Table 1 Cytogenetic and molecular features of chromosomal instability in described patient

1

1p36.33p36.23

arr[hg19] 1p36.33p36.23(849,466-8,096,240)x1–2

CAMTA1, ERRFI1, MIB2, RPL22, PRDM16, DVL1

dup(1)?(p32p34)

1p36.23p36.13

arr[hg19] 1p36.23p36.13(8,931,529-19,215,840)x2–3

PIK3CD, PRDM2, SDHB, CASP9, MTOR, MTHFR, ENO1

nuc ish (STILx3)

LSI STIL Dual Color, Break Apart Rearrangement Probe (Empire Genomic)

1p36.12p31.3

arr[hg19] 1p36.12p31.3(23,146,680-67,365,806)x2–3

MUTYH, RPS6KA1, STIL, IL22RA1, LCK, PTCH2, PPP1R8, JAK1, CSF3R, JUN, SFPQ, CITED4, CDKN2C, RPA2, MPL, YBX1, CLIC4, TSPAN1, TAL1, COL16A1, HNRNPR, MDS2, RSPO1, PRDX1, EPS15, CDC20, PDZK1IP1

1p31.1p21.1

arr[hg19] 1p31.1p21.1(70,493,564-106,636,210)x1–2

BCL10, SEP15, GLMN, RPL5, TGFBR3, GBP1, LPHN2, GFI1

1p13.2q21.1

arr[hg19] 1p13.2q21.1(111,894,976-145,289,186)x1–2

NOTCH2, RHOC, SLC16A1, HIPK1, FAM46C, WDR77, NRAS, BCL2L15, REG4, RAP1A, VTCN1, PDE4DIP

3

der(3)t(1;3)(q12;q22)

3q22.1q24

arr[hg19] 3q22.1q24(133,476,890-146,949,828)x1–2

ATR, FAIM, RNF7

ish der(3)t(1;3)(wcp3+,wcp1+)

WCP1 WCP3 (Cytocell)

3q25.1q29

arr[hg19] 3q25.1q29(151,583,903-197,851,986)x1–2

PLD1, BCL6, MME, PIK3CA, MUC4, TNFSF10, EIF4A2, DLG1, RAP2B, MECOM, TBL1XR1, LPP, GMPS, PAK2, MECOM, MLF1, RARRES1, SOX2, TFRC

4

invisible

4q31.3q35.2

arr[hg19] 4q31.3q35.2(155,500,158-190,957,473)x2–3

ING2, NPY1R, FAT1, SORBS2

5

der(5)t(5;10)(q21;p11)

ish der(5)t(5;10)(wcp5+,wcp10+)

WCP5 WCP10 (Cytocell)

5q21.1q35.3

arr[hg19] 5q21.1q35.3(100,821,228-180,719,789)x1–2

RANBP17, SNX2, ACSL6, TGFBI, ITK, PTTG1, TSLP, LOX, ARHGAP26, SPINK7, IRF1, NR3C1, APC, TNIP1, NSD1, CSNK1A1, NPM1, GNB2L1, NKX2–5, AFF4, MAPK9, FNIP1, EBF1, CSF1R, TLX3, IL3, HDAC3, EGR1, PDGFRB

del(5)(q33)(D5S23,D5S721+,CSF1R-)

LSI 5q33q34 (CSF1R)Orange/D5S23,D5S721Green Probe Set (Vysis)

6

invisible

6q22.1q27

arr[hg19] 6q22.1q27(115,144,178-170,919,482)x2–3

ECT2L, PLAGL1, hsa-mir-548a-2, MLLT4, MYB, IGF2R, AHI1, TNFAIP3, BCLAF1, FGFR1OP, RNF217-AS1, CTGF, CEP85L, AKAP12, CITED2, RNASET2, THBS2, LATS1

9

der(9)t(4;9)(q32;p21),

9p24.3p21.1

arr[hg19] 9p24.3p21.1(203,861–28,849,504)x1–2

CDKN2A, IFNA1, RLN2, MLLT3 (AF9), SH3GL2, CDKN2A, TEK, JAK2, MTAP, KDM4C, PTPRD, PSIP1, RFX3, CDKN2B, MLLT3

WCP 4 (Cytocell)

10

invisible

10p15.3p11.1

arr[hg19] 10p15.3p11.1(100,026-38,258,848)x2–3

BMI1, MLLT10, ABI1, KLF6, GATA3, NET1, AKR1C3, MRC1

11

der(11)t(1;11)(p?32;p13)

11p15.5p13

arr[hg19] 11p15.5p13(230,615-35,363,338)x1–2

HRAS, PAX6, KIAA1549L (C11orf41), WT1, MUC2, CD44, CD151, EIF3F, LMO1, CARS, HTATIP2, FANCF, RRM1, LMO2, MUC6, NUP98

der(11)t(1;11)(wcp1+,wcp11+),

12

del(12)(p13)

12p13.33p12.1

arr[hg19] 12p13.33p12.1(173,786-22,885,159)x1–2

FOXM1, ERC1, KDM5A, ING4, ATF7IP, EPS8, ETV6, MIR200C, RECQL, BCL2L14, CCND2, GUCY2C, ZNF384, CDKN1B, KLRK1, VWF, CD9, ETNK1, GABARAPL1

nuc ish(ETV6x1,RUNXx2)

LSI ETV6(TEL)/RUNX1(AML1) ES Dual Color Translocation Probe Set (Vysis)

16

der(16)t(6;16)(q22;p13)

16p13.3p13.2

arr[hg19] 16p13.3p13.2(85,880-10,023,421)x1–2

TRAP1, AXIN1, CREBBP, PKD1, TSC2, USP7

der(16)t(6;16)(wcp6+,wcp16+)

WCP6 WCP16 (Cytocell)