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Table 3 Summary of subtype verification results

From: DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

Methylation subtype Confirmed subtype a Subtype-like b Unconfirmed subtype c
N Karyotype d RT-PCR e CNA f N Karyotype d Negative for fusion gene g Novel fusion gene h CNA f N
T-ALL* 0/1 (0%) 0 ND ND 0/1 (0%) 0 NA ND ND 1/1 (100%)
HeH* 7/25 (28%) 0 ND 7 18/25 (72%) 8 NA ND 13 0/25 (0%)
t(12;21)* 4/33 (12%) 1 4 ND 22/33 (67%) 0 19 3 ND 7/33 (21%)
11q23/MLL* 3/4 (75%) 1 ND 3 1/4 (25%) 0 1 ND ND 0/4 (0%)
t(1;19)* 0/15 (0%) 0 ND ND 9/15 (60%) 0 9 0 1 6/15 (40%)
dic(9;20)* 3/19 (16%) 0 ND 3 16/19 (84%) 5 NA 0 10 0/19 (0%)
t(9;22)* 0/5 (0%) 0 ND ND 3/5 (60%) 0 3 ND ND 2/5 (40%)
iAMP21* 4/4 (100%) 4 ND 4 0/4 (0%) 0 NA ND ND 0/4 (0%)
  1. *DNA methylation-based subtype group. Asterisks indicate groups classified by DNA methylation.
  2. aNewly classified patients with confirmed verification of their subtype group by at least one verification method.
  3. bNewly classified patients negative for the canonical event that defines their subtype and/or non-canonical event.
  4. cNewly classified patients without a positive or negative result from one of the verification methods.
  5. dNumber of patients with a chromosomal aberration observed in karyotyping results determined at diagnosis in NOPHO centers.
  6. eNumber of patients positive for respective fusion genes by re-analysis by RT-PCR.
  7. fThe number of patients with chromosomal aberrations discovered by array-based copy number alteration (CNA) that support subtype classification.
  8. gThe number of subtype-like patients negative for canonical aberrations by targeted analyses (FISH/RT-PCR) at diagnosis.
  9. hThe number of patients with novel (non-canonical) fusion genes detected.
  10. Abbreviations: NA not applicable, ND not determined.