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Table. 1.

Table. 1.

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 deletionSETD2 exon 1-10 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 deletionCDKN2A whole gene deletionCDKN2B whole gene 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.

Ann Lab Med 2024;44:324~334 https://doi.org/10.3343/alm.2023.0339

© Ann Lab Med