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Supplementary Information

Classification of Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profile

Section I: Diagnostic ALL samples used for class prediction

I: Patient Dataset

132 cases of pediatric ALL were selected from the original 327 diagnostic bone marrow aspirates1 to reanalyze on the higher density U133A and B microarrays. The selection of cases was based on having sufficient numbers of each subtype to build accurate class predictions, rather than reflecting the actual frequency of these groups in the pediatric population. The list of samples that were used in this reanalysis (Table S1), as well as the subtype distribution (Table S2) are shown below.

Table S1. Diagnostic ALL samples used for class prediction (n=132)

BCR-ABL-#1 Hyperdip>50-C18 Pseudodip-#6
BCR-ABL-#2 Hyperdip>50-C21 Pseudodip-C2-N
BCR-ABL-#3 Hyperdip>50-C22 Pseudodip-C3
BCR-ABL-#4 Hyperdip>50-C23 Pseudodip-C5
BCR-ABL-#5 Hyperdip>50-C27-N Pseudodip-C6
BCR-ABL-#6 Hyperdip>50-C32 Pseudodip-C7
BCR-ABL-#7 Hyperdip>50-R4 Pseudodip-C9
BCR-ABL-#8 Hyperdip47-50-C14-N Pseudodip-C14
BCR-ABL-#9 Hyperdip47-50-C3-N Pseudodip-C16-N
BCR-ABL-Hyperdip-#10 Hypodip-#2 Pseudodip-R1-N
BCR-ABL-C1 Hypodip-2M#1 T-ALL-#5
BCR-ABL-R1 Hypodip-C2 T-ALL-#6
BCR-ABL-R2 Hypodip-C5 T-ALL-#7
BCR-ABL-R3 MLL-#1 T-ALL-#8
BCR-ABL-Hyperdip-R5 MLL-#2 T-ALL-#10
E2A-PBX1-#5 MLL-#3 T-ALL-C2
E2A-PBX1-#6 MLL-#4 T-ALL-C6
E2A-PBX1-#9 MLL-#5 T-ALL-C7
E2A-PBX1-#10 MLL-#6 T-ALL-C11
E2A-PBX1-#12 MLL-#7 T-ALL-C15
E2A-PBX1-#13 MLL-#8 T-ALL-C19
E2A-PBX1-2M#1 MLL-2M#1 T-ALL-C21
E2A-PBX1-C2 MLL-2M#2 T-ALL-R5
E2A-PBX1-C3 MLL-C1 T-ALL-R6
E2A-PBX1-C4 MLL-C2 TEL-AML1-#6
E2A-PBX1-C5 MLL-C3 TEL-AML1-#9
E2A-PBX1-C6 MLL-C4 TEL-AML1-#10
E2A-PBX1-C7 MLL-C5 TEL-AML1-#14
E2A-PBX1-C9 MLL-C6 TEL-AML1-2M#1
E2A-PBX1-C10 MLL-R1 TEL-AML1-2M#2
E2A-PBX1-C11 MLL-R2 TEL-AML1-C4
E2A-PBX1-C12 MLL-R3 TEL-AML1-C5
E2A-PBX1-R1 MLL-R4 TEL-AML1-C6
Hyperdip>50-#8 content-C1-N TEL-AML1-C26
Hyperdip>50-#12 content-C2-N TEL-AML1-C28
Hyperdip>50-#14 content-C3-N TEL-AML1-C30
Hyperdip>50-C1 content-C4-N TEL-AML1-C31
Hyperdip>50-C4 content-C7-N TEL-AML1-C32
Hyperdip>50-C6 content-C8 TEL-AML1-C33
Hyperdip>50-C8 content-C9 TEL-AML1-C34
Hyperdip>50-C11 content-C11-N TEL-AML1-C37
Hyperdip>50-C13 content-R1 TEL-AML1-C38
Hyperdip>50-C15 content-R2-N TEL-AML1-C40
Hyperdip>50-C16 Pseudodip-#5 TEL-AML1-R3

Table Key:
The nomenclature used in this paper is identical to that used in Yeoh et. al.,1 and thus should facilitate cross comparisons between the datasets.The nomenclature indicates disease status at the time of the initial study and has not been updated as this dataset was not selected to address the issue of outcome.No analysis has been performed in this study to identify expression profiles associated with outcome.

Subtype Name-C# Dx Sample of patient in CCR Subtype Name-R# Dx Sample of patient who developed a hematologic relapse Subtype Name-# Dx Sample used for subgroup classification only Subtype Name-2M# Dx Sample of patient who later developed 2nd AML Subtype Name-N Dx Sample in novel group Subgroup distribution of ALL cases

Table S2. Subgroup distribution of ALL cases

Subgroup Training Set Test Set
BCR-ABL 11 4
E2A-PBX1 13 5
Hyperdiploid >50 13 4
MLL 15 5
T-ALL 12 2
TEL-AML1 15 5
Other 21 7
Total 100 32