Solving complex karyotypes in leukemia samples using long-read sequencing.
| Authors | |
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| Year of publication | 2023 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | Highly complex karyotypes represent an adverse prognostic marker in leukemia samples. Their detailed study is substantive to identify specific genomic defects contributing to the deterioration of the disease course. Methods of classical and molecular cytogenomics are widely used in laboratory diagnostics to detect chromosomal aberrations, but their resolution is limited. We aim to employ Oxford Nanopore whole genome long-read sequencing to decipher cancer genome in difficult and ambiguous cases of chronic lymphocytic leukemia with complex karyotypes. Methods: Complex karyotype cases were identified and characterized using classical (IL-2/CpG-stimulated chromosomal banding) and molecular (24xCyte Multicolor FISH, CytoScan HD Array) cytogenomics. For long-read sequencing, high molecular weight DNA was isolated using chloroform-isopropanol extraction, fragmented using an injection needle, and short DNA fragments were eliminated (SRE XS Kit). The sequencing libraries were prepared using Ligation Sequencing Kit and sequenced on the MinION or PromethION sequencer. Sequences were aligned to the hg19 human genome reference, and structural variants were identified using the split read method, filtered, and annotated. Results/Conclusion: For each patient, we obtained sequencing data enabling 10× (MinION), or >20× (PromethION) average coverage of the genome. We performed a comprehensive comparison of long-read sequencing results with those of classical and molecular cytogenomics and assessed the benefits and shortcomings of long-read sequencing in deciphering the structure of genomic rearrangements in the tested chronic lymphocytic leukemia cases. Long-read sequencing provides more accurate characterization of breakpoints and majority of genome rearrangement events. |
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