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Table 3 Clinical utility beyond targetable somatic mutations

From: Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

PIP ID Diagnosis Alteration Mutation (change) Clinical utility Implication
Sequence mutations  
 15-63375 AML changed to JMML PTPN11; SETB1 c.181G > T (p.D61Y); c.2602G > A (p.D868N) Diagnostic [31, 46] JMML
 13-72282a T-ALL STAT5B c.2110A > C (p.I704L) Diagnostic [30, 47] Gamma-delta T-cell lymphoma
 15-26188 ALL NT5C2 c.1219G > T (p.D407Y) Pharmacogenomic [32, 33] Affects therapy
 13-45348 AML IDH1 c.394C > T (p.R132C) Diagnostic [48, 49] Maffucci syndrome
 14-53198 AML CEBPA c.939_940insAAG (p.K313_V314insK); c.326_327insC (p.P109fs) Prognostic [50] Improved prognosis
 15-10838 Glioma H3F3A c.83A > T (p.K28M) Prognostic [51] Poor prognosis
 14-37237 Glioblastoma multiforme H3F3A c.83A > T (p.K28M) Prognostic [52, 53] GBM subgroup, K27
 14-35585 Renal cell carcinoma VHL c.497 T > G (p.V166G) Diagnostic [54] Von Hippel Lindau
 14-47205 Nephroblastomatosis PIK3CA c.1035 T > A (p.N345K) Diagnostic [55] Nephroblastomatosis
 14-78154a Medulloblastoma KDM6A c.2989_2990dupAT (p.M997fs) Prognostic [56] Risk stratification, group 4
 14-75899 Neuroblastoma ATRX c.5239delA (p.T1747fs) Prognostic [57] Poor prognosis
 14-10141 Pleuropulmonaryblastoma DICER1 c.5438A > G (p.E1813G) Health Maintenance [58] DICER syndrome
Transcriptome analysis and CNV
 14-24794 AML CBFB-MYH11 Fusion Prognostic [59] Low-risk stratification
 15-64793 B-ALL FOXP1-ABL1 Fusion Prognostic [60] High-risk stratification
 15-84578 AMKL CBFA2T3-GLIS2 Fusion Diagnostic [61]; Prognostic [35] AMKL; Poor prognosis
 14-85546 CML BCR-ABL1 Fusion Diagnostic [59] CML
 13-72282a T-ALL Isochromosome 7q Copy number change Diagnostic [39] Gamma-delta T-cell lymphoma
 15-46387 Rhabdomyosarcoma PAX7-FOXO1 Fusion Diagnostic [62, 63]; Prognostic [64] Rhabdomyosarcoma; High-risk group
 13-81192 Alveolar soft part sarcoma ASPSCR1-TFE3 Fusion Diagnostic [65] Alveolar soft part sarcoma
 13-65217 Ewing sarcoma EWSR1-FLI1 Fusion Diagnostic [66] Ewing sarcoma
 15-47087 Ewing sarcoma EWSR1-FLI1; Low expression of PAX8, FHIT, CASP10, CHD2, with high expression of CHD11, FUS, and MTA1 Fusion; Expression pattern Diagnostic [66]; Prognostic [36] Ewing sarcoma; Poor prognosis
 13-21968 Undifferentiated sarcoma EML4-NTRK3 Fusion Diagnostic [34] Infantile fibrosarcoma
 16-88073 Ependymoma C11orf95-RELA; Alternating gains and losses on chr 11 and 22, consistent with a “chromothripsis-like” pattern Fusion; Copy number change Prognostic [67]; Diagnostic [68] Poor prognosis; RELA-type supratentorial ependymoma
 14-27243 Neuroblastoma MYCN amplified, deletion at 1p and 11q, gain 17q; MYCN over expressed Copy number change; Overexpression Prognostic [69, 70] Risk-based therapy
 14-42817 Neuroblastoma MYCN non-amplified, no LOH at 1p11q; MYCN not over expressed Copy number change; No overexpression Prognostic [69, 70] Risk-based therapy
 15-39486 Neuroblastoma MYCN non-amplified, no LOH at 1p11q; MYCN not over expressed Copy number change; No overexpression Prognostic [69, 70] Risk-based therapy
 14-44070 Neuroblastoma MYCN amplified, loss of 1p, gain of 1q and 17q; MYCN over expressed Copy number change; Overexpression Prognostic [69, 70] Risk-based therapy
 15-88980 Hepatoblastoma Amplification of 11q13.2 including CCND1; Over expression of CCND1 Copy number change; Overexpression Prognostic [71] Good prognosis
 15-49177 Medulloblastoma IMPG2, GABRA5, LAPTM4B, MAB21L2, NPR3, MFAP4, NRL, ZFPM2, TSHZ3, IGF2BP3, GALNT14, GPR98; Loss of 10q22.2-10qter involving PTEN and SUFU, loss of 17p, gain of 17q Overexpression; Copy number change Prognostic [72] Risk stratification, subgroup 3/4
 15-70532 Ependymoma Gain of 1q, loss of 6q Copy number change Prognostic [7375] Poor prognosis
 14-78154a Medulloblastoma KCNA1, RBM24, KLHL13, EN2, SNCAIP, PDE1C, GRM8, KCNIP4, EXPH5, UNC5D, NID2, ST18, GPR12, SH3GL3; i17q Overexpression; Copy number change Prognostic [72] Risk stratification, subgroup 4
 15-40141 Pleomorphic xanthoastrocytoma Gain of chromosome 7, LOH at 9p Copy number change Diagnostic [76] Pleomorphic xanthoastrocytoma
 15-97336 Small round blue cell tumor EWSR1-WT1 Fusion Diagnostic [77] DSRCT
 15-34296 Ependymoma TNC, CALB1, PLAG1, ALDH1L1, RELN Overexpression Prognostic [37] Risk stratification, group A, poor prognosis
 15-80972 ATRT LOH at 22q11.21qter, including SMARCB1; ASCL1 Copy number change; Overexpression Diagnostic [78]; Prognostic [79] ATRT; Improved prognosis
  1. aSame patient
  2. ALL acute lymphoblastic leukemia, AMKL acute megakaryoblastic leukemia, AML acute myeloid leukemia, ATRT atypical teratoid rhaboid tumor, CML chronic myeloid leukemia, CNV copy number variation, JMML juvenile myelomonocytic leukemia