Table 2.
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.