Optical genome mapping in acute myeloid leukemia: a multicenter evaluation

Abstract

Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in >5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.

Graphical abstract

Figure 1.

Concordance of sentinel events between CBA and OGM. ∗does not include t(9;11). CBA, chromosomal banding analysis.

Figure 2.

Illustrative examples of SVs, CNVs, and unknown cytogenetic elements resolved by OGM. (A) Case 93. (i) Circos plot showing a whole genome view of the multiple genomic rearrangements (pink lines) and copy number profiles (inner circle blue boxes indicate gains and red boxes indicate deletions). (ii) Circos plot showing a selected chromosome view of the complex genomic rearrangements (pink lines) and copy number profiles (inner circle blue boxes indicate gains and red boxes indicate deletions) between chromosomes 17, 20, and 22. (iii) Whole genome CNV profile showing an interstitial deletion on 5q as well a gain of chromosome 8. (iv) Single molecule view of patient DNA (blue) mapping to both reference chromosomes 17 and 20 with break points in GLP2R and CSTI3P, respectively. (v) Fine mapping of the chromosome 5 deletion indicates a large 81.5Mb deletion on the q arm of chromosome 5 between genomic coordinates 83 773 239 and 165 326 693 (human genome build GRCh38). (B) Case 75. (i) Karyotype showing the reported t(8;21)(q22;q22) (red boxes) and break points (blue arrows) of the cryptic der(5)t(4;5)(q26;q21.3). (ii) Circos plot showing the t(8;21) (q22;q22) and der(5)t(4;5)(q26;q21.3) (pink lines), deletions (red arrows) at 8q21.3q22.1 and gain (blue arrow) of 4q26q35.2. (iii) CMA profile of deletions and losses shown in panel Bii. (C) Classic AML rearrangements. GRCh38 reference chromosomes with OGM label patterns are shown in green. Assembled sample maps with label patterns are shown in light blue. Label alignments between 2 maps are shown in gray strings. Overlapping genes are shown in purple. (i) Case 82 with inv(3)(q21.3q26.3). (ii) Case 84 with inv(16)(p13.11q22.1).

Figure 2.

Illustrative examples of SVs, CNVs, and unknown cytogenetic elements resolved by OGM. (A) Case 93. (i) Circos plot showing a whole genome view of the multiple genomic rearrangements (pink lines) and copy number profiles (inner circle blue boxes indicate gains and red boxes indicate deletions). (ii) Circos plot showing a selected chromosome view of the complex genomic rearrangements (pink lines) and copy number profiles (inner circle blue boxes indicate gains and red boxes indicate deletions) between chromosomes 17, 20, and 22. (iii) Whole genome CNV profile showing an interstitial deletion on 5q as well a gain of chromosome 8. (iv) Single molecule view of patient DNA (blue) mapping to both reference chromosomes 17 and 20 with break points in GLP2R and CSTI3P, respectively. (v) Fine mapping of the chromosome 5 deletion indicates a large 81.5Mb deletion on the q arm of chromosome 5 between genomic coordinates 83 773 239 and 165 326 693 (human genome build GRCh38). (B) Case 75. (i) Karyotype showing the reported t(8;21)(q22;q22) (red boxes) and break points (blue arrows) of the cryptic der(5)t(4;5)(q26;q21.3). (ii) Circos plot showing the t(8;21) (q22;q22) and der(5)t(4;5)(q26;q21.3) (pink lines), deletions (red arrows) at 8q21.3q22.1 and gain (blue arrow) of 4q26q35.2. (iii) CMA profile of deletions and losses shown in panel Bii. (C) Classic AML rearrangements. GRCh38 reference chromosomes with OGM label patterns are shown in green. Assembled sample maps with label patterns are shown in light blue. Label alignments between 2 maps are shown in gray strings. Overlapping genes are shown in purple. (i) Case 82 with inv(3)(q21.3q26.3). (ii) Case 84 with inv(16)(p13.11q22.1).