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 (72Â %) | n.d. | n.d. | n.d. |
P13 | 34 | 46,XY[8] | del of 10q23.3 | Â | del(10)(q23.2q23.31) | chr10:88,906,902-91,189,599 | 2,282,697 |
del of 17p13.1 | TP53: del (9Â %) | 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 | Â | Â | Â | 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]/ | Â | IGH: dup (58Â %) | +14 | +14 | 107,349,540 | ||
46,XX[3] | Â | Â | 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 | Â | 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 | Â | 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 (75Â %) | del(11)(q13.2qter) | chr11:67,773,863-135,006,516 | 67,232,653 | |||
ATM: del (77Â %) | del(15)(q26.1q26.1) | chr15:93,412,860-93,450,773 | 37,913 | ||||
MLL: del (80Â %) | 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 (94Â %) | del(22)(q11.23q11.23) | chr22:23,584,037-23,592,537 | 8500 | ||||
P43 | 69 | 46,XX, | normal | TFG: dup (15Â %) | 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. | Â | del(6)(q13q14.2) | chr6:73,331,571-84,140,938 | 10,809,367 |
t(6;11)(q15;p12), | Â | Â | del(6)(q16.2q21) | chr6:99,282,580-109,703,762 | 10,421,182 | ||
ins(6;11)(q22.1;q13q14), | Â | Â | del(6)(q22.31q22.33) | chr6:124,125,069-128,841,870 | 4,716,801 | ||
inv(6)(q15q25.3), | Â | ESR1: del (89Â %) | del(6)(q25.1q25.3) | chr6:151,725,897-157,531,913 | 5,806,016 | ||
del(11)(q21q23.2)[8] | Â | Â | 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 (91Â %) | del(11)(p15.1p12) | chr11:20,546,133-37,403,781 | 16,857,648 | ||||
BIRC3: del (90Â %) | del(11)(q14.1q14.3) | chr11:85,157,088-88,557,421 | 3,400,333 | ||||
ATM: del (77Â %) | 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] | Â | 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 | Â | 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, | Â | TBL1XR1: del (68Â %) | 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. | Â | del(5)(q31.3q32) | chr5:142,096,863-145,891,069 | 3,794,206 |
t(16;19)(p11.2;q13.3), | Â | Â | Â | Â | Â | ||
der(5)t(5;9)(q31;p13.2), | Â | CDKN2A/B: del (86Â %) | del(9)(p21.3p21.3) | chr9:21,218,548-23,002,377 | 1,783,829 | ||
der(9)t(5;9)(q31;p13.2), | Â | Â | Â | Â | |||
der(9)t(9;9)(q34;p13.2)[10] | Â | FUS: split (75Â %) | |||||
P66 | 0.5 | 46,XX, | n.d. | MLL: split (70Â %) | 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 | Â | Â | Â |
+4, | Â | Â | +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 (64Â %) | 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 (25Â %) | del(13)(q14.2q14.2) | chr13:48,982,463-49,062,316 | 79,853 | ||
t(10;14)(q24;q11)[10] | Â | Â | 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 (13Â %) | n.d. | n.d. | n.d. |
P32 | 27 | 47,XX, | del of 6q21 | Â | n.d. | n.d. | n.d. |
+21, | del of 6q27 | Â | |||||
t(10;14)(q24;q11), | del of 9p21.3 | CDKN2A/B: del (89Â %) | |||||
del(6)(q15q27)[6] | del of 12p13.2 | ETV6: del (78Â %) | |||||
del of 13q14.3 | DLEU1: del (15Â %) | ||||||
dup of 21q22.1 | RUNX1: dup (78Â %) | ||||||
P35 | 40 | 46,XY,i(9)(q21.11)[2] | Â | Â | 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 | Â | 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 (90Â %) | dup(6)(q23.3q23.3) | chr6:134,245,761-136,118,354 | 1,872,593 | ||
del of 9p21.3 | CDKN2A/B: del (88Â %) | del(9)(p21.3p21.3) | chr9:21,252,517-23,002,377 | 1,749,860 | |||
ABL1: amp (95Â %) | dup(9)(q34.1q34.1) | chr9:133,658,293-134,092,544 | 434,251 | ||||
FGFR2: del (57Â %) | 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] | Â | Â | 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 (61Â %) | 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 (81Â %) | 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 (91Â %) | 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 (18Â %) | 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] | Â | Â | 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 | Â | 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 (10Â %) | 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 (10Â %) | 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] | Â | normal | dup(6)(q25.3q25.3) | chr6:157,944,961-158,033,908 | 88,947 |
del of 7p12.2 | Â | 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] | Â | normal | dup(1)(p13.3p13.3) | chr1:107,921,895-107,970,781 | 48,886 |
del of 7p12.2 | Â | del(7)(p12.2p12.2) | chr7:50,356,873-50,465,376 | 408,503 | |||
del of 9p13.2 | Â | 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 |