Comparison of routine diagnostic test results with OGM results in simple cases
Sample ID | Diagnosis | Karyotype | FISH | RT-PCR/RNA fusion | OGM results (SV tool and/or CNV tool) |
Summary |
---|---|---|---|---|---|---|
2 | AML | 46,XX[20] | NA | NUP98::NSD1 | t(5;11)(q35.3;p15.4) NUP98-NSD1 | Concordant |
3 | AML | 46,XY,inv(16)(p13q22)[23]/46,XY[2] | NA | CBFB::MYH11 | t(16;16)(p13.11;q22.1) CBFB-MYH11 | Concordant |
4 | AML | 46,XX,der(9)ins(9;8)(q13;q22q24.2)[22]/46,XX[1] | NA | NA | MYC amplification |
Concordant Additional by OGM |
5 | AML | 47,XX,+8,t(9;11)(p21;q23)[20] | NA | KMT2A::MLLT3 | +8, t(9;11)(p21.3;q23.3) KMT2A-MLLT3 | Concordant |
6 | AML | 46,XX,t(11;12)(p15;q13)[20] | NA | NUP98::HOXC13 | t(11;12)(p15.4;q13.13) NUP98-HOXC13 | Concordant |
8 | AML | 46,XY,dup(19)(p13.1p13.3)[20]/46,XY[6] | NA | Negative | dup(19)(p13.2p13.2) | Concordant |
9 | AML | 46,XX,t(6;9)(p22;q34)[16]/46,XX[4] | NA | DEK::NUP214 | t(6;9)(p22.3;q34.13) DEK-NUP214 | Concordant |
10 | APL | 46,XY,t(15;17)(q24;q21)[19]/46,XY[1] | NA | PML::RARA | t(15;17)(q24.1;q21) PML-RARA | Concordant |
11 | CML-CP | 46,XY,t(9;22;11)(q34;q11.2;q13)[20] | NA | BCR::ABL1(b3a2, major type) |
t(9;22)(q34.12;q11.23) BCR-ABL1 t(11;22)(q13.1;q11.23) ARL2-SNX15-CABIN1 t(9;11)(q34.11;q13.1) |
Concordant Additional by OGM |
12 | CML- CP | 46,XX,t(3;11;9;22)(p21;q13;q34;q11.2)[20] | NA | BCR::ABL1(b2a2, major type) |
t(9;11)(q34.11;q13.2) t(9;22)(q34.12;q11.23) t(3;22)(p21.31;q11.23) |
Partial concordance |
13 | CML-CP | 46,XY,t(7;9;22)(q22;q34;q11.2)[14] | NA |
BCR::ABL1(b2a2, major type) BCR::ABL1(e1a2, minor type,weakly positive) |
t(7;22)(q22.1;q11.23) t(9;22)(q34.12;q11.23) |
Partial concordance |
14 | PMF | 46,XY,der(6)t(1;6)(q21;p21)[3]/46,XY[17] | NA | NA | del(6)(p21.1p25.3) | Partial concordance |
17 | B-ALL | 46,XY,t(9;22)(q34;q11.2)[3]/47,idem,+21[9]/46,XY[8] | NA | BCR::ABL1(e1a2, minor type) | t(9;22)(q34.12;q11.23) BCR-ABL1+21IKZF1 exon 4-7 deletion |
Concordant Additional by OGM |
18 | B-ALL | 46,XY[30] | Negative for t(11q23) break-apart | Negative |
del(12)(p13.31p12.1) del(17)(p11.2p13.3) dup(17)(p11.2q25.3) t(12;22)(p13.31;q13.2) EP300-ZNF384 |
Concordant Additional by OGM |
19 | B-ALL | 47,XX,+X,t(2;14)(p11.2;q32)[5]/46,XX[20] | NA | Negative for BCR::ABL1 | +X, t(2;14)(p11.2;q32.33) | Concordant |
21 | B-ALL | 46,XY,t(2;12)(p11.2;p13)[5]/46,XY[4] | NA | Negative for BCR::ABL1 | t(2;12)(p12;p13.2)IKZF1 exon 4-7 deletion |
Concordant Additional by OGM |
22 | B-ALL | 46,XY[13] | NA | ETV6::RUNX1 | t(12;21)(p13.2;q22.12) | Concordant |
23 | CLL | 46,XY[20] | Positive for del(13q) | NA | del(13)(q14.3) | Concordant |
*Detection of MYC amplification by OGM was confirmed by FISH.
†IKZF1 exon 4–7 deletion was not called by OGM but was detectable upon manual inspection.
‡Detection of SETD2 exon 1–10 deletion by OGM was confirmed using NGS CNV analysis.
§A false-positive call (ATP5L-KMT2A fusion) was initially called using an RNA fusion panel.
||Detection of the EP300-ZNF384 fusion by OGM was confirmed by Sanger sequencing.
¶Detection of del(12)(p13.31p12.1), del(17)(p11.2p13.3), and dup(17)(p11.2q25.3) by OGM was confirmed by NGS CNV analysis.
**Detection of CDKN2A and CDKN2B whole gene deletion by OGM was confirmed by NGS CNV analysis.
Abbreviations: OGM, optical genome mapping; FISH, fluorescence in situ hybridization; RT-PCR, reverse transcription PCR; SV, structural variant; CNV, copy number variant; APL, acute promyelocytic leukemia; B-ALL, B-lymphoblastic leukemia; CML-CP, chronic myeloid leukemia in chronic phase; PMF, primary myelofibrosis; NA, not available.
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