Supplementary material J Med Genet

Supplementary Table 1. DNA array1 data of the leukemic clone from patient C.2.2.

Chromosome Cytoband Type CN State Size (kb) Full Location Count Interpretation

3 p25.3p25.2 Loss 1 3831,3 chr3:9140941-12972193 SRGAP3, SRGAP3-AS3, THUMPD3, SETD5-AS1, 58 heterozygous deletion del(3)(p25.3p25.2) SETD5, LHFPL4, MTMR14, CPNE9, BRPF1, OGG1, with breakpoints in SRGAP3 and IQSEC1 CAMK1, TADA3, ARPC4, ARPC4-TTLL3, TTLL3, RPUSD3, CIDEC, JAGN1, IL17RE, IL17RC, CRELD1, PRRT3, PRRT3-AS1, EMC3, LOC401052, CIDECP, FANCD2, FANCD2OS, BRK1, VHL, IRAK2, TATDN2, GHRLOS, LINC00852, GHRL, SEC13, ATP2B2, MIR885, LINC00606, SLC6A11, SLC6A1, SLC6A1- AS1, HRH1, ATG7, VGLL4, TAMM41, SYN2, TIMP4, PPARG, TSEN2, C3orf83, MKRN2, RAF1, TMEM40, CAND2, RPL32, SNORA7A, IQSEC1 3 q23q24 Loss 1 4100,6 chr3:139522572-143623204 CLSTN2, TRIM42, SLC25A36, SPSB4, ACPL2, 24 heterozygous deletion del(3)(q23q24) ZBTB38, RASA2, RNF7, GRK7, ATP1B3, TFDP2, GK5, XRN1, ATR, PLS1, TRPC1, PCOLCE2, LOC100507389, PAQR9, LOC100289361, U2SURP, CHST2, SLC9A9, SLC9A9-AS1 3 q11.1q11.2 Loss 1 4000,8 chr3:93519464-97520232 PROS1, ARL13B, STX19, DHFRL1, NSUN3, 9 heterozygous deletion del(3)(q11.1q11.2) LINC00879, LOC100287639, EPHA6, ARL6 4 p16.3q35.2 Gain 3 190889,1 chr4:68345-190957473 multiple genes/whole 891 trisomy 4

7 p12.2p12.2 Loss 1 55,1 chr7:50413611-50468721 IKZF1 1 heterozygous deletion of IKZF1 4-7

8 p23.3q24.3 Gain 3 146137,7 chr8:158048-146295771 multiple genes/whole chromosome 837 trisomy 8

9 p24.3q34.3 Gain 3 140816,5 chr9:203861-141020389 multiple genes/whole chromosome 961 trisomy 9

10 p15.3q26.3 Gain 3 135327,1 chr10:100026-135427143 multiple genes/whole chromosome 921 trisomy 10

10 q21.2q21.3 LOH 3664,2 chr10:62617282-66281499 RHOBTB1, TMEM26, C10orf107, ARID5B, 14 constitutional copy-neutral loss-of- MIR548AV, RTKN2, ZNF365, ADO, EGR2, NRBF2, heterozygosity 10q21.2q21.3 present in JMJD1C, MIR1296, JMJD1C-AS1, REEP3 all 3 alleles 13 q12.2q12.2 Loss 1 132,2 chr13:28684222-28816404 PAN3-AS1, PAN3 2 heterozygous deletion of PAN3 exons 1-6 and PAN3-AS1 14 q11.2q32.12 Gain 3 71852,3 chr14:20511672-92363929 multiple genes/whole chromosome 523 trisomy 14

14 q32.12q32.13 Loss 2 2811,8 chr14:92367890-95179707 FBLN5, TRIP11, ATXN3, NDUFB1, CPSF2, 40 disomic region of otherwise trisomic SLC24A4, RIN3, LGMN, GOLGA5, CHGA, ITPK1, chromosome 14 (1 of 3 alleles deleted) ITPK1-AS1, MOAP1, TMEM251, C14orf142, UBR7, BTBD7, UNC79, COX8C, PRIMA1, FAM181A-AS1, FAM181A, ASB2, LINC00521, OTUB2, DDX24, IFI27L1, IFI27, IFI27L2, PPP4R4, SERPINA10, SERPINA6, SERPINA1, SERPINA11, SERPINA9, SERPINA12, SERPINA4, SERPINA5, SERPINA3, SERPINA13P

Karastaneva A, et al. J Med Genet 2020; 57:427–433. doi: 10.1136/jmedgenet-2019-106339 Supplementary material J Med Genet

Supplementary Table 1. DNA array1 data of the leukemic clone from patient C.2.2.

Chromosome Cytoband Type CN State Size (kb) Full Location Genes Gene Count Interpretation

14 q32.13q32.33 Gain 3 12105,7 chr14:95179769-107285437 multiple genes/whole chromosome 208 trisomy 14

17 q12q25.1 Gain 3 41483,6 chr17:37850697-79354166 multiple genes 688 duplication dup(17)(q12q25.3) with breakpoints in ERBB2 and in LOC100130370 or in BAHCC1 18 p11.32q23 Gain 3 77877,9 chr18:136226-78014123 multiple genes/whole chromosome 342 tisomy 18

21 q11.2q22.3 Gain 4 33090,9 chr21:15006457-48097372 multiple genes/whole chromosome 293 tetrasomy 21

X p22.33q28 Gain 2 155044,3 chrX:168546-155233731 multiple genes/whole chromosome 1021 disomy X

1, The DNA sample was processed on the CytoScan™ HD Array (ThermoFisher, Vienna, Austria) and analyzed using the Chromosome Analysis Suite version 3.1 (ChAS; ThermoFisher/Affymetrix) software package. All aberrations were mapped to the Genome Reference Consortium GRCh37, UCSC genome assembly hg19 reference genome. Genomic segments were filtered according to the following parameters: losses 25 markers genome-wide, 20 markers in leukemia-associated regions; gains 50 markers and 50 kb genome-wide, 25 markers in leukaemia-associated regions; LOH 50 markers and 3 Mb. Copy number variants (CNVs) arising from B-cell and T-cell antigen receptor gene rearrangements as well as all known common benign CNVs were excluded. CN, copy number; kb, kilobases; LOH, loss-of-heterozygosity.

Karastaneva A, et al. J Med Genet 2020; 57:427–433. doi: 10.1136/jmedgenet-2019-106339