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. 2021 Apr;7(2):a005975. doi: 10.1101/mcs.a005975

Table 2.

Genomic characterization

Patient Specimen Major cytogenetic findingsa Fusions CNVs by NGS SNVsb (Tier 1–2), variant allele fraction
1 Bone marrow aspirate Complex and multiclonal; no pathognomonic findings NUP98/KDM5A Complex with numerous CNVs, including loss of RB1, and chromothripsis at varying degrees of subclonalityc None
2 Bone marrow aspirate Balanced translocation between Chromosome 16 homologs CBFA2T3/GLIS2 No significant CNV; suboptimal data quality None
3 Frozen brain mass Karyotype not performed, FISH inconclusive CBFA2T3/GLIS2 No significant CNV; suboptimal data quality None
4 Bone marrow aspirate Pericentric Chromosome 16 inversion CBFA2T3/GLIS2 1q gain None
5 Bone marrow aspirate Balanced translocation between long arms of Chromosomes 16 and 19 CBFA2T3/GLIS2 No significant CNV; suboptimal data quality SETD2 p.(Trp1306*), 16%
6 Bone marrow aspirate Complex and multiclonal with unbalanced translocation between the long arms of Chromosomes 11 and 17 KMT2A/MLLT6 No significant CNV SETD2 p.(Arg441*), 7% EPOR p.(Trp439*) 6%
7 Peripheral blood Not performed/ordered NA Trisomy 21 GATA1 p.(Gln17Valfs*22), 59%
8 Peripheral blood Constitutional trisomy 21 NA Trisomy 21 GATA1 p.(Val74Serfs*63), 95%
9 Peripheral blood NA NA Trisomy 21 GATA1 p.(Ser51Leufs*5), 42%
10 Peripheral blood Constitutional study, PHA-stimulated: trisomy 21 NA Trisomy 21 GATA1 p.(Glu2Glyfs*38), 73%
11 Bone marrow aspirate Constitutional trisomy 21 and subclonal trisomies 8 and 14 NA Trisomy 21 GATA1 p.(Asp65Glyfs*9), 10% RAD21 p.(Tyr3*), 8%
12 Bone marrow aspirate Constitutional trisomy 21 NA Trisomy 21 GATA1 p.(Ser30*), 15% CTCF p.(Tyr502Ilefs*10), 7%
13 Bone marrow aspirate Constitutional trisomy 21 and subclonal trisomy 8 NA Trisomy 21, subclonal trisomy 8 GATA1 p.(Glu39Glyfs*22), 30% CTCF p.(Asp547Valfs*34), 17% SUZ12 p.(Leu385Profs*10), 32% JAK2 p.(Phe694Leu), 22%
14 Bone marrow aspirate Constitutional trisomy 21 Trisomy 21 GATA1 p.(Ser51Leufs*89), 16% GATA1 p.(Ala58Hisfs*14), 38% JAK1 p.(Leu783Phe), 6% SRSF2 p.(Pro95Arg), 6%
15 Peripheral blood Constitutional trisomy 21 Trisomy 21 GATA1 p.(Pro73Pro), 16% NRAS p.(Gly13Asp), 17% PTPN11 p.(Thr411Met), 43%

(FISH) Fluorescence in situ hybridization, (NA) not available, (CNV) copy-number variation, (NGS) next-generation sequencing, (SNV) single-nucleotide variation.

aSee Table 3 for detailed cytogenetic results.

bSee Table 4 for detailed SNV results.

cCNVs characterized by chromosomal microarray instead of NGS.