Supplementary Table 1. Clinical Information for the samples used in the 27K Methylation arrays and HUG133plus2
expression arrays
New Sample ID
A3-1
A3-2
A3-3
A3-4
A3-5
A3-6
A3-7
A3-8
A3-9
A3-10
A3-11
A3-12
A3-13
A3-14
A3-15
A7-1
A7-2
A7-3
A7-4
A7-5
EN-1
EN-2
EN-3
EN-4
EN-5
EN-6
EN-7
Sample type
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Methylation Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Expression Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Supplementary Table 1 (Continued)
New Sample ID
EN-8
EN-9
EN-10
EN-11
EN-12
EA-1
EA-2
EA-3
EA-4
EA-5
CM-1
CM-2
CM-3
CM-4
BM-1
BM-2
BM-3
BM-4
B1
B2
B3
B4
B5
B6
B7
B8
Sample type
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Human Skeletal Muscle
Human Skeletal Muscle
Human Skeletal Muscle
Human Skeletal Muscle
Human Bone Marrow
Human Bone Marrow
Human Bone Marrow
Human Bone Marrow
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
Methylation Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Expression Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Supplementary Table 1 (Continued)
New Sample ID
B9
B10
B11
B12
B13
B14
B15
B16
B17
B18
B19
B20
B21
B22
B23
B24
B25
B26
B27
B28
B29
B30
B31
B32
B33
B34
B35
Sample type
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX3-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
PAX7-FOXO1 Fusion-Positive RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Methylation Array
Expression Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Supplementary Table 1 (Continued)
New Sample ID
B36
B37
B38
B39
B40
B41
B42
Sample type
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Fusion-Negative RMS
Abbreviation: RMS, rhabdomyosarcoma.
Methylation Array
Expression Array
Yes
Yes
Yes
Yes
Yes
Yes
Yes