58% and 41%, respectively.[4] While it is more frequent in older and higher-risk patients, the Ph-like subtype has also been identified in NCI standard-risk patients. In a COG study, 13.6% of 1,023 NCI standard-risk B-ALL patients were found to have Ph-like ALL; these patients had an inferior EFS compared with non–Ph-like standard-risk patients (82% vs. 91%), although no difference in OS (93% vs. 96%) was noted.[107] In one study of 40 Ph-like patients, the adverse prognostic significance of this subtype appeared to be abrogated when patients were treated with risk-directed therapy on the basis of MRD levels.[108]
      The hallmark of Ph-like ALL is activated kinase signaling, with 50% containing CRLF2 genomic alterations [104,109] and half of those cases containing concomitant JAK mutations.[110] Additional information about Ph-like ALL cases with CRLF2 genomic alterations is provided below.
      Many of the remaining cases of Ph-like ALL have been noted to have a series of translocations with a common theme of involvement of kinases, including ABL1, ABL2, CSF1R, JAK2, and PDGFRB.[4,105] Fusion proteins from these gene combinations have been noted in some cases to be transformative and have responded to tyrosine kinase inhibitors both in vitro and in vivo,[105] suggesting potential therapeutic strategies for these patients. The prevalence of targetable kinase fusions in Ph-like ALL is lower in NCI standard-risk patients (3.5%) than in NCI high-risk patients (approximately 30%).[107] Point mutations in kinase genes, aside from those in JAK1 and JAK2, are uncommon in Ph-like ALL cases.[8]
      Genomic alterations in CRLF2, a cytokine receptor gene located on the pseudoautosomal regions of the sex chromosomes, have been identified in 5% to 10% of cases of B-ALL; they represent approximately 50% of cases of Ph-like ALL.[111-113] The chromosomal abnormalities that commonly lead to CRLF2 overexpression include translocations of the IGH locus (chromosome 14) to CRLF2 and interstitial deletions in pseudoautosomal regions of the sex chromosomes, resulting in a P2RY8-CRLF2 fusion.[8,109,111,112] These two genomic alterations are associated with distinctive clinical and biological characteristics. The P2RY8-CRLF2 fusion is observed in 70% to 75% of pediatric patients with CRLF2 genomic alterations, and it occurs in younger patients (median age, approximately 4 years vs. 14 years for patients with IGH-CRLF2).[114,115] P2RY8-CRLF2 occurs not infrequently with established chromosomal abnormalities (e.g., hyperdiploidy, iAMP21, dic(9;20)), while IGH-CRLF2 is generally mutually exclusive with known cytogenetic subgroups. CRLF2 genomic alterations are observed in approximately 60% of patients with Down syndrome ALL, with P2RY8-CRLF2 fusions being more common than IGH-CRLF2 (approximately 80% vs. 20%).[112,114]
      CRLF2 abnormalities are strongly associated with the presence of IKZF1 deletions. Other recurring genomic alterations found in association with CRLF2 alterations include deletions in genes associated with B-cell differentiation (e.g., PAX5, BTG1, EBF1, etc.) and cell cycle control (CDKN2A), as well as genomic alterations activating JAK-STAT pathway signaling (e.g., IL7R and JAK mutations).[4,109,110,112,116]
      IGH-CRLF2 and P2RY8-CRLF2 commonly occur as an early event in B-ALL development and show clonal prevalence.[117] However, in some cases they appear to be a late event and show subclonal prevalence.[117] Loss of the CRLF2 genomic abnormality in some cases at relapse confirms the subclonal nature of the alteration in these cases.[114,118]
      Although the results of several retrospective studies suggest that CRLF2 abnormalities may have adverse prognostic significance on univariate analyses, most do not find this abnormality to be an independent predictor of outcome.[109,111,112,119,120] For example, in a large European study, increased expression of CRLF2 was not associated with unfavorable outcome in multivariate analysis, while IKZF1 deletion and Ph-like expression signatures were associated with unfavorable outcome.[106] Controversy exists about whether the prognostic significance of CRLF2 abnormalities should be analyzed on the basis of CRLF2 overexpression or on the presence of CRLF2 genomic alterations.[119,120]
      Approximately 9% of Ph-like ALL cases result from rearrangements that lead to overexpression of a truncated erythropoietin receptor (EPOR).[121] The C-terminal region of the receptor that is lost is the region that is mutated in primary familial congenital polycythemia and that controls stability of the EPOR. The portion of the EPOR remaining is sufficient for JAK-STAT activation and for driving leukemia development.
    • IKZF1 deletions
      IKZF1 deletions, including deletions of the entire gene and deletions of specific exons, are present in approximately 15% of B-ALL cases. Less commonly, IKZF1 can be inactivated by deleterious point mutations.[103] Cases with IKZF1 deletions tend to occur in older children, have a higher WBC count at diagnosis, and are therefore, more common in NCI high-risk patients than in NCI standard-risk patients.[2,103,116,122] A high proportion of Ph-like cases have a deletion of IKZF1,[3,116] and ALL arising in children with Down syndrome appears to have elevated rates of IKZF1 deletions.[123] IKZF1 deletions are also common in cases with CRLF2 genomic alterations and in Ph-like ALL.[79,102,116]
      Multiple reports have documented the adverse prognostic significance of an IKZF1 deletion, and most studies have reported that this deletion is an independent predictor of poor outcome on multivariate analyses.[79,102,103,106,116,124-129]; [130][Level of evidence: 2Di] However, the prognostic significance of IKZF1 may not apply equally across ALL biological subtypes, as illustrated by the apparent lack of prognostic significance in patients with ERG deletion.[79-81] Similarly, the prognostic significance of the IKZF1 deletion also appeared to be minimized in a cohort of COG patients with DUX4-rearranged ALL and with ERG transcriptional dysregulation that frequently occurred by ERG deletion.[6] The Associazione Italiana di Ematologia e Oncologia Pediatrica (AIEOP)–Berlin-Frankfurt-Münster (BFM) group reported that IKZF1 deletions were significant adverse prognostic factors only in B-ALL patients with high end-induction MRD and in whom co-occurrence of deletions of CDKN2A, CDKN2B, PAX5, or PAR1 (in the absence of ERG deletion) were identified.[131]
      There are few published results of changing therapy on the basis of IKZF1 gene status. The Malaysia-Singapore group published results of two consecutive trials. In the first trial (MS2003), IKZF1 status was not considered in risk stratification, while in the subsequent trial (MS2010), IKZF1-deleted patients were excluded from the standard-risk group. Thus, more IKZF1-deleted patients in the MS2010 trial received intensified therapy. Patients with IKZF1-deleted ALL had improved outcomes in MS2010 compared with patients in MS2003, but interpretation of this observation is limited by other changes in risk stratification and therapeutic differences between the two trials.[132][Level of evidence: 2A]

T-cell ALL cytogenetics/genomics

Multiple chromosomal translocations have been identified in T-cell ALL that lead to deregulated expression of the target genes. These chromosome rearrangements fuse genes encoding transcription factors (e.g., TAL1/TAL2, LMO1 and LMO2, LYL1, TLX1, TLX3, NKX2-I, HOXA, and MYB) to one of the T-cell receptor loci (or to other genes) and result in deregulated expression of these transcription factors in leukemia cells.[15,16,133-137] These translocations are often not apparent by examining a standard karyotype, but can be identified using more sensitive screening techniques, including FISH or PCR.[16] Mutations in a noncoding region near the TAL1 gene that produce a super-enhancer upstream of TAL1 represent nontranslocation genomic alterations that can also activate TAL1 transcription to induce T-cell ALL.[138]
Translocations resulting in chimeric fusion proteins are also observed in T-cell ALL.[139]
  • A NUP214-ABL1 fusion has been noted in 4% to 6% of T-cell ALL cases and is observed in both adults and children, with a male predominance.[140-142] The fusion is cytogenetically cryptic and is seen in FISH on amplified episomes or, more rarely, as a small homogeneous staining region.[142] T-cell ALL may also uncommonly show ABL1 fusion proteins with other gene partners (e.g., ETV6, BCR, and EML1).[142] ABL tyrosine kinase inhibitors, such as imatinib or dasatinib, may demonstrate therapeutic benefits in this T-cell ALL subtype,[140,141,143] although clinical experience with this strategy is very limited.[144-146]
  • Gene fusions involving SPI1 (encoding the transcription factor PU.1) were reported in 4% of Japanese children with T-cell ALL.[147] Fusion partners included STMN1 and TCF7. T-cell ALL cases with SPI1 fusions had a particularly poor prognosis; six of seven affected individuals died within 3 years of diagnosis of early relapse.
  • Other recurring gene fusions in T-cell ALL patients include those involving MLLT10, KMT2A, and NUP98.[15]
Notch pathway signaling is commonly activated by NOTCH1 and FBXW7 gene mutations in T-cell ALL, and these are the most commonly mutated genes in pediatric T-cell ALL.[15,148] NOTCH1-activating gene mutations occur in approximately 50% to 60% of T-cell ALL cases, and FBXW7-inactivating gene mutations occur in approximately 15% of cases, with the result that approximately 60% of cases have Notch pathway activation by mutations in at least one of these genes.[149]
The prognostic significance of NOTCH1/FBXW7 mutations may be modulated by genomic alterations in RAS and PTEN. The French Acute Lymphoblastic Leukaemia Study Group (FRALLE) and the Group for Research on Adult Acute Lymphoblastic Leukemia groups reported that patients having mutated NOTCH1/FBXW7 and wild-type PTEN/RAS constituted a favorable-risk group while patients with PTEN or RAS mutations, regardless of NOTCH1/FBXW7 status, have a significantly higher risk of treatment failure.[139,150] In the FRALLE study, 5-year cumulative incidence of relapse and disease-free survival (DFS) were 50% and 46% for patients with mutated NOTCH1/FBXW7 and mutated PTEN/RAS versus 13% and 87% for patients with mutated NOTCH1/FBXW7 and wild-type PTEN/RAS.[139] The overall 5-year DFS in the FRALLE study was 73%, and additional research is needed to determine whether the same prognostic significance for NOTCH1/FBXW7 and PTEN/RAS mutations will apply to current treatment regimens, which produce overall 5-year DFS rates that approach 90%.[151]
Early T-cell precursor ALL cytogenetics/genomics
Detailed molecular characterization of early T-cell precursor ALL showed this entity to be highly heterogeneous at the molecular level, with no single gene affected by mutation or copy number alteration in more than one-third of cases.[152] Compared with other T-cell ALL cases, the early T-cell precursor group had a lower rate of NOTCH1 mutations and significantly higher frequencies of alterations in genes regulating cytokine receptors and RAS signaling, hematopoietic development, and histone modification. The transcriptional profile of early T-cell precursor ALL shows similarities to that of normal hematopoietic stem cells and myeloid leukemia stem cells.[152]
Studies have found that the absence of biallelic deletion of the TCR-gamma locus (ABGD), as detected by comparative genomic hybridization and/or quantitative DNA-PCR, was associated with early treatment failure in patients with T-cell ALL.[153,154] ABGD is characteristic of early thymic precursor cells, and many of the T-cell ALL patients with ABGD have an immunophenotype consistent with the diagnosis of early T-cell precursor phenotype.

Mixed phenotype acute leukemia (MPAL) cytogenetics/genomics

For acute leukemias of ambiguous lineage, the WHO classification system is summarized in Table 1.[155,156] The criteria for lineage assignment for a diagnosis of MPAL are provided in Table 2.[19]
Table 1. Acute Leukemias of Ambiguous Lineage According to the World Health Organization Classification of Tumors of Hematopoietic and Lymphoid Tissuesa
ConditionDefinition
NOS = not otherwise specified.
aBéné MC: Biphenotypic, bilineal, ambiguous or mixed lineage: strange leukemias! Haematologica 94 (7): 891-3, 2009.[155] Obtained from Haematologica/the Hematology Journal website http://www.haematologica.orgExit Disclaimer.
Acute undifferentiated leukemiaAcute leukemia that does not express any marker considered specific for either lymphoid or myeloid lineage
Mixed phenotype acute leukemia with t(9;22)(q34;q11.2); BCR-ABL1Acute leukemia meeting the diagnostic criteria for mixed phenotype acute leukemia in which the blasts also have the (9;22) translocation or the BCR-ABL1 rearrangement
Mixed phenotype acute leukemia with t(v;11q23); KMT2A (MLL) rearrangedAcute leukemia meeting the diagnostic criteria for mixed phenotype acute leukemia in which the blasts also have a translocation involving the KMT2A gene
Mixed phenotype acute leukemia, B/myeloid, NOSAcute leukemia meeting the diagnostic criteria for assignment to both B and myeloid lineage, in which the blasts lack genetic abnormalities involving BCR-ABL1 or KMT2A
Mixed phenotype acute leukemia, T/myeloid, NOSAcute leukemia meeting the diagnostic criteria for assignment to both T and myeloid lineage, in which the blasts lack genetic abnormalities involving BCR-ABL1 or KMT2A
Mixed phenotype acute leukemia, B/myeloid, NOS—rare typesAcute leukemia meeting the diagnostic criteria for assignment to both B and T lineage
Other ambiguous lineage leukemiasNatural killer–cell lymphoblastic leukemia/lymphoma
Table 2. Lineage Assignment Criteria for Mixed Phenotype Acute Leukemia According to the 2016 Revision to the World Health Organization Classification of Myeloid Neoplasms and Acute Leukemiaa
LineageCriteria
aAdapted from Arber et al.[19]
bStrong defined as equal to or brighter than the normal B or T cells in the sample.
Myeloid lineageMyeloperoxidase (flow cytometry, immunohistochemistry, or cytochemistry); or monocytic differentiation (at least two of the following: nonspecific esterase cytochemistry, CD11c, CD14, CD64, lysozyme)
T lineageStrongb cytoplasmic CD3 (with antibodies to CD3 epsilon chain); or surface CD3
B lineageStrongb CD19 with at least one of the following strongly expressed: CD79a, cytoplasmic CD22, or CD10; or weak CD19 with at least two of the following strongly expressed: CD79a, cytoplasmic CD22, or CD10
The classification system for MPAL includes two entities that are defined by their primary molecular alteration: MPAL with BCR-ABL1 translocation and MPAL with KMT2A rearrangement. The genomic alterations associated with the MPAL, B/myeloid, NOS (B/M MPAL) and MPAL, T/myeloid, NOS (T/M MPAL) entities are distinctive, as described below:
  • B/M MPAL.
    • Among 115 MPAL cases for which genomic characterization was performed, 35 (30%) were B/M MPAL. There were an additional 16 MPAL cases (14%) with KMT2A rearrangements, 15 of whom showed a B/myeloid immunophenotype.
    • Approximately one-half of B/M MPAL cases had rearrangements of ZNF384 with recurrent fusion partners, including TCF3 and EP300. These cases had gene expression profiles indistinguishable from B-ALL cases with ZNF384 rearrangements.[90]
    • Approximately two-thirds of B/M MPAL cases had RAS pathway alterations, with NRAS and PTPN11 being the most commonly altered genes.[90]
    • Genes encoding epigenetic regulators (e.g., MLLT3, KDM6A, EP300, and CREBBP) are mutated in approximately two-thirds of B/M MPAL cases.[90]
  • T/M MPAL.
    • Among 115 MPAL cases for which genomic characterization was performed, 49 (43%) were T/M MPAL.[90] The genomic features of the T/M MPAL cases shared commonalities with those of early T-cell precursor (ETP) ALL, suggesting that T/M MPAL and ETP ALL are similar entities along the spectrum of immature leukemias.
    • Compared with T-cell ALL, T/M MPAL showed a lower rate of alterations in the core T-cell ALL transcription factors (TAL1, TAL2, TLX1, TLX3, LMO1, LMO2, NKX2-1, HOXA10, and LYL1) (63% vs. 16%, respectively).[90] A similar lower rate was also observed for ETP ALL.
    • CDKN2A/B and NOTCH1 mutations, which are present in approximately two-thirds of T-cell ALL cases, were much less common in T/M MPAL cases. By contrast, WT1 mutations occurred in approximately 40% of T/M MPAL, but in less than 10% of T-cell ALL cases.[90]
    • RAS and JAK-STAT pathway mutations were common in the T/M MPAL and ETP ALL cases, while the PI3K signaling pathway is more commonly altered in T-cell ALL.[90] For T/M MPAL, the most commonly mutated signaling pathway gene was FLT3 (43% of cases). FLT3 mutations tended to be mutually exclusive with RAS pathway mutations.
    • Genes encoding epigenetic regulators (e.g., EZH2 and PHF6) were mutated in approximately two-thirds of T/M MPAL cases.[90]

Gene polymorphisms in drug metabolic pathways

A number of polymorphisms of genes involved in the metabolism of chemotherapeutic agents have been reported to have prognostic significance in childhood ALL.[157-159] For example, patients with mutant phenotypes of thiopurine methyltransferase (TPMT, a gene involved in the metabolism of thiopurines, such as mercaptopurine), appear to have more favorable outcomes,[160] although such patients may also be at higher risk of developing significant treatment-related toxicities, including myelosuppression and infection.[161,162] Patients with homozygosity for TPMT variants associated with low enzymatic activity tolerate only very low doses of mercaptopurine (approximately 10% of the standard dose) and are treated with reduced doses of mercaptopurine to avoid excessive toxicity. Patients who are heterozygous for this mutant enzyme gene generally tolerate mercaptopurine without serious toxicity, but they do require more frequent dose reductions for hematologic toxicity than do patients who are homozygous for the normal allele.[163,164]
Germline variants in NUDT15 that reduce or abolish activity of this enzyme also lead to diminished tolerance to thiopurines.[163,165] The variants are most common in East Asians and Hispanics, and they are rare in Europeans and Africans. Patients homozygous for the risk variants tolerate only very low doses of mercaptopurine, while patients heterozygous for the risk alleles tolerate lower doses than do patients homozygous for the wild-type allele (approximately 25% dose reduction on average), but there is broad overlap in tolerated doses between the two groups.[163,166]
Gene polymorphisms may also affect the expression of proteins that play central roles in the cellular effects of anticancer drugs. As an example, patients who are homozygous for a polymorphism in the promoter region of CEP72 (a centrosomal protein involved in microtubule formation) are at increased risk of vincristine neurotoxicity.[167]
Genome-wide polymorphism analysis has identified specific single nucleotide polymorphisms associated with high end-induction MRD and risk of relapse. Polymorphisms of interleukin-15, as well as genes associated with the metabolism of etoposide and methotrexate, were significantly associated with treatment response in two large cohorts of ALL patients treated on SJCRH and COG protocols.[168] Polymorphic variants involving the reduced folate carrier and methotrexate metabolism have been linked to toxicity and outcome.[169,170] While these associations suggest that individual variations in drug metabolism can affect outcome, few studies have attempted to adjust for these variations; it is unknown whether individualized dose modification on the basis of these findings will improve outcome.
(Refer to the PDQ summary on Childhood Acute Lymphoblastic Leukemia Treatment for information about the treatment of childhood ALL.)

Acute Myeloid Leukemia (AML)

Comprehensive molecular profiling of pediatric and adult AML has shown that AML is a disease demonstrating both commonalities and differences across the age spectrum.[171,172]
  • Pediatric AML, in contrast to AML in adults, is typically a disease of recurring chromosomal alterations (refer to Table 3 for a list of common gene fusions).[171,173] Within the pediatric age range, certain gene fusions occur primarily in children younger than 5 years (e.g., NUP98 gene fusions, KMT2A gene fusions, and CBFA2T3-GLIS2), while others occur primarily in children aged 5 years and older (e.g., RUNX1-RUNX1T1, CBFB-MYH11, and NPM1-RARA).
  • Pediatric patients with AML have low rates of mutations, with most cases showing less than one somatic change in protein-coding regions per megabase.[172] This mutation rate is somewhat lower than that observed in adult AML and is much lower than the mutation rate for cancers that respond to checkpoint inhibitors (e.g., melanoma).[172]
  • The pattern of gene mutations differs between pediatric and adult AML cases. For example, IDH1/IDH2, TP53, RUNX1, and DNMT3A mutations are more common in adult AML than in pediatric AML, while NRAS and WT1 mutations are significantly more common in pediatric AML.[171,172]
Genetic analysis of leukemia blast cells (using both conventional cytogenetic methods and molecular methods) is performed on children with AML because both chromosomal and molecular abnormalities are important diagnostic and prognostic markers.[173-179] Clonal chromosomal abnormalities are identified in the blasts of about 75% of children with AML and are useful in defining subtypes with both prognostic and therapeutic significance.
Detection of molecular abnormalities can also aid in risk stratification and treatment allocation. For example, mutations of NPM and CEBPA are associated with favorable outcomes while certain mutations of FLT3 portend a high risk of relapse, and identifying the latter mutations may allow for targeted therapy.[180-183]
The 2016 revision to the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia emphasizes that recurrent chromosomal translocations in pediatric AML may be unique or have a different prevalence than in adult AML.[19] The pediatric AML chromosomal translocations that are found by conventional chromosome analysis and those that are cryptic (identified only with fluorescence in situ hybridization or molecular techniques) occur at higher rates than in adults. These recurrent translocations are summarized in Table 3.[19] Table 3 also shows, in the bottom three rows, additional relatively common recurrent translocations observed in children with AML.[177,178,184]
Table 3. Common Pediatric Acute Myeloid Leukemia (AML) Chromosomal Translocations
Gene Fusion ProductChromosomal TranslocationPrevalence in Pediatric AML (%)
aCryptic chromosomal translocation.
KMT2A (MLL) translocated11q23.325.0
NUP98-NSD1at(5;11)(q35.3;p15.5)7.0
CBFA2T3-GLIS2ainv(16)(p13.3;q24.3)3.0
NUP98-KDM5A4at(11;12)(p15.5;p13.5)3.0
DEK-NUP214t(6;9)(p23;q34.1)1.7
RBM15(OTT)-MKL1(MAL)t(1;22)(p13.3;q13.1)0.8
MNX1-ETV6t(7;12)(q36.3;p13.2)0.8
KAT6A-CREBBPt(8;16)(p11.2;p13.3)0.5
RUNX1-RUNX1T1t(8;21)(q22;q22)13–14
CBFB-MYH11inv(16)(p13.1;q22) or t(16;16)(p13.1;q22)4–9
PML-RARAt(15;17)(q24;q21)6–11
The genomic landscape of pediatric AML cases can change from diagnosis to relapse, with mutations detectable at diagnosis dropping out at relapse and, conversely, with new mutations appearing at relapse. In a study of 20 cases for which sequencing data were available at diagnosis and relapse, a key finding was that the variant allele frequency at diagnosis strongly correlated with persistence of mutations at relapse.[185] Approximately 90% of the diagnostic variants with variant allele frequency greater than 0.4 persisted to relapse, compared with only 28% with variant allele frequency less than 0.2 (P < .001). This observation is consistent with previous results showing that presence of the FLT3-ITD mutation predicted for poor prognosis only when there was a high FLT3-ITD allelic ratio.
Specific recurring cytogenetic and molecular abnormalities are briefly described below. The abnormalities are listed by those in clinical use that identify patients with favorable or unfavorable prognosis, followed by other abnormalities. The nomenclature of the 2016 revision to the WHO classification of myeloid neoplasms and acute leukemia is incorporated for disease entities where relevant.

Molecular abnormalities associated with a favorable prognosis

Molecular abnormalities associated with a favorable prognosis include the following:
  • Core-binding factor (CBF) AML includes cases with RUNX1-RUNX1T1 and CBFB-MYH11 fusion genes that disrupt the activity of core-binding factor, which contains RUNX1 and CBFB. These are specific entities in the 2016 revision to the WHO classification of myeloid neoplasms and acute leukemia.
    • AML with t(8;21)(q22;q22.1); RUNX1-RUNX1T1: In leukemias with t(8;21), the RUNX1 (AML1) gene on chromosome 21 is fused with the RUNX1T1 (ETO) gene on chromosome 8. The t(8;21) translocation is associated with the FAB M2 subtype and with granulocytic sarcomas.[186,187] Adults with t(8;21) have a more favorable prognosis than do adults with other types of AML.[174,188] Children with t(8;21) have a more favorable outcome than do children with AML characterized by normal or complex karyotypes,[174,189-191] with 5-year overall survival (OS) of 74% to 90%.[177,178,192] The t(8;21) translocation occurs in approximately 12% of children with AML.[177,178,192]
    • AML with inv(16)(p13.1;q22) or t(16;16)(p13.1;q22); CBFB-MYH11: In leukemias with inv(16), the CBFB gene at chromosome band 16q22 is fused with the MYH11 gene at chromosome band 16p13. The inv(16) translocation is associated with the FAB M4Eo subtype.[193] Inv(16) confers a favorable prognosis for both adults and children with AML,[174,189-191] with a 5-year OS of about 85%.[177,178] Inv(16) occurs in 7% to 9% of children with AML.[177,178,192] As noted above, cases with CBFB-MYH11 and cases with RUNX1-RUNX1T1 have distinctive secondary mutations; CBFB-MYH11 secondary mutations are primarily restricted to genes that activate receptor tyrosine kinase signaling (NRAS, FLT3, and KIT).[194,195]
    • AML with t(16;21)(q24;q22); RUNX1-CBFA2T3: In leukemias with t(16;21)(q24;q22), the RUNX1 gene is fused with the CBFA2T3 gene, and the gene expression profile is closely related to that of AML cases with t(8;21) and RUNX1-RUNX1T1.[196] These patients present at a median age of 7 years and are rare, representing approximately 0.1% to 0.3% of pediatric AML cases. Among 23 patients with RUNX1-CBFA2T3, five presented with secondary AML, including two patients who had a primary diagnosis of Ewing sarcoma. Outcome for the cohort of 23 patients was favorable, with a 4-year EFS of 77% and a cumulative incidence of relapse of 0%.[196]
    Both RUNX1-RUNX1T1 and CBFB-MYH11 subtypes commonly show mutations in genes that activate receptor tyrosine kinase signaling (e.g., NRAS, FLT3, and KIT); NRAS and KIT are the most commonly mutated genes for both subtypes. KIT mutations may indicate increased risk of treatment failure for patients with core-binding factor AML, although the prognostic significance of KIT mutations may be dependent on the mutant-allele ratio (high ratio unfavorable) and/or the specific type of mutation (exon 17 mutations unfavorable).[194,195] A study of children with RUNX1-RUNX1T1 AML observed KIT mutations in 24% of cases (79% being exon 17 mutations) and RAS mutations in 15%, but neither were significantly associated with outcome.[192]
    Although both RUNX1-RUNX1T1 and CBFB-MYH11 fusion genes disrupt the activity of core-binding factor, cases with these genomic alterations have distinctive secondary mutations.[194,195]
    • RUNX1-RUNX1T1 cases also have frequent mutations in genes regulating chromatin conformation (e.g., ASXL1 and ASXL2) (40% of cases) and genes encoding members of the cohesin complex (20% of cases). Mutations in ASXL1 and ASXL2 and mutations in members of the cohesin complex are rare in CBFB-MYH11 leukemias.[194,195]
    • A study of 204 adults with RUNX1-RUNX1T1 AML found that ASXL2 mutations (present in 17% of cases) and ASXL1 or ASXL2 mutations (present in 25% of cases) lacked prognostic significance.[197] Similar results, albeit with smaller numbers, were reported for children with RUNX1-RUNX1T1 AML and ASXL1 and ASXL2 mutations.[198]
  • Acute promyelocytic leukemia (APL) with PML-RARA: APL represents about 7% of children with AML.[178,199] AML with t(15;17) is invariably associated with APL, a distinct subtype of AML that is treated differently than other types of AML because of its marked sensitivity to arsenic trioxide and the differentiating effects of all-trans retinoic acid. The t(15;17) translocation or other more complex chromosomal rearrangements may lead to the production of a fusion protein involving the retinoid acid receptor alpha and PML.[200] The WHO 2016 revision does not include the t(15;17) cytogenetic designation to stress the significance of the PML-RARA fusion, which may be cryptic or result from complex karyotypic changes.[19]
    Utilization of quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) for PML-RARA transcripts has become standard practice.[201] Quantitative RT-PCR allows identification of the three common transcript variants and is used for monitoring response on treatment and early detection of molecular relapse.[202] Other much less common translocations involving the retinoic acid receptor alpha can also result in APL (e.g., t(11;17)(q23;q21) involving the PLZF gene).[203-205] Identification of cases with the t(11;17)(q23;q21) is important because of their decreased sensitivity to all-trans retinoic acid.[200,203]
  • AML with mutated NPM1: NPM1 is a protein that has been linked to ribosomal protein assembly and transport as well as being a molecular chaperone involved in preventing protein aggregation in the nucleolus. Immunohistochemical methods can be used to accurately identify patients with NPM1 mutations by the demonstration of cytoplasmic localization of NPM.[206] Mutations in the NPM1 protein that diminish its nuclear localization are primarily associated with a subset of AML with a normal karyotype, absence of CD34 expression,[207] and an improved prognosis in the absence of FLT3–internal tandem duplication (ITD) mutations in adults and younger adults.[207-212]
    Studies of children with AML suggest a lower rate of occurrence of NPM1 mutations in children compared with adults with normal cytogenetics. NPM1 mutations occur in approximately 8% of pediatric patients with AML and are uncommon in children younger than 2 years.[180,181,213,214] NPM1 mutations are associated with a favorable prognosis in patients with AML characterized by a normal karyotype.[180,181,214] For the pediatric population, conflicting reports have been published regarding the prognostic significance of an NPM1 mutation when a FLT3-ITD mutation is also present. One study reported that an NPM1 mutation did not completely abrogate the poor prognosis associated with having a FLT3-ITD mutation,[180,215] but other studies showed no impact of a FLT3-ITD mutation on the favorable prognosis associated with an NPM1 mutation.[172,181,214]
  • AML with biallelic mutations of CEBPA: Mutations in the CEBPA gene occur in a subset of children and adults with cytogenetically normal AML.[216] In adults younger than 60 years, approximately 15% of cytogenetically normal AML cases have mutations in CEBPA.[211] Outcomes for adults with AML with CEBPA mutations appear to be relatively favorable and similar to that of patients with core-binding factor leukemias.[211,217] Studies in adults with AML have demonstrated that CEBPA double-mutant, but not single-mutant, AML is independently associated with a favorable prognosis,[218-221] leading to the WHO 2016 revision that requires biallelic mutations for the disease definition.[19]
    CEBPA mutations occur in 5% to 8% of children with AML and have been preferentially found in the cytogenetically normal subtype of AML with FAB M1 or M2; 70% to 80% of pediatric patients have double-mutant alleles, which is predictive of a significantly improved survival, similar to the effect observed in adult studies.[182,222] Although both double-mutant and single-mutant alleles of CEBPA were associated with a favorable prognosis in children with AML in one large study,[182] a second study observed inferior outcome for patients with single CEBPA mutations.[222] However, very low numbers of children with single-allele mutants were included in these two studies (only 13 total patients), which makes a conclusion regarding the prognostic significance of single-allele CEBPA mutations in children premature.[182] In newly diagnosed patients with double-mutant CEBPA AML, germline screening should be considered in addition to usual family history queries, because 5% to 10% of these patients are reported to have a germline CEBPA mutation.[216]
  • Myeloid leukemia associated with Down syndrome (GATA1 mutations): GATA1 mutations are present in most, if not all, Down syndrome children with either transient abnormal myelopoiesis (TAM) or acute megakaryoblastic leukemia (AMKL).[223-226] GATA1 mutations were also observed in 9% of non–Down syndrome children and 4% of adults with AMKL (with coexistence of amplification of the Down syndrome Critical Region on chromosome 21 in 9 of 10 cases).[227] GATA1 is a transcription factor that is required for normal development of erythroid cells, megakaryocytes, eosinophils, and mast cells.[228]
    GATA1 mutations confer increased sensitivity to cytarabine by down-regulating cytidine deaminase expression, possibly providing an explanation for the superior outcome of children with Down syndrome and M7 AML when treated with cytarabine-containing regimens.[229]

Molecular abnormalities associated with an unfavorable prognosis

Molecular abnormalities associated with an unfavorable prognosis include the following:
  • Chromosomes 5 and 7: Chromosomal abnormalities associated with poor prognosis in adults with AML include those involving chromosome 5 (monosomy 5 and del(5q)) and chromosome 7 (monosomy 7).[174,188,230] These cytogenetic subgroups represent approximately 2% and 4% of pediatric AML cases, respectively, and are also associated with poor prognosis in children.[177,188,230-234]
    In the past, patients with del(7q) were also considered to be at high risk of treatment failure, and data from adults with AML support a poor prognosis for both del(7q) and monosomy 7.[179] However, outcome for children with del(7q), but not monosomy 7, appears comparable to that of other children with AML.[178,233] The presence of del(7q) does not abrogate the prognostic significance of favorable cytogenetic characteristics (e.g., inv(16) and t(8;21)).[174,233,235]
    Chromosome 5 and 7 abnormalities appear to lack prognostic significance in AML patients with Down syndrome who are aged 4 years and younger.[236]
  • AML with inv(3)(q21.3;q26.2) or t(3;3)(q21.3;q26.2); GATA2, MECOM: MECOM at chromosome 3q26 codes for two proteins, EVI1 and MDS1-EVI1, both of which are transcription regulators. The inv(3) and t(3;3) abnormalities lead to overexpression of EVI1 and to reduced expression of GATA2.[237,238] These abnormalities are associated with poor prognosis in adults with AML,[174,188,239] but are very uncommon in children (<1% of pediatric AML cases).[177,190,240]
    Abnormalities involving MECOM can be detected in some AML cases with other 3q abnormalities and are also associated with poor prognosis.
  • FLT3 mutations: Presence of a FLT3-ITD mutation appears to be associated with poor prognosis in adults with AML,[241] particularly when both alleles are mutated or there is a high ratio of the mutant allele to the normal allele.[242,243] FLT3-ITD mutations also convey a poor prognosis in children with AML.[183,215,244-247] The frequency of FLT3-ITD mutations in children is lower than that observed in adults, especially for children younger than 10 years, for whom 5% to 10% of cases have the mutation (compared with approximately 30% in adults).[246-248]
    The prognostic significance of FLT3-ITD is modified by the presence of other recurring genomic alterations. The prevalence of FLT3-ITD is increased in certain genomic subtypes of pediatric AML, including those with the NUP98-NSD1 fusion gene, of which 80% to 90% have FLT3-ITD.[249,250] Approximately 15% of patients with FLT3-ITD have NUP98-NSD1, and patients with both FLT3-ITD and NUP98-NSD1 have a poorer prognosis than do patients who have FLT3-ITD without NUP98-NSD1.[250] For patients who have FLT3-ITD, the presence of either WT1 mutations or NUP98-NSD1 fusions is associated with poorer outcome (EFS rates below 25%) than for patients who have FLT3-ITD without these alterations.[172] Conversely, when FLT3-ITD is accompanied by NPM1 mutations, the outcome is relatively favorable and is similar to that of pediatric AML cases without FLT3-ITD.[172]
    For APL, FLT3-ITD and point mutations occur in 30% to 40% of children and adults.[242,245,246,251-255] Presence of the FLT3-ITD mutation is strongly associated with the microgranular variant (M3v) of APL and with hyperleukocytosis.[245,253,256,257] It remains unclear whether FLT3 mutations are associated with poorer prognosis in patients with APL who are treated with modern therapy that includes all-trans retinoic acid and arsenic trioxide.[251,252,255,256,258-261]
    Activating point mutations of FLT3 have also been identified in both adults and children with AML, although the clinical significance of these mutations is not clearly defined. Some of these point mutations appear to be specific to pediatric patients.[172]
  • AML with t(16;21)(p11;q22); FUS-ERG: In leukemias with t(16;21)(p11;q22), the FUS gene is joined with the ERG gene, producing a distinctive AML subtype with a gene expression profile that clusters separately from other cytogenetic subgroups.[196] These patients present at a median age of 8 to 9 years and are rare, representing approximately 0.3% to 0.5% of pediatric AML cases. For a cohort of 31 patients with FUS-ERG AML, outcome was poor, with a 4-year EFS of 7% and a cumulative incidence of relapse of 74%.[196]

Other molecular abnormalities observed in pediatric AML

Other molecular abnormalities observed in pediatric AML include the following:
  • KMT2A (MLL) gene rearrangements: KMT2A gene rearrangement occurs in approximately 20% of children with AML.[177,178] These cases, including most AMLs secondary to epipodophyllotoxin,[262] are generally associated with monocytic differentiation (FAB M4 and M5). KMT2A rearrangements are also reported in approximately 10% of FAB M7 (AMKL) patients (see below).[227,263]
    The most common translocation, representing approximately 50% of KMT2A-rearranged cases in the pediatric AML population, is t(9;11)(p22;q23), in which the KMT2A gene is fused with MLLT3(AF9) gene.[264] The WHO 2016 revision defined AML with t(9;11)(p21.3;q23.3); MLLT3-KMT2A as a distinctive disease entity. However, more than 50 different fusion partners have been identified for the KMT2A gene in patients with AML.
    The median age for 11q23/KMT2A-rearranged cases in children is approximately 2 years, and most translocation subgroups have a median age at presentation of younger than 5 years.[264] However, significantly older median ages are seen at presentation of pediatric cases with t(6;11)(q27;q23) (12 years) and t(11;17)(q23;q21) (9 years).[264]
    Outcome for patients with de novo AML and KMT2A gene rearrangement is generally reported as being similar to that for other patients with AML.[174,177,264,265] However, as the KMT2A gene can participate in translocations with many different fusion partners, the specific fusion partner appears to influence prognosis, as demonstrated by a large international retrospective study evaluating outcome for 756 children with 11q23- or KMT2A-rearranged AML.[264] For example, cases with t(1;11)(q21;q23), representing 3% of all 11q23/KMT2A-rearranged AML, showed a highly favorable outcome, with a 5-year event-free survival (EFS) of 92%.
    While reports from single clinical trial groups have variably described more favorable prognosis for patients with AML who have t(9;11)(p21.3;q23.3)/MLLT3-KMT2A, the international retrospective study did not confirm the favorable prognosis for this subgroup.[174,177,264,266-268] An international collaboration evaluating pediatric AMKL patients observed that the presence of t(9;11), which was seen in approximately 5% of AMKL cases, was associated with an inferior outcome compared with other AMKL cases.[263]
    KMT2A-rearranged AML subgroups that appear to be associated with poor outcome include the following:
    • Cases with the t(10;11) translocation are a group at high risk of relapse in bone marrow and the CNS.[174,178,269] Some cases with the t(10;11) translocation have fusion of the KMT2A gene with the AF10-MLLT10 at 10p12, while others have fusion of KMT2A with ABI1 at 10p11.2.[270,271] An international retrospective study found that these cases, which present at a median age of approximately 1 year, have a 5-year EFS of 20% to 30%.[264]
    • Patients with t(6;11)(q27;q23) have a poor outcome, with a 5-year EFS of 11%.
    • Patients with t(4;11)(q21;q23) also have a poor outcome, with a 5-year EFS of 29%.[264]
    • A follow-up study by the international collaborative group demonstrated that additional cytogenetic abnormalities further influenced outcome of children with KMT2A translocations, with complex karyotypes and trisomy 19 predicting poor outcome and trisomy 8 predicting a more favorable outcome.[272]
  • AML with t(6;9)(p23;q34.1); DEK-NUP214: t(6;9) leads to the formation of a leukemia-associated fusion protein DEK-NUP214.[273,274] This subgroup of AML has been associated with a poor prognosis in adults with AML,[273,275,276] and occurs infrequently in children (less than 1% of AML cases). The median age of children with DEK-NUP214 AML is 10 to 11 years, and approximately 40% of pediatric patients have FLT3-ITD.[277,278]
    t(6;9) AML appears to be associated with a high risk of treatment failure in children, particularly for those not proceeding to allogeneic stem cell transplantation.[177,274,277,278]
  • Molecular subgroups of non–Down syndrome acute megakaryoblastic leukemia (AMKL): AMKL accounts for approximately 10% of pediatric AML and includes substantial heterogeneity at the molecular level. Molecular subtypes of AMKL are listed below.
    • CBFA2T3-GLIS2: CBFA2T3-GLIS2 is a fusion resulting from a cryptic chromosome 16 inversion (inv(16)(p13.3q24.3)).[279-283] It occurs almost exclusively in non–Down syndrome AMKL, representing 16% to 27% of pediatric AMKL and presenting with a median age of 1 year.[227,281,284,285] It appears to be associated with unfavorable outcome,[227,279,283-285] with EFS at 2 years less than 20% in two reports that included 28 patients.[227,283,285]
    • KMT2A-rearranged: Cases with KMT2A translocations represent 10% to 17% of pediatric AMKL, with MLLT3 (AF9) being the most common KMT2A fusion partner.[227,263,284] KMT2A-rearranged cases appear to be associated with inferior outcome among children with AMKL, with OS rates at 4 to 5 years of approximately 30%.[227,263,284] An international collaboration evaluating pediatric AMKL observed that the presence of t(9;11)/MLLT3-KMT2A, which was seen in approximately 5% of AMKL cases (n = 21), was associated with an inferior outcome (5-year OS, approximately 20%) compared with other AMKL cases and other KMT2A-rearrangements (n = 17), each with a 5-year OS of 50% to 55%.[263] Inferior outcome was not observed for patients (n = 17) with other KMT2A-rearrangements.
    • NUP98-KDM5A4: NUP98-KDM5A4 is observed in approximately 10% of pediatric AMKL cases [227,284] and is observed at much lower rates in non-AMKL cases.[285] NUP98-KDM5A4 cases showed a trend towards inferior prognosis, although the small number of cases studied limits confidence in this assessment.[227,284]
    • RBM15-MKL1: The t(1;22)(p13;q13) translocation that produces RBM15-MKL1 is uncommon (<1% of pediatric AML) and is restricted to acute megakaryocytic leukemia (AMKL).[177,285-290] Studies have found that t(1;22)(p13;q13) is observed in 10% to 18% of children with AMKL who have evaluable cytogenetics or molecular genetics.[227,263,284] Most AMKL cases with t(1;22) occur in infants, with the median age at presentation (4–7 months) being younger than that for other children with AMKL.[263,281,291] Cases with detectable RBM15-MKL1 fusion transcripts in the absence of t(1;22) have also been reported because these young patients usually have hypoplastic bone marrow.[288]
      An international collaborative retrospective study of 51 t(1;22) cases reported that patients with this abnormality had a 5-year EFS of 54.5% and an OS of 58.2%, similar to the rates for other children with AMKL.[263] In another international retrospective analysis of 153 cases with non–Down syndrome AMKL who had samples available for molecular analysis, the 4-year EFS for patients with t(1;22) was 59% and OS was 70%, significantly better than AMKL patients with other specific genetic abnormalities (CBFA2T3/GUS2, NUP98/KDM5A4, KMT2A rearrangements, monosomy 7).[284]
    • HOX-rearranged: Cases with a gene fusion involving a HOX cluster gene represented 15% of pediatric AMKL in one report.[227] This report observed that these patients appear to have a relatively favorable prognosis, although the small number of cases studied limits confidence in this assessment.
    • GATA1 mutated: GATA1-truncating mutations in non–Down syndrome AMKL arise in young children (median age, 1–2 years) and are associated with amplification of the Down syndrome critical region on chromosome 21.[227] These patients represented approximately 10% of non–Down syndrome AMKL and appeared to have a favorable outcome if there were no prognostically unfavorable fusion genes also present, although the number of patients studied was small (n = 8).[227]
  • t(8;16) (MYST3-CREBBP): The t(8;16) translocation fuses the MYST3 gene on chromosome 8p11 to CREBBP on chromosome 16p13. t(8;16) AML rarely occurs in children. In an international Berlin-Frankfurt-Münster (BFM) AML study of 62 children, presence of this translocation was associated with younger age at diagnosis (median, 1.2 years), FAB M4/M5 phenotype, erythrophagocytosis, leukemia cutis, and disseminated intravascular coagulation.[292] Outcome for children with t(8;16) AML appears similar to other types of AML.
    A substantial proportion of infants diagnosed with t(8;16) AML in the first month of life show spontaneous remission, although AML recurrence may occur months to years later.[292-298] These observations suggest that a watch and wait policy could be considered in cases of t(8;16) AML diagnosed in the neonatal period if close long-term monitoring can be ensured.[292]
  • t(7;12)(q36;p13): The t(7;12)(q36;p13) translocation involves ETV6 on chromosome 12p13 and variable breakpoints on chromosome 7q36 in the region of MNX1 (HLXB9).[299] The translocation may be cryptic by conventional karyotyping and in some cases may be confirmed only by FISH.[300-302] This alteration occurs virtually exclusively in children younger than 2 years, is mutually exclusive with the KMT2A (MLL) rearrangement, and is associated with a high risk of treatment failure.[177,178,214,300,301,303]
  • NUP98 gene fusions: NUP98 has been reported to form leukemogenic gene fusions with more than 20 different partners.[304] In the pediatric AML setting, the two most common fusion genes are NUP98-NSD1 and NUP98-KDM5A4 (JARID1A), with the former observed in one report in approximately 15% of cytogenetically normal pediatric AML and the latter observed in approximately 10% of pediatric AMKL (see above).[227,249,281] AML cases with either NUP98 fusion gene show high expression of HOXA and HOXB genes, indicative of a stem cell phenotype.[274,281]
    The NUP98-NSD1 fusion gene, which is often cytogenetically cryptic, results from the fusion of NUP98 (chromosome 11p15) with NSD1 (chromosome 5q35).[249,250,274,305-308] This alteration occurs in approximately 4% to 7% of pediatric AML cases.[19,184,249,274,307] The highest frequency in the pediatric population is in the 5- to 9-year age group (approximately 8%), with lower frequency in younger children (approximately 2% in children younger than 2 years). NUP98-NSD1 cases present with high WBC count (median, 147 × 109/L in one study).[249,250] Most NUP98-NSD1 AML cases do not show cytogenetic aberrations.[249,274,305] A high percentage of NUP98-NSD1 cases (74% to 90%) have FLT3-ITD.[184,249,250]
    A study that included 12 children with NUP98-NSD1 AML reported that although all patients achieved CR, presence of NUP98-NSD1 independently predicted poor prognosis, and children with NUP98-NSD1 AML had a high risk of relapse, with a resulting 4-year EFS of approximately 10%.[249] In another study that included children (n = 38) and adults (n = 7) with NUP98-NSD1 AML, presence of both NUP98-NSD1 and FLT3-ITD independently predicted poor prognosis; patients with both lesions had a low CR rate (approximately 30%) and a low 3-year EFS rate (approximately 15%).[250]
  • RUNX1 mutations: AML with mutated RUNX1, which is a provisional entity in the 2016 WHO classification of AML and related neoplasms, is more common in adults than in children. In adults, the RUNX1 mutation is associated with a high risk of treatment failure. In a study of children with AML, RUNX1 mutations were observed in 11 of 503 patients (approximately 2%). Six of 11 patients with RUNX1-mutated AML failed to achieve remission and their 5-year EFS was 9%, suggesting that the RUNX1 mutation confers a poor prognosis in both children and adults.[309]
  • RAS mutations: Although mutations in RAS have been identified in 20% to 25% of patients with AML, the prognostic significance of these mutations has not been clearly shown.[214,310-312] Mutations in NRAS are observed more commonly than mutations in KRAS in pediatric AML cases.[214,313] RAS mutations occur with similar frequency for all Type II alteration subtypes, with the exception of APL, for which RAS mutations are seldom observed.[214]
  • KIT mutations: Mutations in KIT occur in approximately 5% of AML, but in 10% to 40% of AML with core-binding factor abnormalities.[214,313-315]
    The presence of activating KIT mutations in adults with this AML subtype appears to be associated with a poorer prognosis compared with core-binding factor AML without KIT mutations.[314,316,317] The prognostic significance of KIT mutations occurring in pediatric core-binding factor AML remains unclear,[318-321] although the largest pediatric study reported to date observed no prognostic significance for KIT mutations.[322]
  • WT1 mutations: WT1, a zinc-finger protein regulating gene transcription, is mutated in approximately 10% of cytogenetically normal cases of AML in adults.[323-326] The WT1 mutation has been shown in some,[323,324,326] but not all studies [325] to be an independent predictor of worse disease-free survival, EFS, and OS of adults.
    In children with AML, WT1 mutations are observed in approximately 10% of cases.[327,328] Cases with WT1 mutations are enriched among children with normal cytogenetics and FLT3-ITD, but are less common among children younger than 3 years.[327,328] AML cases with NUP98-NSD1 are enriched for both FLT3-ITD and WT1 mutations.[249] In univariate analyses, WT1 mutations are predictive of poorer outcome in pediatric patients, but the independent prognostic significance of WT1 mutation status is unclear because of its strong association with FLT3-ITD and its association with NUP98-NSD1.[249,327,328] The largest study of WT1 mutations in children with AML observed that children with WT1 mutations in the absence of FLT3-ITD had outcomes similar to that of children without WT1 mutations, while children with both WT1 mutation and FLT3-ITD had survival rates less than 20%.[327]
  • DNMT3A mutations: Mutations of the DNMT3A gene have been identified in approximately 20% of adult AML patients and are uncommon in patients with favorable cytogenetics but occur in one-third of adult patients with intermediate-risk cytogenetics.[329] Mutations in this gene are independently associated with poor outcome.[329-331] DNMT3A mutations are virtually absent in children.[332]
  • IDH1 and IDH2 mutations: Mutations in IDH1 and IDH2, which code for isocitrate dehydrogenase, occur in approximately 20% of adults with AML,[333-337] and they are enriched in patients with NPM1 mutations.[334,335,338] The specific mutations that occur in IDH1 and IDH2 create a novel enzymatic activity that promotes conversion of alpha-ketoglutarate to 2-hydroxyglutarate.[339,340] This novel activity appears to induce a DNA hypermethylation phenotype similar to that observed in AML cases with loss of function mutations in TET2.[338]
    Mutations in IDH1 and IDH2 are rare in pediatric AML, occurring in 0% to 4% of cases.[332,341-345] There is no indication of a negative prognostic effect for IDH1 and IDH2 mutations in children with AML.[341]
  • CSF3R mutations: CSF3R is the gene encoding the granulocyte colony-stimulating factor (G-CSF) receptor, and activating mutations in CSF3R are observed in 2% to 3% of pediatric AML cases.[346] These mutations lead to enhanced signaling through the G-CSF receptor, and they are primarily observed in AML with either CEBPA mutations or with core-binding factor abnormalities (RUNX1-RUNX1T1 and CBFB-MYH11).[346] The clinical characteristics of and prognosis for patients with CSF3R mutations do not seem to be significantly different from those of patients without CSF3R mutations.
    Activating mutations in CSF3R are also observed in patients with severe congenital neutropenia. These mutations are not the cause of severe congenital neutropenia, but rather arise as somatic mutations and can represent an early step in the pathway to AML.[347] In one study of patients with severe congenital neutropenia, 34% of patients who had not developed a myeloid malignancy had CSF3R mutations detectable in peripheral blood neutrophils and mononuclear cells, while 78% of patients who had developed a myeloid malignancy showed CSF3R mutations.[347] A study of 31 patients with severe congenital neutropenia who developed AML or MDS observed CSF3R mutations in approximately 80%, and also observed a high frequency of RUNX1 mutations (approximately 60%), suggesting cooperation between CSF3R and RUNX1 mutations for leukemia development within the context of severe congenital neutropenia.[348]
(Refer to the PDQ summary on Childhood Acute Myeloid Leukemia/Other Myeloid Malignancies Treatment for information about the treatment of childhood AML.)
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