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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