Table 2 Cytogenetic, aCGH and FISH Results.

RAEB-2

43~44,XY,-5,der(5)add(5)(p15.3) del(5)(q34),der(7)dup(?7)(p15p22) t(7;15)(q31;q11.2),add(12)(p13), der(15)t(7;15), add(17)(p13),-18, der(19)t(?5;19)(p15.1;p13.3),+mar1[cp2/ 45~46, sl,-Y,-mar1,+mar2x2 [cp3]/ 42~46,sl,r(12) (p11.2q24.3),-der(15) t(7;15),-mar1[8]/ 42-46,sl, dic(6;12) (p10;q10),add(12)(p13),add(17)(p11.2), +add(18)(q23),add(20) (p13),-mar1[cp3]/42~45, sdl3,psu dic (18;19)(p11.2;p13.3)t(?5;19) (p15.1;p13.3)[cp4]

arr 5p15.33p15.31(387,034-7,150,950)x1,5q22.2(112,073,070-112,236,540)x1, 5q23.1q35.3(119,285,451-180,616,147)x1,6p25.3p25.2(326,849-2,927,819)x1, 7p14.1(40,423,354-42,301,602)x1,7p13q11.22(44,583,533-67,706,469)x1, 7q11.22(69,795,761-71,039,199)x1,7q21.3(94,315,008-94,637,930)x1,7q21.3 q36.3(96,419,102-158,788,150)x1,11q14.1q25(84,811,642-34,301,424)x3~4, 12p13.33(74,345-1,781,320)x3,12p13.32p13.31(4,144,817-6,740,664)x3, 12p13.31(7,454,167-7,781,482)x1,12p13.31(7,909,595-8,174,285)x3,12p13.2 (10,290,689-10,555,515)x1,12p12.3 p12.2(16,484,810-20,837,343)x1,12p12.1 (23,481,114-23,903,637)x3,12p11.22p11.1(27,792,939-33,636,183)x1,17q11.2 (26,415,260-26,685,081)x1,18p11.32p11.22 (905,705-10,600,909)x1,18q21.32 q23(55,877,565-76,103,395)x1,19p13.3(211,754-719,804)x1,20p11.23 (19,446,369-19,632,379)x1

5q22.2/APC loss (73%) (164 kb)

5q23.1q35.5 loss (69.2%) (61.3 Mb)

11q14.1q25 gain (42%) (49.5 Mb)

12p13.32/CCND2 gain (67%) (2.6 Mb)

12p12.3p12.2 loss (79%) (4.3 Mb)

12p12.1/SOX5 gain (23%) (422 kb)

17q11.2/NF1 loss (33%) (270kb)

18p11.32p11.22 loss (21%) (9.6 Mb)

18q21.32q23 loss (48%) (20.2 Mb)

20p11.23/SLC24A3 loss (50%) (186 kb)

t-MDS

(RAEB-1)

45,XY,-7,add(18)(p11.2) [20]

arr 7p22.3q36.3(106,470-158,788,150)x1,9p24.3p13.1(188,707-38,662,411)x3, 18p11.32p11.21(140,284-14,065,199)x1

Monosomy 7 (80%) (158 Mb)

aCGH defined der(18)t(9;18)(p13.1; p11.32)

RCUD

40,X,-Y,der(5;12)(q10;q10),-7,-13, der (?5;15)(p10;q10),der(17;?21) (q10;q10) ,-18,-22,+mar[3]/80,slx2 [3]/46,XY[14]

arr 5q32q33.1(145,784,050-150,381,359)x1~2,7p22.3q36.3(106,470-158,615,766) x1~2,13q14.12 q33.3(45,226,907-108,905,138)x1~2,18p11.32q23(140,284-76,103,395)x1~2

FISH non-informative: 2n/4n clones present.

Loss of Y not detected by aCGH.

RAEB-2

46,XX,der(1)t(1;5)(p13;q13),-4,del(5) (q13),+der(?)t(1;?) (p13;?)[9]/ 46,XX[11]

arr(1-22,X)x2 Normal Female

5q deletion (0.7%) (within background)

Suspect low-level clonality

t-MDS

(RAEB-1)

46,XY,t(3;12)(p25;q13)[16]/46,XY[4]

arr(1-22)x2,(XY)x1 Normal Male

Balanced translocation

t-MDS

(RAEB-1)

46,XY,del(5)(q15q31)[13]/46,XY[6]

arr 5q14.1q33.3(80,739,035-157,165,622)x1

del(5q) (17.5%) (76.4 Mb)

RAEB-2

46,XX,t(2;6)(q33;p11.2),r(11)(p15q23)[18]/46,idem,del(X)(q24q28)[2]

arr 2q33.1q37.3(202,851,669-242,436,891)x1,6p22.2p22.1(25,845,975-26,237,877)x1,6p12.3(47,118,924-47,484,069)x1,11p13(32,426,278-33,841,461)x1,11p13q14.1(35,917,783-79,934,744)x3,11q14.1q25(84,987,721-134,431,368)x1

2q33.1q37.3 deletion (87%) (39.6 Mb)

RCMD

46,XX,+1,der(1;7)(q10;p10)[20]

arr 1q21.1-1q44(1444111146-247189904)x3,7q11.21-7q36.3(61991850-158615766)x1,?13q21.1-13q21.33(56,970,230 -71,102,396)x1~2

del(7q) (48.5%) (96.6 Mb)

suspected 13q deletion - unable to confirm

t-MDS

(RAEB-2)

43~47,XX,+2[2],del(3)(q23q29)[3],-4[4], add(4)(p14)[3],del(5)(q13)[17],del(6) (q23q27)[3],del(7)(q21.2q36)[17], +8[2],+9[2],+11[3],add(11)(p15)[16], add(12)(p11.2)[2],-13[13],+14[2],-17[7],-18[9],-20[5],del(20)(q11.2q13.3)[2], der(21)t(9;21)(q22;q22)[15],+mar1[6], +mar2[12],+mar3[2][cp17]/46,XX[3]

arr 3q22.2q29(136,891,829-199,230,435)x3,5q14.1q34(80,739,035-162,985,861) x1,6p25.3p22.1(89,702-27,735,846)x1,6p21.33p21.1(31,007,155-44,123,999)x3, 7q21.3(94,315,008-94,637,930)x3,7q21.3q36.3(95,908,715-155,963,689)x1, 8q24.13q24.3(123,825,412-145,957,473)x3,11p15.5p15.4(896,316-7,391,465)x1, 11q23.1q25(111,095,142-134,431,368)x3,12q13.13(50,423,182-52,714,396)x3, 13q12.11q12.3(18,448,674-30,094,861)x3,13q13.1q34(31,498,180-114,103,243) x1,17q21.31(41,288,422-41,528,254)x3,18p11.32p11.22(140,284-10,487,828)x1, 18q21.2q23(51,018,278-76,103,395)x1,20q11.23q12(35,843,902-39,677,519)x1, 20q13.2(52,310,955-52,627,305)x1,21q22.2q22.3(39,838,925-45,584,697)x1, 22q11.22q11.23(21,330,008-21,978,854)x3

12q13.13/SP1 gain (25%) (2.3 Mb)

17q21.31/MAPT gain (22.5%) (240 kb)

Array reproducibility confirmed same CNAs detected on right and left PIC aspirates. Follow-up study confirmed 5q, 7q and most deletions.

RAEB-1

46,XY,del(20)(q11.2q13.3)[2]/46,XY[18]

arr(1-22)x2,(XY)x1 Normal Male

20q deletion (2%) Low-level clonality

RAEB-2

46,XX,del(5)(q13q33)[10]/46,sl, del(11)(q13q23)[8]/46,XX[2]

arr 5q14.3q34(87,963,057-162,985,861)x1,11q14.1q23.1(79,505,241-111,400,572)x1~2

5q deletion (38.4%) (75 Mb)

MLL FISH (0.4%) (WNL)

Relapsed AML

(RAEB-T)

46,XY,i(7)(p10)[17]/46,XY[3]

arr 7p22.3q11.21(106,470-62,303,249)x3,7q11.22q36.3(67,538,481-158,788,150)x1

del(7q) (60.0%) (91 Mb)

RARS

46,XY,del(5)(q15q31)[20]

arr 5q21.1q32(98,042,952-145,952,287)x1

del(5q) (70.7%) (47.9 Mb)

RAEB-2

46,XY,del(11)(q13q25)[20]

arr 11q14.1q25(84,811,642-132,230,180)x1

fibrotic MDS (RAEB-1)

44,XY,add(5)(q13),del(9)(p10),der(11;15)(q10;q10),der(13)t(7;13;?) (13pter- > 13q22 : :7q31- > 7q32::?), der(18)t ?11;18)(p11.2;q23),psu dic(20;7) (:7p11.2->7q11.2::20p13- > 20qter)[24]

arr 5q21.1q35.3(102,768,888-180,616,147)x1,7p22.3p11.1(106,470-7,622,921)x1, 7q11.21q22.3(61,991,850-107,152,110)x1,7q31.33q32.3(126,838,584-130,116,345)x1,7q36.1q36.3(148,606,208-158,788,150)x1,12p13.32p13.31 (4,144,817-8,174,285)x3,2p13.2p12.3(10,290,689-16,828,705)x1,12p12.2 p12.1(20,350,473-23,903,637)x3,13q21.1q21.2(57,084,770-59,940,562)x1, 18q22.1q23(62,148,705-76,103,395)x1

del(5q) loss (70%) (77.8 Mb)

chr7 CEP7/D7S486 (7q31): normal

CDKN2A/2B 9p21 loss (44.5%)

12p13.32p13.31/CCND2 gain (49.3%) (4.0 Mb)

12p13.2-12p12.3/EMP1 loss (75.0%) (6.5 Mb)

1212p12.2-12p12.1/SOX5 gain (54.5%) (3.5 Mb)

RAEB2 -> AML

45,X,-Y,del(4)(q12q21),-5,add(7)(q11.2), ?t(7;21;12) (q22;q22;p12),?del(17)(p13), +mar[1]/ 45,sl,add(19)(q13.3)[6]/

90,sdl1x2[1]/46,XY[12]

arr 4p15.31p14(20,201,929-38,418,177)x1,4q13.1q21.23(59,479,326-85,831,534)x1,4q22.1q27(88,240,778-121,956,556)x1,5p13.2p12(38,353,657-42,684,423)x1,5q14.1q21.1(76,836,011-98,453,706)x1,5q23.3q35.3(127,839,105- 180,616,147)x1,7q22.2q36.3(105,379,216-155,347,034)x1,12p13.2p11.1 (10,290,689-33,636,183)x1,17p13.3p11.2(0-17,929,998)x1,19p13.3(211,754-383,987)x1,19p13.3(2,139,294-2,922,392)x3,19p13.3p13.2(5,893,471-7,959,704)x3,19p13.2p13.13(9,747,145-13,087,968)x1,19p13.12p13.11 (14,852,729-19,194,051)x3,21q11.2q22.2(14,429,720-40,367,306)x3

del(5q) (54.3% 2n/4.9% 4n)

del(7q) (50.7% 2n/5.5% 4n)

19p13.2/MAP2K7 gain (42.6% 2n/3.5% 4n) (2.1 Mb)

19p13.12p13.11/MAP1 S gain (44%) (4.3 Mb)

RAEB-2

47,XX,+9,del(20)(q11.2q13.1)[2]/46,XX[4] Limited Study

arr 9p24.3q34.3(188,707-140,168,105)x3,20q11.23 q13.12(35,843,902-45,321,690)x1

trisomy 9 (16.5%)

del(20q) (10.2%)

t-MDS (RAEB-1)

46,XX,der(7)del(7)(p10)del(7)(q22)[13]/ 45,XX-7[6]/46,XX[1]

arr 7p22.3p11.2(106,470-55,599,166)x1,7q21.3q36.3(94,315,008-158,593,771)x1

del(7q)/ monosomy 7 (84.5%)

t-MDS

(RAEB-1)

45,XY,-7[11]/46,XY[9]

arr 7p22.3q36.3(106,470-158,593,771)x1,12q21.31q23.1(84,097,500-95,218,964)x1

monosomy 7 (70%)

del(12)q21.3q23 (75%) (11 Mb)

RAEB-2 and Multiple myeloma

46,XY,del(5)(q15q33)[21]

arr 5q21.1q33.2(98,272,436-153,873,892)x1

del(5q)/-5 (80.5%)

trisomy 5 (1.0%) by non-targeted FISH. Plasma cell specific FISH: 30/30 cells = 100.0% Trisomy 5

AML arising from MPD

47,XX,+8[20]

arr 1p21.3p12(96,795,246-119,008,810)x2~3,8p23.3q24.3(345,060-146,236,298)x3,21q22.12(35,028,342-35,371,865)x1~2

trisomy 8 (82.5%)

1p21.3p12 dup (32%) (22 Mb)

RUNX1 deletion (10%) (344 kb)

t-MDS → AML

46,XX,del(7)(q22q32)[20]

arr 3q26.1q29(166,401,814-199,230,435)x3,7q21.3q36.3(94,315,008-158,788,150)x1,21q22.12(35,028,342-35,371,865)x1~2

del(7q) (91.5%) (64.5 Mb)

3q gain with EVI1 break (94%) (32.8 Mb)

RUNX1 deletion (5.0%) (344 kb)

hypoplastic MDS

45,XX,-7,del(12)(p11.2p13)[20]

arr 7p22.3q36.3(106,470-158,788,150)x1,12p13.1p11.1(12,890,018-33,636,183)x1

Monosomy 7 (39.7%) (158.7 Mb)

12p12.1/KRAS loss (58.5%) (20.7 Mb)

ETV6/RUNX1 FISH: normal

5q- syndrome

46,XX,del(5)(q11.2q31)[19]/

46,XX[1]

arr 5q14.3q33.3(87,963,057-158,280,854)x1,12p13.1p12.2(12,961,431-20,567,792)x1~2

del(5q) (65.5%) (70.3 Mb)

12p13.1p12.2/EMP1 deletion (17%) (7.6 Mb)

t-MDS

45,XY,-5,add(17)(p11.2),-18,+mar[6]/ 46,XY[17]

arr(1-22)x2,(XY)x1 Normal Male

TP53 deletion (5.0%)

t-AML

RAEB-T

47,XX,+8[5]/46,XX[15]

arr 8p23.3q24.3(345,060-146,236,298)x2~3,21q22.12(35,028,342-35,371,865)x1~2

Trisomy 8 (22.5%) RUNX1 loss (1.0% or WNL) RP11-77g18 (344 kb)

RAEB-2

46,XY[20]

arr(1-22)x2,(XY)x1 Normal Male

8q24.3/CTD-3034E3: normal (CNV)

t-MDS (RCMD-RS)

46,XY,del(3)(p21),der(5;15)(p10;q10), der(6)del(6)(p11.2p21.1)del(6) (p23p25), ?del(16)(q22q24),-17,+ider(?),+r [19]/ 46,XY[1]

arr 3p26.3p14.1(46,141-71,438,751)x1,5q15q35.3(92,810,609-180,616,147)x1, 6p25.3p22.1(89,702-27,761,655)x1,6p21.33p21.1(31,007,155-44,123,999)x3, 6p12.3p11.2(45,390,156-58,131,862)x1,15q11.2q13.1(22,577,151-26,079,398) x1,17p13.3p13.1(0-8,045,204)x1

del(5q) (73.4%)

16q22/CBFB FISH: normal

TP53 deletion (71.7%)

Primary myelo-fibrosis

46,XY,+1,der(1;7)(q10;p10)[20]/

46,XY[1]

arr 1q21.1q44(144,111,146-246,864,638)x3,5q32(145,643,075-145,952,287)x1, 7q11.21q36.3(61,991,850-158,615,766)x1,12p13.1(12,890,018-13,268,329)x1~2, 13q14.2q14.3(47,759,453-49,406,099)x1,17q11.2(26,415,260-27,249,359)x1

5q32/TCERG1 (77%) (309 kb)

12p13.1/EMP1 deletion (6.0%) (378 kb)

13q14.2q14.3/RB(91%) (1.65 Mb)

17q11.2/NF1 deletion (75%) (834 kb)

normal

46,XX,+1,der(1;7)(q10;p10)[5]/

46,XX[15]

arr(1-22,X)x2 Normal Female

del(7q) (3.0%) and 3p12.1 deletion (70%) (CNV)