Download Supplementary Figure 1 Nucleotide and Amino acid sequence of the

Supplementary Figure 1
Nucleotide and Amino acid sequence of the 3’RACE product in 290F8 and 394D7 cases
MYB exon 15
CAG GAT GTG ATC AAA CAG GAA TCT GAT GAA TCT GGA ATT GTT GCT GAG TTT CAA GAA AAT
Q
D
V
I
K
Q
E
S
D
E
S
G
I
V
A
E
F
Q
E
N
GGA CCA CCC TTA CTG AAG AAA ATC AAA CAA GAG GTG GAA TCT CCA ACT GAT AAA TCA GGA
G
P
P
L
L
K
K
I
K
Q
E
V
E
S
P
T
D
K
S
G
AAC TTC TTC TGC TCA CAC CAC TGG GAA GGG GAC AGT CTG AAT ACC CAA CTG TTC ACG CAG
N
F
F
C
S
H
H
W
E
G
D
S
L
N
T
Q
L
F
T
Q
ACC TCG CCT GTG GCA GAT GCA CCG AAT ATT CTT ACA AGC TCC GTT TTA ATG GCA CCA GCA
T
S
P
V
A
D
A
P
N
I
L
T
S
S
V
L
M
A
P
A
TCA GAA GAT GAA GAC AAT GTT CTC AAA GCA TTT ACA GTA CCT AAA AAC AGG TCC CTG GCG
S
E
D
E
D
N
V
L
K
A
F
T
V
P
K
N
R
S
L
A
NFIB 3’UTR
AGC CCC TTG CAG GTC TTG CAC GCC CCT CCC TTA CCC AGA ACT GCA GAG CTT CAG GAT GGC
S
P
L
Q
V
L
H
A
P
P
L
P
R
T
A
E
L
Q
D
G
GAA GGT CAC CCA AGG GCA TGA GTA GGG AGT GGT GTC TCC AAC CAT CAG TTC CGT GGC ACT
E
G
H
P
R
A
*
GTT CAG CCT TTG TGT GCT GCC CTG CCA CCC ACC ACT CAC AGT GCC TCT GAA GCG TGT TAC
AUAP primer
CCC TGG AGT GAC GTG AGC ATT TGA GGC TTG TCT AAA AAA AAA AAA AAA AAA AAG TAC TAG
TCG ACG CGT GGC
Supplementary Figure 2
Nucleotide and Amino acid sequence of the 3’RACE product in 288F7 case
MYB exon 13
CAG GAT GTG ATC AAA CAG GAA TCT GAT GAA TCT GGA ATT GTT GCT GAG TTT CAA GAA AAT
Q
D
V
I
K
Q
E
S
D
E
S
G
I
V
A
E
F
Q
E
N
MYB intron 13
GGA CCA CCC TTA CTG AAG AAA ATC AAA CAA GAG GTA AAC ACG CAA CCC TTT GGA AGC AAC
G
P
P
L
L
K
K
I
K
Q
E
V
N
T
Q
P
F
G
S
N
AAG CTG AGA ATC CTG CCC CCT TTA TTC CTT GTG TGC AGC TTG ATG TGT CTG CCA TTG GCA
K
L
R
I
L
P
P
L
F
L
V
C
S
L
M
C
L
P
L
A
CTG TGC AAC ACC ACG ACT TTT CGT GCA AGA TTT TCA TAC AAG GTG CAG CGA AAA GGT ACT
L
C
N
T
T
T
F
R
A
R
F
S
Y
K
V
Q
R
K
G
T
GCC AGA CTG TAG GCA TCA TCA ACC TTT CCT TTG GGA AGC CAA GCC ATC TCT ATC TAC TTC
A
R
L
*
A
S
S
T
F
P
L
G
S
Q
A
I
S
I
Y
F
EFR3A intron 22 (Chr8q24.22)
ATG TTT GGA CAG AAA AGT TCA TAG AGC CTG TAT AGA CCA TTT ACG TGA AGT TTA AGA ACA
M
F
G
Q
K
S
S
*
AGC ACC ACT AAT CTT CAG TGA TGG AGA TCA GAA CAT AGT TGT TGC ATG TGG ATG TAT GTG
TAT GGG TAT GTC AGA GTG GGG AGA AAT TGA CTG GTT AGG GAC ATG AAA CAT TTT GGG GGT
GAT TGA AAG TGT TCA GTA TCT CTT GAA CCT AGG AGG TGG AGG TTA CAG TGA GCC AAG ATC
ACA CAA TTG CAC TCC AGC CTG GGT GAC AAG AGT AAA ACT CCA TCT CAA AAA AAA AAA AAA
AUAP primer
AAA AGT ACT AGT CGA CGC GTG GCC
Supplementary Figure 3
Nucleotide and Amino acid of the 3’RACE product in 542A1 case
MYB exon 14
CAG GAT GTG ATC AAA CAG GAA TCT GAT GAA TCT GGA ATT GTT GCT GAG TTT CAA GAA AAT
Q
D
V
I
K
Q
E
S
D
E
S
G
I
V
A
E
F
Q
E
N
GGA CCA CCC TTA CTG AAG AAA ATC AAA CAA GAG GTG GAA TCT CCA ACT GAT AAA TCA GGA
G
P
P
L
L
K
K
I
K
Q
E
V
E
S
P
T
D
K
S
G
AAC TTC TTC TGC TCA CAC CAC TGG GAA GGG GAC AGT CTG AAT ACC CAA CTG TTC ACG CAG
N
F
F
C
S
H
H
W
E
G
D
S
L
N
T
Q
L
F
T
Q
NFIB 3’UTR
ACC TCG CCT GTG GCA GAT GCA CCG AAT GGT TTT GAA AAC TGT GCT ACA GGG ACT GAT GTG
T
S
P
V
A
D
A
P
N
G
F
E
N
C
A
T
G
T
D
V
GCA AAT ATA TCT CTT TAT GCA GAA GGA AGT CTT TTT TTT TCT TTT TTT TTT TTT TAA GAA
A
N
I
S
L
Y
A
E
G
S
L
F
F
S
F
F
F
F
*
GTA TGG CTT TTT ATG CAT CCT TCA TCG AGG GCA TTG AAG TTG CAT GGA CTG ATA AAA GTT
AUAP primer
GAT GCA AAA CAA GAA AGA AAC AAA CAA AAA AAA AAA AAA AGT ACT AGT CGA CGC GTG GCC
Supplementary Figure 4
Nucleotide and Amino acid sequence of the 3’RACE product in 318H3 case
MYB exon 8b
AGA CAC TAT AAT GAT GAA GAC CCT GAG AAG GAA AAG CGA ATA AAG GAA TTA GAA TTG CTC
R
H
Y
N
D
E
D
P
E
K
E
K
R
I
K
E
L
E
L
L
MYB exon 9b
CTA ATG TCA ACC GAG AAT GAG CTA AAA GGA CAG CAG GTG CTA CCA ACA CAG AAC CAC ACA
L
M
S
T
E
N
E
L
K
G
Q
Q
V
L
P
T
Q
N
H
T
TGC AGC TAC CCC GGG TGG CAC AGC ACC ACC ATT GCC GAC CAC ACC AGA CCT CAT GGA GAC
C
S
Y
P
G
W
H
S
T
T
I
A
D
H
T
R
P
H
G
D
AGT GCA CCT GTT TCC TGT TTG GGA GAA CAC CAC TCC ACT CCA TCT CTG CCA GCG GAT CCT
S
A
P
V
S
C
L
G
E
H
H
S
T
P
S
L
P
A
D
P
GGC TCC CTA CCT GAA GAA AGC GCC TCG CCA GCA AGG TGC ATG ATC GTC CAC CAG GGC ACC
G
S
L
P
E
E
S
A
S
P
A
R
C
M
I
V
H
Q
G
T
ATT CTG GAT AAT GTT AAG AAC CTC TTA GAA TTT GCA GAA ACA CTC CAA TTT ATA GAT TCT
I
L
D
N
V
K
N
L
L
E
F
A
E
T
L
Q
F
I
D
S
MYB exon 11
TTC TTA AAC ACT TCC AGT AAC CAT GAA AAC TCA GAC TTG GAA ATG CCT TCT TTA ACT TCC
F
L
N
T
S
S
N
H
E
N
S
D
L
E
M
P
S
L
T
S
ACC CCC CTC ATT GGT CAC AAA TTG ACT GTT ACA ACA CCA TTT CAT AGA GAC CAG ACT GTG
T
P
L
I
G
H
K
L
T
V
T
T
P
F
H
R
D
Q
T
V
MYB intron 11
AAA ACT CAA AAG GAA AAT ACT GTA TAG GAC CTC TTC TGA CAT CCC CAG GAA TAT TAT ATG
K
T
Q
K
E
N
T
V
*
NFIB 3’UTR
ATT AGA AGC CAA GGG ATG AGT AAG CAG TCA TTT TTA TTC AAT AAA GCC TTC CTT TCC AAG
TGT CAA ATA GGA CAC CCA TCT TAC CGG CCA ATG TCC AAA ATT ACG GTT TGA ACA TAA TTG
GAG AAC CTT TCC TTC AAG CAG AAA CAA GCA ACT GAG GGA AAA AGA AAC ACA ACA ATA GTT
AUAP primer
TAA GAA ATT TTT TTT TTA AAT AAA AAA AAA AAA AAA AGT ACT AGT CGA CGC CGT GGC
Supplementary Figure 5
Nucleotide and Amino acid sequence of the 3’RACE product in 405B2 case
MYB exon 15
CAG GAT GTG ATC AAA CAG GAA TCT GAT GAA TCT GGA ATT GTT GCT GAG TTT CAA GAA AAT
Q
D
V
I
K
Q
E
S
D
E
S
G
I
V
A
E
F
Q
E
N
GGA CCA CCC TTA CTG AAG AAA ATC AAA CAA GAG GTG GAA TCT CCA ACT GAT AAA TCA GGA
G
P
P
L
L
K
K
I
K
Q
E
V
E
S
P
T
D
K
S
G
AAC TTC TTC TGC TCA CAC CAC TGG GAA GGG GAC AGT CTG AAT ACC CAA CTG TTC ACG CAG
N
F
F
C
S
H
H
W
E
G
D
S
L
N
T
Q
L
F
T
Q
ACC TCG CCT GTG GCA GAT GCA CCG AAT ATT CTT ACA AGC TCC GTT TTA ATG GCA CCA GCA
T
S
P
V
A
D
A
P
N
I
L
T
S
S
V
L
M
A
P
A
TCA GAA GAT GAA GAC AAT GTT CTC AAA GCA TTT ACA GTA CCT AAA AAC AGG TCC CTG GCG
S
E
D
E
D
N
V
L
K
A
F
T
V
P
K
N
R
S
L
A
Inverted PDCD1LG2 intron 3 (9p24.2)
AGC CCC TTG CAG GAA GGC AGA CTC CTG TGG CCT GTA TAG CCT AGG AAC GTG ACA GCC AAT
S
P
L
Q
E
G
R
L
L
W
P
V
*
AGG AAG CAA GAC GGG AAC ACT AGA GGG TGG ACT GGA GGG AGA AGG GAA GGT ATT TCT CCC
TTA TGC TCT ATA CTT TTG TGG CCT CTC CAG CAG AAG ATG TAT CTC TTC CCT GGC TCC AGA
TAC CAA TGG ACA GGC CCA CTG GGT TCC AGT GTC TGT CAA GTG ACT TTA ATC CCT GGG CTC
CAT TAA CCC TGC CTT CCC CCT TTT CAC TAT AGC CTA GTG GTA GGA GCA GCT TTC TGC TAT
TGC TAA TTT CTG AAT TGC TTC CCT GTT CTC TGT TTG GCT TCT CAG TCT CCC TCA TTA AAA
GAA TTA CTA GTT TCA GCT TTA GAT TTC CAC AGG TTT AAA TGG TTT CTG TTT CCC TGG TTT
GTT CTG GCT GTC TGA CAG ATA TGT TAC AAG CAA TGC TGT AAT TTC TGA AAT AAA GAT GAA
AUAP primer
ATG TAT ACA TGG TAA AAA AAA AAA AAA AAA GTA CTA GTC GAC GCG TGG CCC
Supplementary Figure 6
Massively paired-end sequencing data by Solexa.
2 upper panels indicate the 485F7, FISH positive but fusion transcript negative, reading results.
2 lower panels show the results of 325E5, both FISH and transcript positive tumor.
Supplementary Figure 7
Verification of the novel NFIB-AIG1 gene fusion identified by pair-end sequencing; A) Two
NFIB-AIG1 gene fusion variants are noted by RT-PCR. B) sequencing analysis confirming the
NFIB exon 2 link to AIG1 exon 4 (variant 1) and exon 5 (variant 2).
Supplementary Figure 8
The representation of CNV at narrow regions around MYB and NFIB genes in 485F7 case. The
upper panel shows the region around MYB gene. The lower panel shows that one copy still lost
around NFIB region.