Table S1Comparison of MLL fusions detected by cytogenetics, fluorescent in situ hybridization (FISH), Long distance Inverse polymerase chain reaction (LDI-PCR) and Anchored multiplex PCR enrichment (AMP-E)

Patient No. / Age at Diagnosis (yrs) / Sex / Diagnosis / Karyotype/FISH / Blast Percentage at Diagnosis / MLL partner gene detected by FISH / MLL(KMT2A) fusion detected by / RNA fusion transcript detected by AMP-E
LDI-PCR
gDNA / AMP-E
RNA
1 / 13.80 / F / ALL / 46,XX,t(4;11)(q21;q23) / 94 / Yes / MLL-AFF1 (MLL: Exon 10 - AFF1:Intron 3) / MLL - AFF1 (exon 8- exon 5) / 1
2 / 16.00 / M / ALL / 47, XY, +X, t(4;11) (q21;q23) / 90 / Yes / MLL-AFF1 (intron11 -Intron 3) / MLL-AFF1 (exon9/10- exon5) / 2
3 / 0.67 / M / ALL / 46, XY, t(4;11) (q21; q23) / 83 / Yes / MLL-AFF1 (intron9 -Intron 3) / MLL-AFF1 (Exon8- Exon5 ) Exon8- exon5 intergenic chr4 / 2
4 / 0.58 / F / ALL / 46 XX t(4:11) (q21:q23) FISH 5'MLLsep 3' MLL / 92 / Yes / MLL-AFF1 (Exon 10 -Intron 3) / MLL-AFF1 (exon8- exon5 ) Exon8- exon5 intergenic chr4 / 2
5 / 13.00 / M / ALL / FISH showed 5' and 3' MLLsep in 100% of cells but partner chr not identified in karyotype / 90 / No / MLL-AFF1 (Intron 11- Intron 3) / MLL-AFF1 (exon9/10- exon5) / 3
6 / 0.42 / M / ALL / 46, XY, inv (2) (p13q33), t(4;11) (q21;q23) / 90 / Yes / 2p16 - MLL (2p16 - Intron 12)
MLL-AFF1 (Intron 10 - Intron 3) / MLL-AFF1 (Exon9- Exon5) / 1
7 / 15.00 / M / ALL / 46, XY, t(4;11) (q21;q23) / 95 / Yes / MLL-AFF1 (Exon10 - Intron 4)
AFF1-MLL (Intron 4- Intron 10) / MLL-AFF1 (Exon9-Exon6) / 1
8 / 11.00 / F / ALL / 46,XX,t(4;11)(q21;q23) / 95 / Yes / MLL-AFF1 (Intron 11- Intron 3) / MLL-AFF1 (exon10- exon5 intergenic chr4 ) / 1
9 / 0.67 / F / ALL / 46, XX, t(4;11) (q21;q23) / 91.9 / Yes / AFF1-MLL (Intron 4- Intron 11)
MLL-AFF1 (Intron11 -Intron 4) / MLL-AFF1 (Exon9/10 - Exon6) / 2
10 / 16.00 / M / ALL / 46, XY, t(4;11) (q21;q23) / 97 / Yes / MLL-AFF1 (Intron 9- Intron 5) / MLL-AFF1 (Exon 8 -Exon7) / 1
11 / 0.25 / F / ALL / 46, XX, t(4;11)(q21;q23) / 85 / Yes / MLL-AFF1 (intron11 -Intron 3) / MLL-AFF1 (exon9/10- exon5) / 2
12 / 15.00 / M / ALL / 46,XY,t(4;11)(q21;q23) / 92 / Yes / AFF1-MLL (Intron 10- Intron 11)
MLL-AFF1 (Intron11 -Intron 10) / MLL-AFF1 (exon9/10- exon12) / 2
13 / 3.00 / F / ALL / 46,XX,t(4;11)(q21;q23) / 95 / Yes / MLL-AFF1 (Exon12 -Intron 3) / MLL-AFF1 (Exon9/10-Exon5) Intergenic chr 4 / 5
14 / 0.25 / F / ALL / 46, XX, t(4;11) (q21;q23), / 94 / Yes / MLL-AFF1 (Intron9 -Intron 4) / MLL-AFF1 (Exon8- Exon6) / 1
15 / 0.92 / M / ALL / 46, XY [18] nucish(MLLx2) (5'MLLsep 3'MLLx1) / 90 / No / MLL-MLLT3 (Intron 11 -Intron 5) / MLL -MLLT3 ( Exon9- Exon6) / 1
16 / 5.00 / M / ALL / 46, XY, t(9;11) (p22;q23) / 95 / Yes / MLL-MLLT3 (Intron 9 -Intron 9) / MLL-MLLT3 (Exon8-exon10) / 1
17 / 0.58 / M / ALL / nucish (KMT2Ax2) (5'KMT2A sep 3'KMT2A 89/100 / 90 / No / MLL-MLLT3 (Intron 11 -Intron 5) / AMP-E assay unable to detect fusion
18 / 1.08 / F / ALL / nucish (KMTAx2)(5'KMT2A sep 3"KMT2Ax1) / 95 / No / MLL-MLLT3 (Intron 11 -Intron 5)
MLLT3-MLL (Intron 5-Intron 3) / MLL-MLLT3 (Exon9- Exon6) / 1
19 / 3.00 / M / ALL / 47, XY, +X, t(11;19)(q23;p13.3) / 90 / Yes / MLLT1-MLL (Intron1 - Intron 11) / MLL-MLLT1 (exon9/10-exon2) / 2
20 / 0.08 / F / ALL / 47, XX, +X, t(11;19) (q23;p13.3) / 93 / Yes / MLL-MLLT1 (Intron10 -Intron 1) / MLL-MLLT1 (exon9-exon2) / 1
21 / 1.50 / M / ALL / 47,XY,+X,add(1)(q?42),add(3)(p25),t(11;19)(q23;p13,del(11)(q13q23)? / 82 / No / LDI-PCR unable to find breakpoint / MLL-MLLT1 ( Exon8 - Exon 4) / 2
22 / 1.68 / M / ALL / 46,XY,t(10;11)(p?,q23) / 98 / No / MLL-MLLT10 (Intron 11 – Intron 9) / MLL- MLLT10 (exon 9/10- exon 9) / 1
23 / 3.00 / F / ALL / 46,XX,t(6;11)(q27;q23) / 90 / Yes / MLL-MLLT4 (Intron 10- Intron1) / MLL-MLLT4 (Exon9- Exon2) / 1
24 / 0.67 / F / ALL / 46, XX, t(1;11) (p32;q23) / 95 / Yes / MLL-EPS15 (Intron 10- 1p32 spliced fusion)
TNXB-MLL (Intron 2- Intron 11) / MLL-EPS15 (Exon9- Exon2) / 1
25 / 1.67 / M / ALL / 46, XY, t(2;11) (q33;q23), add (11) (q23) / 90 / Yes / MLL-AFF3 (Intron 11- Intron 4) / MLL-AFF3 (Exon9/10 -Exon7) / 3
26 / 14.00 / M / ALL / 46,XY,t(?7;11)(?p22;q23) / 95 / No / MLL-TNRC18 (Intron9 - Intron 15)
ZC3H12C- MLL( Exon6 UTR - Intron 9) / MLL-TNRC18 (Exon 7/8- Exon 16) / 1
27 / 16.00 / F / AML / 47, XX, +8, t(9;11) (p22;q23) / 82.6 / Yes / MLL-MLLT3 (Intron9 - Intron 5) / MLL-MLLT3 (exon8-exon6) / 1
28 / 11.00 / M / t- AML / 46,XY,t(9;11)(p22;q23) / 98 / Yes / MLL-MLLT3 (Intron 9- Intron 4) / MLL-MLLT3 (Exon9- Exon6) / 1
29 / 0.67 / M / AML / 46,XY,t(9;11)(p22;q23) MLL rearrangement on FISH / 94 / Yes / MLL-MLLT3 (Intron 9 -Intron 5) / MLL-MLLT3 (exon8-exon6) / 1
30 / 1.08 / M / AML / 47,XY,t(9;11)(p21;q23) / 65 / Yes / MLL-MLLT3 (Intron11 –Intron 5) / MLL-MLLT3 (exon9/10-exon6) / 2
31 / 1.15 / M / AML / 46,XY,t(9;11)(p22;q23) / 92 / Yes / MLL-MLLT3 (Intron9 –Intron 5) / MLL-MLLT3 (exon8-exon6) / 2
32 / 7.79 / F / AML / 46,XX,t(9;11)(p22;q23) / 93 / Yes / MLL-MLLT3 (Intron11 –Intron 5) / MLL-MLLT3 (exon9/10-exon6) / 2
33 / 2.59 / M / AML / 46,XY,t(9;11)(p22;q23) / 93 / Yes / MLL-MLLT3 (Intron 10 –Intron 5) / MLL - MLLT3 (Exon 8- Exon 5) / 1
34 / 15.4 / M / AML / 47,XY,t(10;11)(p1?2;q23) / 92 / No / MLL-MLLT10 (Intron9 –Intron 9) / MLL-MLLT10 (exon8 – exon10) / 1
35 / 1.6 / F / AML / 46, XX, t (10; 11)) (q23 ;?) / 93 / No / MLL-MLLT10 (Intron11 –Intron 8) / MLL-MLLT10 (exon9/10 – exon9 / 2
36 / 0.50 / F / AML / 46,XX,t(11;19)(q23;p13.1) MLL rearrangement on FISH / 8 / Yes / MLL-ELL (Intron11- Intron1) / MLL-ELL (exon 9/10 -exon2) / 2
37 / 2.93 / F / AML / 46, XX, t (11; 19) (q23; p13.?1) / 88 / Yes / MLL-ELL (MLL: Intron 11-ELL: Intron 1 / MLL – ELL (exon 9/10 – exon 2) / 2
38 / 3.57 / M / t-AML / 46,XY,t(11;19)(p13;q23) / 25 / Yes / MLL-ELL (MLL: Intron 11 -ELL: Intron 1) / MLL - ELL (exon 9/10- exon 2) / 3
39 / 2.07 / M / AML / 46,XY,t(3;11)(p21;q23) / 57 / Yes / MLL - DCP1A (Intron 10 - Intron 5)
DCP1A-MLL (Intron 5- Intron 10) / MLL-DCP1A (exon9- exon6) / 1