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Table 1 Patient characteristics, distribution, and total RNA preparation method

From: New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures

Sample

Diagnosis

Blast cells (%)

Gold standard classification

Age (m-y)

RNA preparation method

Microarrays

#1

Pre-pre-B-ALL

95

t(4;11)

6 m

A,B,C

3

#2

c-ALL

70

t(9;22)

14 y

A,B,C

3

#3

Early-T-ALL

83

negative

16 y

A,B,C

3

#4

c-ALL

90

t(12;21)

13 y

A,B,C

3

#5

Pre-B-ALL

98

t(1;19)

10 y

A,B,C

3

#6

c-ALL

87

hyperdiploid (DI = 1,233)

2 y

A,B,C

3

#7

c-ALL

93

negative

16 y

A,B,C

3

#8

AML

89

negative*

16 y

A,B,C

3

#9

c-ALL/Pro-B

85

t(9;22)

5 y

A,B,C

3

#10

Early-T-ALL

94

negative

4 y

A,B,C

3

#11

c-ALL

88

t(12;21)

2 y

A,B,C

3

#12

prepreB/c-ALL

96

Hyperdiploid (DI = 1,244)

11 y

A,B,C

3

#13

c-ALL

95

negative

3 y

A,B,C

3

#14

Pre-B-ALL

87

negative

12 y

A,B,C

3

#15

c-ALL

94

t(12;21)

8 y

A,B,C

3

#16

AML

93

t(9;11)

6 y

A,B,C

3

#17

Early-T-ALL

87

negative

9 y

A,B,C

3

#18

Early-T-ALL

93

negative

9 y

A,B,C

3

#19

c-ALL

93

hyperdiploid (DI = 1,160)

2 y

A,B,C

3

#20

prepreB/c-ALL

85

negative

3 y

A,B,C

3

#21

mature T-ALL

94

negative

4 y

A,B,C

3

#22

Pre-B-ALL

95

negative

7 y

A,B,C

3

#23

prepreB/c-ALL

94

negative

4 y

A,B,C

3

#24

c-ALL

86

negative

5 y

A,B,C

3

TOTAL

     

72

#25

AML

89

negative**

4 y

A,A,A,B,B,B,C,C,C

9

#26

AML

77

t(1;11)

6 m

A,A,A,B,B,B,C,C,C

9

#27

prepreB/CALL

92

negative

4 y

A,A,A,B,B,B,C,C,C

9

TOTAL (replicates)

     

27

TOTAL in Study

     

99

  1. Negative = negative for all gold standard tests regarding recurrent translocations. Age at diagnosis is expressed as months (m) or years (y). Method A: QIAshredder homogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by RNeasy purification; Method B: TRIzol RNA isolation. Method C: TRIzol RNA isolation followed by RNeasy purification. Samples #1–24 have been extracted in triplicates; Samples #25, #26, and #27 have been extracted in multiple technical replicates (n = 3). (*) Karyotype information: 46, XY; (**) Karyotype information: 46, XY der(9p) [3]/46, XY [19].