Using long read sequencing to capture complex translocations in multiple myeloma
Multiple myeloma (MM) is a blood cancer, characterized by accumulation of cancerous plasma cells, terminally differentiated B cells, in the bone marrow. The malignant plasma cells crowd out healthy bone marrow cells, which weakens the immune system and causes adverse effects on the body. Patients with MM usually have one hallmark translocation. KMS11 is an atypical MM cell line that has three hallmark translocations: t(4;14), t(8;14), and t(14;16). The t(4;14) translocation leads to overexpression of NSD2 and FGFR31*. With current short read sequencing techniques, the der(14) chromosome, from which FGFR3 is overexpressed, is missed but captured by FISH analysis. Accurate detection of translocations, even complex translocations, is important as their detection can affect clinical treatment decisions for patients. Long read sequencing can resolve complex translocations missed with short reads, increasing the detection of derivatives like the der(14), FGFR3 overexpressing derivative.
We compared pre-existing Illumina short read sequencing data produced by a HiSeq2500 to new long read sequencing data produced by the Oxford Nanopore Technologies (ONT) PromethION. Translocated chromosomes were reconstructed through analyses utilizing the Integrated Genomics Viewer (IGV) tool. Using the ONT data, we found the t(8;14) event is a secondary event occurring on a duplicated copy of the original der(14), based on the specific breakpoint location, making it a t(4;8;14) event. The Illumina data only detected the t(4;8;14) haplotype, whereas the ONT data was able to identify the FGFR3 haplotype, proving the t(4;14) occurred before the t(4;8;14).
*Fonseca, R et al. International Myeloma Working Group (2009). International Myeloma Working Group molecular classification of multiple myeloma: spotlight review. Leukemia, 23(12), 2210–2221. https://doi.org/10.1038/leu.2009.174
