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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
|
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BCR-ABL-#2
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Hyperdip>50-C21
|
Pseudodip-C2-N
|
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BCR-ABL-#3
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Hyperdip>50-C22
|
Pseudodip-C3
|
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BCR-ABL-#4
|
Hyperdip>50-C23
|
Pseudodip-C5
|
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BCR-ABL-#5
|
Hyperdip>50-C27-N
|
Pseudodip-C6
|
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BCR-ABL-#6
|
Hyperdip>50-C32
|
Pseudodip-C7
|
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BCR-ABL-#7
|
Hyperdip>50-R4
|
Pseudodip-C9
|
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BCR-ABL-#8
|
Hyperdip47-50-C14-N
|
Pseudodip-C14
|
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BCR-ABL-#9
|
Hyperdip47-50-C3-N
|
Pseudodip-C16-N
|
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BCR-ABL-Hyperdip-#10
|
Hypodip-#2
|
Pseudodip-R1-N
|
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BCR-ABL-C1
|
Hypodip-2M#1
|
T-ALL-#5
|
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BCR-ABL-R1
|
Hypodip-C2
|
T-ALL-#6
|
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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
|
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E2A-PBX1-#5
|
MLL-#3
|
T-ALL-C2
|
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E2A-PBX1-#6
|
MLL-#4
|
T-ALL-C6
|
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E2A-PBX1-#9
|
MLL-#5
|
T-ALL-C7
|
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E2A-PBX1-#10
|
MLL-#6
|
T-ALL-C11
|
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E2A-PBX1-#12
|
MLL-#7
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T-ALL-C15
|
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E2A-PBX1-#13
|
MLL-#8
|
T-ALL-C19
|
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E2A-PBX1-2M#1
|
MLL-2M#1
|
T-ALL-C21
|
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E2A-PBX1-C2
|
MLL-2M#2
|
T-ALL-R5
|
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E2A-PBX1-C3
|
MLL-C1
|
T-ALL-R6
|
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E2A-PBX1-C4
|
MLL-C2
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TEL-AML1-#6
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E2A-PBX1-C5
|
MLL-C3
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TEL-AML1-#9
|
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E2A-PBX1-C6
|
MLL-C4
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TEL-AML1-#10
|
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E2A-PBX1-C7
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MLL-C5
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TEL-AML1-#14
|
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E2A-PBX1-C9
|
MLL-C6
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TEL-AML1-2M#1
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E2A-PBX1-C10
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MLL-R1
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TEL-AML1-2M#2
|
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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
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TEL-AML1-C26
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Hyperdip>50-#12
|
content-C2-N
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TEL-AML1-C28
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Hyperdip>50-#14
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content-C3-N
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TEL-AML1-C30
|
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Hyperdip>50-C1
|
content-C4-N
|
TEL-AML1-C31
|
|
Hyperdip>50-C4
|
content-C7-N
|
TEL-AML1-C32
|
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Hyperdip>50-C6
|
content-C8
|
TEL-AML1-C33
|
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Hyperdip>50-C8
|
content-C9
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TEL-AML1-C34
|
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Hyperdip>50-C11
|
content-C11-N
|
TEL-AML1-C37
|
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Hyperdip>50-C13
|
content-R1
|
TEL-AML1-C38
|
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Hyperdip>50-C15
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content-R2-N
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TEL-AML1-C40
|
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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
|
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T-ALL
|
12
|
2
|
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TEL-AML1
|
15
|
5
|
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Other
|
21
|
7
|
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Total
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100
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32
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back to table
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