Table 3 Clinical utility beyond targetable somatic mutations

 15-63375

AML changed to JMML

PTPN11; SETB1

c.181G > T (p.D61Y); c.2602G > A (p.D868N)

Diagnostic [31, 46]

JMML

 13-72282^a

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

 14-78154^a

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

 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

 13-72282^a

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 [73–75]

Poor prognosis

 14-78154^a

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