Chr

Cytoband

Start

End

Length (bps)

Length (Kb)

Modification

No. probes

Probe density

Mean copy number

P-value

Overlapping RefSeq genes

1

1p32.2

58018411

58102775

84364

84

Amplification

13

6489.54

3.04943

0.00180806

Intron of DAB1 (--−)

2

2p21

47182709

47259414

76705

77

Deletion

11

6973.18

1.17658

0.00445066

Contained within TTC7A (+)

2

2p25.1

9784529

9857416

72887

73

Deletion

10

7288.7

1.18714

0.000653079

None

2

2q14.2

119893616

120103405

209789

210

Deletion

26

8068.81

1.35894

0.00581587

C1QL2 (--−), STEAP3 (+), region overlaps with 20.78% of C2orf76 (--−)

3

3p26.1

6394113

6490483

96370

96

Deletion

14

6883.57

1.30877

0.0468727

None

4

4q23

100164895

100319304

154409

154

Deletion

12

12867.4

1.37538

0.0193024

ADH1A (--−), ADH1B (--−), ADH1C (--−), region overlaps with 37.3% of LOC100507053 (+)

5

5q31.1

131646277

131969143

322866

323

Deletion

27

11958

1.37316

0.00514616

C5orf56 (+), IL5 (--−), IRF1 (--−), LOC553103 (--−), MIR3936 (--−), SLC22A5 (+), region overlaps with 10.4% of SLC22A4 (+), 23.7% of RAD50 (+)

5

5q33.1

150982753

151040778

58025

58

Deletion

10

5802.5

1.18605

0.00123703

Region overlaps with 0.2% of SPARC (--−)

6

6p12.1

53226579

53361010

134431

134

Deletion

13

10340.8

1.2829

0.0113972

None

6

6p25.1

6598746

6665270

66524

67

Deletion

14

4751.71

1.27237

0.0131841

Region overlaps with 36.6% of LY86--−AS1 (--−), 84.9% of LY86 (+)

7

7p13

44783038

45237489

454451

454

Deletion

39

11652.6

1.46163

0.0140781

CCM2 (+), H2AFV (--−), MIR4657 (--−), MYO1G (--−), NACAD (--−), PPIA (+), PURB (--−), RAMP3 (+), SNHG15 (--−), SNORA5A (--−), SNORA5B (--−), SNORA5C (--−), SNORA9 (--−), TBRG4 (--−), ZMIZ2 (+)

7

7q35

145066826

145882546

815720

816

Amplification

27

30211.9

2.91072

2.99E--−05

Region overlaps with 8.5% of CNTNAP2 (+)

10

10q22.1

72660683

73858777

1198094

1198

Deletion

184

6511.38

1.58835

0.00311729

C10orf105 (--−), C10orf54 (--−), CDH23 (+), CHST3 (+), LOC102723377 (--−), MIR7152 (+), PSAP (--−), SLC29A3 (+), SPOCK2 (--−), UNC5B (+), UNC5B--−AS1 (--−), region overlaps with 0.2% of ASCC1 (--−)

11

11p15.1

19576970

19620319

43349

43

Deletion

10

4334.9

1.19839

0.000673858

MIR4486 (+), intron of NAV2 (+)

13

13q14.11

40883885

40954431

70546

71

Deletion

10

7054.6

1.21126

0.0203006

Region overlaps with 47.0% of LINC00598 (--−)

16

16p13.3

86671

2372535

2285864

2286

Deletion

131

17449.3

1.55843

0.00107079

ARHGDIG (+), AXIN1 (--−), BAIAP3 (+), BRICD5 (--−), C16orf13 (--−), C16orf91 (--−), C1QTNF8 (--−), CACNA1H (+), CAPN15 (+), CASKIN1 (--−), CCDC154 (--−), CCDC78 (--−), CHTF18 (+), CLCN7 (--−), CRAMP1L (+), DECR2 (+), DNASE1L2 (+), E4F1 (+), ECI1 (--−), EME2 (+), FAHD1 (+), FAM173A (+), FAM195A (+), FBXL16 (--−), GFER (+), GNG13 (--−), GNPTG (+), HAGH (--−), HAGHL (+), HBA1 (+), HBA2 (+), HBM (+), HBQ1 (+), HBZ (+), HN1L (+), HS3ST6 (--−), IFT140 (--−), IGFALS (--−, ITFG3 (+), JMJD8 (--−), LINC00235 (--−), LINC00254 (--−), LMF1 (--−),

LMF1--−AS1 (+), LOC100134368 (+), LUC7L (--−), MAPK8IP3 (+), MEIOB (--−), METRN (+), MIR1225 (--−), MIR3176 (+), MIR3177 (+), MIR3180--−5 (--−), MIR3677 (+), MIR4516 (+), MIR4717 (+), MIR5587 (+), MIR6511B1 (--−), MIR6511B2 (--−), MIR662 (+), MIR940 (+), MLST8 (+), MPG (+), MRPL28 (--−), MRPS34 (--−), MSLN (+), MSRB1 (--−), NARFL (--−), NDUFB10 (+), NHLRC4 (+), NME3 (--−), NME4 (+), NOXO1 (--−), NPRL3 (--−), NPW (+), NTHL1 (--−), NUBP2 (+), PDIA2 (+), PGP (-­−), PIGQ (+), PKD1 (--−), POLR3K (-­−), PRR25 (+), PRR35 (+), PTX4 (--−), RAB11FIP3 (+), RAB26 (+), RAB40C (+), RGS11 (--−), RHBDF1 (--−), RHBDL1 (+), RHOT2 (+), RNF151 (+), RNPS1 (--−), RPL3L (--−), RPS2 (--−), RPUSD1 (--−), SLC9A3R2 (+), SNHG9 (+), SNORA10 (--−), SNORA64 (--−), SNORA78 (+), SNORD60 (--−), SNRNP25 (+), SOX8 (+), SPSB3 (--−), SSTR5 (+), SSTR5--−AS1 (--−), STUB1 (+), SYNGR3 (+), TBL3 (+), TELO2 (+), TMEM204 (+), TMEM8A (--−), TPSAB1 (+), TPSB2 (--−), TPSD1 (+), TPSG1 (--−), TRAF7 (+), TSC2 (+), TSR3 (--−), UBE2I (+), UNKL (--−), WDR24 (--−), WDR90 (+), WFIKKN1 (+), ZNF598 (--−), region overlaps with 2.0% of ABCA3 (--−)

16

16q22.1

68713776

68766540

52764

53

Deletion

10

5276.4

1.18734

0.0108732

Region overlaps with 36.4% of CDH3 (+)

16

16q24.3

88856351

90156776

1300425

1300

Deletion

95

13688.7

1.53951

0.00253683

ACSF3 (+), AFG3L1P (+), ANKRD11 (--−), APRT (--−), CBFA2T3 (--−), CDH15 (+), CDK10 (+), CDT1 (+), CENPBD1 (--−), CHMP1A (--−), CPNE7 (+), DBNDD1 (--−), DEF8 (+), DPEP1 (+), FANCA (--−), GALNS (--−), GAS8 (+), GAS8--−AS1 (--−), LINC00304 (+), LOC100129697 (+), LOC100287036 (+), LOC101927817 (+), LOC400558 (+), MC1R (+), PABPN1L (--−), PRDM7 (--−), RPL13 (+), SLC22A31 (--−), SNORD68 (+), SPATA2L (--−), SPATA33 (+), SPG7 (+), SPIRE2 (+), TCF25 (+), TRAPPC2L (+), TUBB3 (+), URAHP (--−), VPS9D1 (--−), VPS9D1--−AS1 (+), ZNF276 (+), ZNF778 (+)

17

17q21.31

44120955

44267657

146702

147

Amplification

27

5433.41

2.66323

0.0147722

Contained within KANSL1 (--−)

17

17q21.33--− 17q22

50041539

52770545

2729006

2729

Amplification

175

15594.3

2.42975

0.0147755

C17orf112 (+), KIF2B (+), region overlaps with 7.1% of CA10 (--−), 7.2% of CA10 (--−), 7.2% of CA10 (--−)

20

20q12

40524911

40574279

49368

49

Amplification

10

4936.8

3.22544

0.000732926

None

20

20q13.32

58180686

58302046

121360

121

Amplification

10

12136

3.15384

0.00611637

LOC100506384 (--−), intron of PHACTR3 (+), region overlaps with 4.8% of PHACTR3 (+), 41.5% of PHACTR3 (+), 81.1% of PHACTR3 (+)

21

21q22.2

39949569

40032072

82503

83

Deletion

10

8250.3

1.18693

0.0143156

Contained within ERG (--−), region overlaps with 8.9% of ERG (--−)

21

21q22.3

43461765

43534781

73016

73

Deletion

10

7301.6

0.937121

0.0138014

UMODL1--−AS1 (--−), region overlaps with 59.4% of UMODL1 (+), 70.8% of UMODL1 (+)

22

22q12.3

34634252

34899238

264986

265

Amplification

34

7793.71

2.61709

0.00171403

None