Table 1.

Comparison of alteration frequencies

Tumor type and gene alterationFMPublished frequencyFisher exact test
Neuroblastoma
ALK point mutation14.3% (33/230)9.2% (22/240)P = 0.0865
PTPN11 point mutation1.3% (3/230)2.9% (7/240)P = 0.3396
ATRX point mutation1.8% (4/227)a2.5% (6/240)P = 0.7522
ATRX focal deletion4.0% (9/227)a7.1% (17/240)P = 0.1610
MYCN point mutation0.9% (2/230)1.7% (4/240)P = 0.6859
MYCN focal amplification25.7% (59/230)32.0% (77/240)P = 0.1284
NRAS point mutation2.6% (6/230)0.8% (2/240)P = 0.1677
ALL
ETV6–RUNX1 rearrangement12.0% (10/83)19.4% (47/242)P = 0.1362
TCF3–PBX1 rearrangement2.4% (2/83)a7.0% (17/242)P = 0.1749
BCR–ABL1 rearrangement1.1% (1/89)3.7% (9/242)P = 0.2986
MLL rearrangement4.8% (4/83)a11.4% (16/140)P = 0.1442
P2RY8–CRLF2 rearrangement4.8% (4/83)a7% (19/272)P = 0.6151
PAX5 rearrangement6.0% (5/83)a2.2% (10/446)P = 0.0697
PICALM-MLLT10 rearrangement2.4% (2/83)a9.5% (4/42)P = 0.1778
AML
FLT3 internal tandem duplication5.5% (4/73)16.5% (15/91)P = 0.0472
NPM1 point mutation4.1% (3/73)7.8% (23/295)P = 0.4422
CEBPA point mutation6.8% (5/73)4.5% (38/847)P = 0.3785
Fusion-negative RMS
NRAS point mutation6.7% (3/45)11.7% (11/94)P = 0.5482
FGFR4 point mutation4.4% (2/45)9.6% (9/94)P = 0.5030
PIK3CA point mutation2.2% (1/45)7.4% (7/94)P = 0.4370
BCOR point mutation6.7% (3/45)7.4% (7/94)P = 1.00
FBXW7 point mutation0% (0/45)7.4% (7/94)P = 0.0960
KRAS point mutation2.2% (1/45)6.4% (6/94)P = 0.4279
TP53 point mutation20% (9/45)5.3% (5/94)P = 0.0132
NF1 point mutation4.4% (2/45)5.3% (5/94)P = 1.00
HRAS point mutation2.2% (1/45)4.3% (4/94)P = 1.00
Medulloblastoma
CTNNB1 point mutation3.1% (1/32)6.5% (6/92)P = 0.6760
PTCH1 point mutation12.5% (4/32)7.6% (7/92)P = 0.4722
MLL2 point mutation6.3% (2/32)8.7% (8/92)P = 1.00
SMARCA4 point mutation3.1% (1/32)4.30% (4/92)P = 1.00
TP53 point mutation9.4% (3/32)3.3% (3/92)P = 0.1775
BCOR point mutation0% (0/31)a3.3% (3/92)P = 0.5712
DDX3X point mutation0% (0/5)a7.6% (7/92)P = 1.00
MYC amplification3.1% (1/32)1.1% (1/92)P = 0.4511
MYCN amplification12.5% (4/32)4.30% (4/92)P = 0.2025
  • Abbreviation: FM, Foundation Medicine dataset.

  • aCorrects for the gene not being assayed on all versions of the test.