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Table 1 Summary of aberrations detected by metaphase directed FISH, interphase FISH to determine the percentage of specific aberrations, and aCGH in 34 ALL patients

From: High rates of submicroscopic aberrations in karyotypically normal acute lymphoblastic leukemia

Case number Age [y] Metaphase directed FISH MLPA LSPs for genes aCGH – affected cytobands Localization acc. to GRCH37/hg19 Size of imbalance [bp]
B-ALLs
P1 1 46,XX normal normal dup(11)(p15.5p15.4) chr11:1,960,555-3,626,932 1,666,377
P8 30 47,XY,+21[5]/46,XY[2] dup of 21q22.12 RUNX1: dup (72 %) n.d. n.d. n.d.
P13 34 46,XY[8] del of 10q23.3   del(10)(q23.2q23.31) chr10:88,906,902-91,189,599 2,282,697
del of 17p13.1 TP53: del (9 %) del(17)(p13.1p13.1) chr17:7,579,695-8,281,928 702,233
P17 27 46,XX[7] n.d. normal normal n.d. n.d.
P23 59     del(3)(p25.3p25.3) chr3:10,179,706-10,385,195 205,489
  del of 7p12.2   del(7)(p12.2p12.2) chr7:50,337,405-50,482,274 144,869
    del(10)(q23.3q23.3) chr10:89,570,600-89,676,741 106,141
    del(11)(q14.2q14.2) chr11:85,683,188-85,944,362 261,174
47,XX,+14[2]/   IGH: dup (58 %) +14 +14 107,349,540
46,XX[3]    del(15)(q26.1q26.1) chr15:93,390,484-93,463,312 72,828
    del(17)(p13.1p13.1) chr17:7,581,198-7,922,308 341,110
del(17)(q11.2q11.2) chr17:30,259,053-30,271,653 12,600
del(18)(q21.32q21.32) chr18:57,517,756-57,718,190 200,434
del(21)(q22.3q22.3) chr21:45,527,941-45,565,198 37,257
P28 84 46,XY, del of 7p12.2   del(7)(p12.2p12.2) chr7:50,353,062-50,444,269 91,207
t(9;22)(q34;q11), del of 9p21.3 CDKN2A/B: del (75 %) del(9)(pterp11.2) chr9:0–47,212,321 47,212,321
del(11)(q13q25)[7] del of 9p13.2   del(9)(q34.2qter) chr9:136,917,580-141,213,431 4,295,851
    del(10)(q23.3q23.3) chr10:89,619,806-89,731,258 111,452
del of 11q22.3 BIRC3: del (75 %) del(11)(q13.2qter) chr11:67,773,863-135,006,516 67,232,653
ATM: del (77 %) del(15)(q26.1q26.1) chr15:93,412,860-93,450,773 37,913
MLL: del (80 %) dup(20)(q11.23q12) chr20:37,305,876-39,130,131 1,824,255
  del(20)(q12q13.12) chr20:39,245,111-45,524,952 6,279,841
  dup(20)(q13.12q13.12) chr20:45,524,953-45,780,811 255,858
  del(20)(q13.12q13.32) chr20: 45,780,812-58,067,678 12,286,866
  del(21)(q22.2q22.2) chr21:39,764,621-39,807,169 42,548
BCR: del (94 %) del(22)(q11.23q11.23) chr22:23,584,037-23,592,537 8500
P43 69 46,XX, normal TFG: dup (15 %) dup(3)(q12.2q12.2) chr3:100,360,682-100,444,109 83,427
der(4)(4pter- > 4q21.3::11q23.3-    del(7)(q21.2q21.2) chr7:92,252,341-92,475,197 222,856
>11q23.3::4q21.3- > 4qter),   MLL: ins (75 %)
der(11)(11pter- > 11q23.3::11q23.3- > 11q24.2::11p15.4- > 11pter),
der(11)(11qter- > 11q24.2::11p15.4- > 11qter)[5]
P48 39 46,XY, n.d.   del(6)(q13q14.2) chr6:73,331,571-84,140,938 10,809,367
t(6;11)(q15;p12),    del(6)(q16.2q21) chr6:99,282,580-109,703,762 10,421,182
ins(6;11)(q22.1;q13q14),    del(6)(q22.31q22.33) chr6:124,125,069-128,841,870 4,716,801
inv(6)(q15q25.3),   ESR1: del (89 %) del(6)(q25.1q25.3) chr6:151,725,897-157,531,913 5,806,016
del(11)(q21q23.2)[8]    del(7)(p12.2p12.2) chr7:49,991,954-51,207,236 1,215,282
  dup(11)(p15.5p15.4) chr11:1,925,114-3,143,116 1,218,002
WT1: del (91 %) del(11)(p15.1p12) chr11:20,546,133-37,403,781 16,857,648
BIRC3: del (90 %) del(11)(q14.1q14.3) chr11:85,157,088-88,557,421 3,400,333
ATM: del (77 %) del(11)(q22.1q22.3) chr11:100,992,179-114,667,959 13,675,780
del(13)(q14.2q14.2) chr13:48,980,623-49,148,073 167,450
P49 39 46,XX[10] n.d. normal dup(11)(p15.5p15.4) chr11:2,016,406-3,430,378 3,430,378
P51 59 46,XX[6] normal normal del(10)(p12.1p12.1) chr10:28,057,099-28,220,314 163,215
del(15)(q26.1q26.1) chr15:93,412,860-93,450,773 37,913
del(X)(q21.1q21.1) chrX:76,875,639-77,157,819 282,180
P52 21 46,XY[4]   normal del(6)(p21.1p21.1) chr6:45,395,872-45,409,919 14,047
   del(7)(q21.2q21.2) chr7:92,149,393-92,495,958 346,565
del of 10q23.3   del(10)(q23.3q23.3) chr10:89,610,886-89,722,948 112,062
   del(11)(q14.2q14.2) chr11:85,683,188-85,944,362 261,174
   del(15)(q26.1q26.1)) chr15:93,433,130-93,450,773 17,643
   del(17)(q23.1q23.1) chr17:57,698,768-57,913,528 214,760
del(20)(q13.2q13.2) chr20:52,151,411-52,629,609 478,198
del(X)(p22.33p22.33) chrX:1,327,561-1,684,270 1,684,270
P53 34 46,XY[5] normal normal dup(22)(q11.21q11.21) chr22:18,706,001-21,561,514 2,855,514
P55 19 46,XY[6] del of 17p13.1 TP53: del (100 %) del(17)(pterp11.2) chr17:0–20,219,464 20,219,464
−20 −20 63,025,520
P56 47 45,XY,-21[2]/ normal normal del(12)(pterp11.21) chr12:0–31,260,891 31,260,891
46,XY[4]
P57 56 46,XY[3] normal normal normal n.d. n.d.
P58 20 46,XX,   TBL1XR1: del (68 %) del(3)(q26.32q26.32) chr3:176,825,586-177,697,157 871,571
der(14)(pter- > q32::q32- > q13::q32- > qter)[10] del of 9p21.3 CDKN2A/B: del (74 %) del(9)(p21.3p21.3) chr9:21,252,517-24,289,720 3,037,203
  del(10)(p15.3p15.3) chr10:1,491,986-1,582,072 90,086
   IGH: split (78 %) dup(14)(q13q32.33) chr14:35,918,265-106,513,022 70,594,757
del(16)(q13q13) chr16:57,275,940-57,331,138 55,198
del(21)(q22.2q22.2) chr21:39,764,621-39,895,171 130,550
P64 5 46,XX, n.d.   del(5)(q31.3q32) chr5:142,096,863-145,891,069 3,794,206
t(16;19)(p11.2;q13.3),      
der(5)t(5;9)(q31;p13.2),   CDKN2A/B: del (86 %) del(9)(p21.3p21.3) chr9:21,218,548-23,002,377 1,783,829
der(9)t(5;9)(q31;p13.2),     
der(9)t(9;9)(q34;p13.2)[10]   FUS: split (75 %)
P66 0.5 46,XX, n.d. MLL: split (70 %) dup(11)(p15.5p15.4) chr11:1,008,688-3,669,161 3,669,161
der(10)(10pter- > 10p12.31::11q23.3- > 11q23.3::10p12.31- > 10q11.23::14q24.2- > 14qter),   IGH: inv (100 %)
der(11)(10qter- > 10q11.23::11p15.3- > 11q23.3::10p12.31- > 10p12.31::11q23.3- > 11qter),
der(14)t(11;14)(q15.3;q24.2), inv(14)(q11q23)[8]
T-ALLs
P5 22 46,XX[12] normal normal normal n.d. n.d.
P6 16 47,XY, normal normal    
+4,    +4 +4 191,154,276
der(3)t(3;5)(p23;q31.1),
der(5)t(3;5)(p23;q35.3),
der(5)t(5;10)(q31.1;p12.3),
der(10)t(5;10)(q35.3;p12.3)[8]/
46,XY[13]
P7 26 46,XY, del of 9p21.3 CDKN2A/B: del (64 %) del(9)(p21.3p21.3) chr9:21,817,082-23,515,821 1,698,739
t(2;9;18)(p23.2;p21.3;q21.33), del of 13q14.2 RB1: del (25 %) del(13)(q14.2q14.2) chr13:48,982,463-49,062,316 79,853
t(10;14)(q24;q11)[10]    del(16)(p13.3p13.3) chr16:3,154,954-4,568,792 1,413,838
P18 36 46,XY[5] dup of 18q21.2 DCC: dup (13 %) n.d. n.d. n.d.
P32 27 47,XX, del of 6q21   n.d. n.d. n.d.
+21, del of 6q27  
t(10;14)(q24;q11), del of 9p21.3 CDKN2A/B: del (89 %)
del(6)(q15q27)[6] del of 12p13.2 ETV6: del (78 %)
del of 13q14.3 DLEU1: del (15 %)
dup of 21q22.1 RUNX1: dup (78 %)
P35 40 46,XY,i(9)(q21.11)[2]    del(2)(q34q34) chr2:213,811,279-214,150,984 339,705
   dup(7)(pterp14.1) chr7:0–38,218,586 38,218,586
   del(7)(q21.2q21.2) chr7:92,252,341-92,460,773 208,432
   del(7)(q36.3qter) chr7:156,881,580-159,138,663 2,257,083
del of 9p21.3 CDKN2A/B: del (92 %) del(9)(pterp11.2) chr9:0–47,212,321 47,212,321
del of 9p13.2   dup(9)(q21.11qter) chr9:71,035,265-141,213,431 70,178,166
del(10)(q23.2q23.31) chr10:89,570,600-89,728,844 158,244
del(11)(q22.2q22.2) chr11:102,106,046-102,529,831 423,785
del(13)(q14.2q14.2) chr13:49,004,123-49,122,923 118,800
del(15)(q26.1q26.1) chr15:93,390,484-93,466,292 75,808
del(16)(p13.3p13.3) chr16:3,808,951-3,839,782 30,831
del(18)(q21.32q21.32) chr18:57,517,756-57,617,796 100,040
del(20)(q13.2q13.2) chr20:52,151,411-52,574,928 423,517
P38 22 46,XY[3] normal normal normal n.d. n.d.
P61 18 46,XX,der(2)t(2;7)(q37.3;q34), t(7;10)(q34;q24.1 ~ 25.1) [4]/    del(1)(p36.31p36.23) chr1:5,958,728-7,238,618 1,279,890
   del(4)(p16.3p14) chr4:3,072,509-38,882,925 35,810,416
46,XX[3] dup of 6q23.3 MYB: amp (90 %) dup(6)(q23.3q23.3) chr6:134,245,761-136,118,354 1,872,593
del of 9p21.3 CDKN2A/B: del (88 %) del(9)(p21.3p21.3) chr9:21,252,517-23,002,377 1,749,860
ABL1: amp (95 %) dup(9)(q34.1q34.1) chr9:133,658,293-134,092,544 434,251
FGFR2: del (57 %) del(10)(q25.1q26.3) chr10:112,392,101-135,534,737 23,124,636
B- or T ALLs (not clinically well defined)
P11 26 46,XY[8] n.d. normal normal n.d. n.d.
P16 17 46,XX[7]    del(1)(q25.3q31.1) chr1:184,771,633-185,825,795 1,054,162
   del(4)(p15.33p15.31) chr4:12,322,760-18,779,457 6,456,697
   del(4)(q21.22q24) chr4:82,992,997-106,476,929 23,483,932
   del(7)(pterp14.2) chr7:0–36,320,986 36,320,986
dup of 7q22.1 RELN: dup (61 %) dup(7)(q21.3q22.3) chr7:96,048,870-106,348,693 10,299,823
   del(9)(p23p22.2) chr9:12,656,733-17,466,907 4,810,174
del of 9p21.3 CDKN2A/B: del (81 %) del(9)(p21.3p21.3) chr9:20,279,653-22,555,566 2,275,913
   del(10)(p14p13) chr10:6,889,266-12,484,159 5,594,893
del of 12p13.2 ETV6: del (91 %) del(12)(p13.2p13.1) chr12:11,761,018-12,934,870 1,173,852
del(18)(p11.32p11.31) chr18:2,741,687-3,231,531 489,844
P21 62 46,XY[11] n.d. normal normal normal normal
P24 23 46,XY[12] dup of 18q21.2 DCC: dup (18 %) n.d. n.d. n.d.
P30 46 46,XY[6] normal normal n.d. n.d. n.d.
P33 76 45,X,-X[8]    del(4)(q24q24) chr4:106,036,993-106,601,946 564,953
   del(7)(q21.2q21.2) chr7:92,080,855-92,475,197 394,342
   dup(7)(q36.2q36.2) chr7:153,039,830-154,467,634 1,427,804
del of 10q23.3   del(10)(q23.3q23.3) chr10:89,610,886-89,698,312 87,426
   del(15)(q21.2q21.2) chr15:51,826,924-51,919,665 92,741
   del(15)(q26.1q26.1) chr15:93,433,130-93,450,773 17,643
del of 17p13.1 TP53: del (10 %) del(17)(p13.1p13.1) chr17:7,583,457-8,156,734 573,277
   del(17)(q11.2q11.2) chr17:30,259,193-30,267,204 8011
dup of 18q21.2 DCC: dup (10 %) dup(18)(q21.2q21.2) chr18:49,105,579-51,431,815 2,326,236
del(20)(q13.2q13.2) chr20:52,151,411-52,554,455 403,044
del(21)(q22.12q22.12) chr21:36,253,465-36,426,708 173,243
-X -X 155,270,560
P46 63 46,XY[8]   normal dup(6)(q25.3q25.3) chr6:157,944,961-158,033,908 88,947
del of 7p12.2   del(7)(p12.2p12.2) chr7:50,452,798-50,492,798 40,000
   dup(17)(q12q12) chr17:36,046,040-36,095,204 49,164
P47 59 46,XX[6]   normal dup(1)(p13.3p13.3) chr1:107,921,895-107,970,781 48,886
del of 7p12.2   del(7)(p12.2p12.2) chr7:50,356,873-50,465,376 408,503
del of 9p13.2   del(9)(p13.2p13.2) chr9:37,006,073-37,320,759 314,686
dup(9)(q31.1q31.1) chr9:104,126,808-104,167,077 40,269
del(15)(q26.1q26.1) chr15:93,390,484-93,450,773 60,289
del(18)(q21.32q21.32) chr18:57,517,756-57,718,190 200,434
del(19)(p13.3p13.3) chr19:0–2,787,457 2,787,457
  1. bp basepairs, LSP locus-specific probes as specified in Additional file 2: Table S2, y year