Table 3 Summary of statistically significant smaller copy number alterations (p-value < = 0.05) and genes in the region

chr1:142,898,654-143,481,059

582

q21.1

Loss

26.67

<0.001

0

has-mir-3118-2, has-mir-3118-2

chr2:127,807,016-127,821,014

14

q14.3

Loss

20.00

0.021

1

BIN1

chr2:141,745,577-141,790,622

45

q22.1

Gain

20.00

0.005

1

LRP1B

chr2:236,033,001-236,677,413

644

q37.2

Gain

20.00

0.005

1

AGAP1

chr3:196,726,226-196,756,289

30

q29

Loss

20.00

0.002

2

MFI2, MIF2-AS1

chr4:1,792,487-1,809,740

17

p16.3

Loss

33.33

<0.001

1

FGFR3

FGFR3

chr4:69,305,095-69,412,970

108

q13.2

Gain

40.00

<0.001

2

TMPRSS11E, UGT2B17

chr7:13,933,308-14,336,685

403

p21.2

Gain

46.67

<0.001

1

ETV1

ETV1

chr7:38,306,193-38,380,749

75

p14.1

Loss

33.33

<0.001

1

TARP

chr7:156,798,142-156,928,704

131

q36.3

Loss

46.67

<0.001

2

MNX1, LOC645249

chr8:145,737,034-145,741,006

4

q24.3

Loss

40.00

<0.001

1

RECQL4

RECQL4

chr9:139,390,677-139,425,667

35

q34.3

Loss

26.67

0.003

1

NOTCH1

NOTCH1

chr10:3,514,976-3,988,938

474

p15.2 - p15.1

Gain

26.67

0.008

1

KLF6

chr10:89,581,346-89,717,798

136

q23.31

Loss

20.00

0.021

3

CFL1P1, KLLN, PTEN

PTEN

chr11:65,263,143-65,279,263

16

q13.1

Gain

26.67

0.003

1

MALAT1

chr16:2,104,905-2,135,150

30

p13.3

Loss

20.00

0.021

1

TSC2

TSC2

chr16:79,628,093-79,633,200

5

q23.2

Gain

20.00

0.003

1

MAF

MAF

chr16:89,550,964-89,780,717

229753

q24.3

Gain

20.00

0.003

12

ANKRD11, SPG7, SNORD68, RPL13, CPNE7, DPEP1, CHMP1A, C16orf55, CDK10, SPATA2L, VPS9D1, LOC100128881

chr17:79,848,607-79,974,997

126390

q25.3

Loss

26.67

0.02

11

ALYREF, ANAPC11, NPB, PCYT2, SIRT7, MAFG, MAFG-AS1, PYCR1, MYADML2, NOTUM, ASPSCR1

ASPSCR1

chr18:14,827,524-15,293,288

465764

p11.21

Loss

53.33

<0.001

2

ANKRD30B, MIR3156-2

chr19:42,402,083-42,413,495

11412

q13.2

Loss

40.00

<0.001

1

ARHGEF1

chrX:66,252,360-66,809,186

556827

q12

Gain

33.33

<0.001

1

AR