Cytogenetic and molecular genetics of the 20 patients with near-haploid and low-hypodiploid ALL
| Patient . | PCGP ID . | Ploidy group . | Next-generation sequencing . | Karyotype . | Genomic lesion . |
|---|---|---|---|---|---|
| 1 | SJHYPO122 | Near haploid | WES | *48(24,X,+21)x2[20]/46,XY[1] | NF1 Y2455*; RB1 L317fs; CDKN2A/B deletion |
| 2 | SJBALL156 | Near haploid | WES | *50(25,X,+14,+21)x2,del(1)(q42),add(11)(p15)[5]/46,XY[4] | KRAS G12D and EP300 D1399N |
| 3 | SJBALL014876 | Near haploid | WES | *53(26,X,+10,+14,+21)x2,del(9)(p22),i(9)(q10),+mar[4]/53,idem,+9,-mar[16]/46,XX[1] | CREBBP S1432fs, WHSC1 E1099K, USH2A I1326M, NF1 P678fs |
| 4 | SJHYPO143 | Near haploid | WES | 27,X,+X,+18,+21,+mar[6]/54,idemx2[3]/46,XX [15] | No mutations in key pathways |
| 5 | SJHYPO128 | Near haploid | WES | 27,X,+X,+14,+21,+22[13]/54,idemx2,-X,+10,-14,+17,+18,-21,-22,+mar[7] | NF1 T2600fs |
| 6 | SJHYPO123 | Near haploid†,‡ | WGS, RNA-seq | 27,X,+Y,+13,+18,+21[8]/35,idem,+1,+2,+3,+5,+6,+7,+11,+15[6]/46,XY[14] | NF1 deletion of exons 33-41; histone cluster (6p22) deletion |
| 7 | SJHYPO146 | Near haploid† | WGS, WES | 27,X,+Y,+17,+18,+21[5]/54,idemx2[6]/46,XY[8] | NF1 T2133fs and deletion; CREBBP E1240K and deletion; PAX5 G25E |
| 8 | SJHYPO124 | Near haploid‡ | WES | 30,X,+Y,+4,+8,+10,+14,+18,+21[4]/60,idemx2[14]/46,XY[2] | NF1 E470* |
| 9 | SJHYPO141 | Low hypodiploid§ | WES (germ line) | 33,X,+1,+2,+6,+10,+11,+12,+18,+19,+21,+22[6]/46,XX [14] | Not available for tumor |
| 10 | SJHYPO22048 | Low hypodiploid§ | WES (germ line) | 34,X,+Y,+1,+5,+6,+7,+10,+11,+15,+17,+19,+21[13]/62,idemx2,-X,-Y,-1,+3,-5,-6,-7,-10,-11,+14,-15,-17,+18,-19,+20,+22[4]/46,XY[3] | Not available for tumor |
| 11 | SJBALL014875 | Low hypodiploid | WES | 35,X,+1,+5,+6,+9,+11,+12,+14,+18,+19,+20,+21,+22[11]/46,XY[9] | MAPK mutation |
| 12 | SJHYPO135 | Low hypodiploid | WES | 35,X,+X,+1,+2,+4,+5,+6,+8,+11,+12,+16,+19,+21[10]/67,idemx2,-2,-5,-6,+10,+10,-11,-12,-12,+14,-16,-16,+18,-19,+20,+22[5]/46,XX[2] | RB1 V654M; TP53 C283Y |
| 13 | SJHYPO125 | Low hypodiploid‡ | WES | 35,X,+X,+1,der(1)t(1;7)(p36.1;q11.2)c,+5,+6,+8,+10,+11,+14,+18,+19,+21,+22[9]/67,idemx2,-5,-14,-19[9] | No mutations in key pathways |
| 14 | SJHYPO138 | Low hypodiploid§ | WES (germ line) | 35,X,+Y,+1,+5,+6,+8,+9,+10,+11,+18,+19,+21,+22[20] | Not available for tumor |
| 15 | SJHYPO126 | Low hypodiploid‡ | WES | 35,X,+1,+5,+6,+8,+10,+11,+14,+15,+18,+19,+21,+22[8]/64,idemx2,-5,-10,-11,-14,-15,-19[9]/46,XX[3] | IKZF2 exon 5 deletion; TP53 I162fs mutation (germ line) |
| 16 | SJHYPO144 | Low hypodiploid | WES | 36,X,+Y,+1,+5,+6,+8,+10,+11,+14,+15,+18,+19,+21,+22[16]/46,XY [4] | TP53 L32_E4splice |
| 17 | SJHYPO139 | Low hypodiploid | WES | 36,X,+Y,+1,+2,+5,+6,+8,+9,+10,+11,+17,+19,+21,+22[5]/72,idemx2[2]/46,XY[13] | TP53 R175H; IKZF2 deletion |
| 18 | SJHYPO140 | Low hypodiploid† | WES | 37,X,+Y,+1,+5,+6,+8,+9,+10,+11,+14,+18,+19,+20,+21,+22[11]/74,idemx2[10]/46,XY[3] | RB1 mutation |
| 19 | SJBALL108 | Low hypodiploid | WES | 38,X,+1,+2,+5,+6,+8,+9,del(9)(p13),ins(10;11)(q26;q21q24),+11,+14,+15,+16,+18,+19,+20,+21,+22[7]/38,idem,del(2)(p13p23)[4]/46,XX[9] | PAX5, CDKN2A/B deletion |
| 20 | SJHYPER22044 | Low hypodiploid* | NA | 73(40,X,+Y,+1,+4,+5,+6,+8,+9,+10,+11,+13,+14,+15,+17,+18,+20,+21,+22)x2,-4,-5,-11,-13,-14,-15,-20[11]/46,XY[9] | No focal deletions; LOH of chromosomes 2,3,4,7,11,12,13,15,16,17 |
| Patient . | PCGP ID . | Ploidy group . | Next-generation sequencing . | Karyotype . | Genomic lesion . |
|---|---|---|---|---|---|
| 1 | SJHYPO122 | Near haploid | WES | *48(24,X,+21)x2[20]/46,XY[1] | NF1 Y2455*; RB1 L317fs; CDKN2A/B deletion |
| 2 | SJBALL156 | Near haploid | WES | *50(25,X,+14,+21)x2,del(1)(q42),add(11)(p15)[5]/46,XY[4] | KRAS G12D and EP300 D1399N |
| 3 | SJBALL014876 | Near haploid | WES | *53(26,X,+10,+14,+21)x2,del(9)(p22),i(9)(q10),+mar[4]/53,idem,+9,-mar[16]/46,XX[1] | CREBBP S1432fs, WHSC1 E1099K, USH2A I1326M, NF1 P678fs |
| 4 | SJHYPO143 | Near haploid | WES | 27,X,+X,+18,+21,+mar[6]/54,idemx2[3]/46,XX [15] | No mutations in key pathways |
| 5 | SJHYPO128 | Near haploid | WES | 27,X,+X,+14,+21,+22[13]/54,idemx2,-X,+10,-14,+17,+18,-21,-22,+mar[7] | NF1 T2600fs |
| 6 | SJHYPO123 | Near haploid†,‡ | WGS, RNA-seq | 27,X,+Y,+13,+18,+21[8]/35,idem,+1,+2,+3,+5,+6,+7,+11,+15[6]/46,XY[14] | NF1 deletion of exons 33-41; histone cluster (6p22) deletion |
| 7 | SJHYPO146 | Near haploid† | WGS, WES | 27,X,+Y,+17,+18,+21[5]/54,idemx2[6]/46,XY[8] | NF1 T2133fs and deletion; CREBBP E1240K and deletion; PAX5 G25E |
| 8 | SJHYPO124 | Near haploid‡ | WES | 30,X,+Y,+4,+8,+10,+14,+18,+21[4]/60,idemx2[14]/46,XY[2] | NF1 E470* |
| 9 | SJHYPO141 | Low hypodiploid§ | WES (germ line) | 33,X,+1,+2,+6,+10,+11,+12,+18,+19,+21,+22[6]/46,XX [14] | Not available for tumor |
| 10 | SJHYPO22048 | Low hypodiploid§ | WES (germ line) | 34,X,+Y,+1,+5,+6,+7,+10,+11,+15,+17,+19,+21[13]/62,idemx2,-X,-Y,-1,+3,-5,-6,-7,-10,-11,+14,-15,-17,+18,-19,+20,+22[4]/46,XY[3] | Not available for tumor |
| 11 | SJBALL014875 | Low hypodiploid | WES | 35,X,+1,+5,+6,+9,+11,+12,+14,+18,+19,+20,+21,+22[11]/46,XY[9] | MAPK mutation |
| 12 | SJHYPO135 | Low hypodiploid | WES | 35,X,+X,+1,+2,+4,+5,+6,+8,+11,+12,+16,+19,+21[10]/67,idemx2,-2,-5,-6,+10,+10,-11,-12,-12,+14,-16,-16,+18,-19,+20,+22[5]/46,XX[2] | RB1 V654M; TP53 C283Y |
| 13 | SJHYPO125 | Low hypodiploid‡ | WES | 35,X,+X,+1,der(1)t(1;7)(p36.1;q11.2)c,+5,+6,+8,+10,+11,+14,+18,+19,+21,+22[9]/67,idemx2,-5,-14,-19[9] | No mutations in key pathways |
| 14 | SJHYPO138 | Low hypodiploid§ | WES (germ line) | 35,X,+Y,+1,+5,+6,+8,+9,+10,+11,+18,+19,+21,+22[20] | Not available for tumor |
| 15 | SJHYPO126 | Low hypodiploid‡ | WES | 35,X,+1,+5,+6,+8,+10,+11,+14,+15,+18,+19,+21,+22[8]/64,idemx2,-5,-10,-11,-14,-15,-19[9]/46,XX[3] | IKZF2 exon 5 deletion; TP53 I162fs mutation (germ line) |
| 16 | SJHYPO144 | Low hypodiploid | WES | 36,X,+Y,+1,+5,+6,+8,+10,+11,+14,+15,+18,+19,+21,+22[16]/46,XY [4] | TP53 L32_E4splice |
| 17 | SJHYPO139 | Low hypodiploid | WES | 36,X,+Y,+1,+2,+5,+6,+8,+9,+10,+11,+17,+19,+21,+22[5]/72,idemx2[2]/46,XY[13] | TP53 R175H; IKZF2 deletion |
| 18 | SJHYPO140 | Low hypodiploid† | WES | 37,X,+Y,+1,+5,+6,+8,+9,+10,+11,+14,+18,+19,+20,+21,+22[11]/74,idemx2[10]/46,XY[3] | RB1 mutation |
| 19 | SJBALL108 | Low hypodiploid | WES | 38,X,+1,+2,+5,+6,+8,+9,del(9)(p13),ins(10;11)(q26;q21q24),+11,+14,+15,+16,+18,+19,+20,+21,+22[7]/38,idem,del(2)(p13p23)[4]/46,XX[9] | PAX5, CDKN2A/B deletion |
| 20 | SJHYPER22044 | Low hypodiploid* | NA | 73(40,X,+Y,+1,+4,+5,+6,+8,+9,+10,+11,+13,+14,+15,+17,+18,+20,+21,+22)x2,-4,-5,-11,-13,-14,-15,-20[11]/46,XY[9] | No focal deletions; LOH of chromosomes 2,3,4,7,11,12,13,15,16,17 |
LOH, loss of heterozygosity; NA, not available; PCGP, Pediatric Cancer Genome Project; WES, whole exome sequencing; WGS, whole genome sequencing.
Chromosome number reflected doubling of the hypodiploid clone.
Also Ph-like.
Genome sequencing previously reported.
No diagnostic material available for genomic analysis.