Hematological Whole Genome and Transcriptome Sequencing as a New Diagnostic Tool for Acute Leukemias

Various research projects have shown that new technologies such as whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) provide added value for patients with acute leukemia. In the coming year, the MLL will be offering both diagnostics using classical methods as well as WGS/WTS analysis for acute leukemia. We want to pass this added clinical value on to our patients while at the same time learning from the knowledge gained. We also want to put WGS/WTS to the test in order to validate their clinical benefit.

In a publication by Duncavage et al. in the New England Journal of Medicine (NEJM. 2021;384(10):924-935), it was shown that whole genome sequencing can reliably gather the information currently being collected by chromosome analysis and molecular genetic methods and that it can also identify other prognostically and therapeutically relevant alterations. In our own projects at the MLL on acute lymphoblastic leukemia (ALL; Walter et al. BMC Cancer. 2021;21(1):886), we also managed to accomplish even more detailed classification of patients using transcriptome analysis. This demonstrates the added value that these new technologies could provide to patients in the future.

This additional diagnostic benefit for the patient is a major focus for us. We are aware that using whole genome sequencing to diagnose leukemia involves a change for both the doctor and the patient, as it is necessary to provide the patient with specific information and prepare separate declaration of consent. We want to make it very clear that we are conducting an analysis of the “hematological/clinical genome” with our approach. As with conventional molecular genetics, we use bone marrow as our starting material. At the same time, we also use peripheral blood (or separated T cells) to diagnose acute myeloid leukemia in order to eliminate any germline changes from the sequencing data, since the investigation is aimed at somatic changes within the leukemia cells. Any germline predispositions that are unrelated to the acute leukemia are therefore excluded from the investigation, being deliberately sorted out in our analytical pipeline. The preparation process for WGS/WTS diagnostics uses DNA and RNA from the corresponding sample. After sequencing, the data are specifically examined for various diagnostically and prognostically relevant alterations. On the one hand, we examine changes in copy numbers, traditionally covered by chromosome analysis. The WGS analysis produces a higher level of resolution here, also allowing for smaller alterations to be discovered that remain undetected at the resolution of normal chromosome banding analysis. In addition, we also see copy-neutral losses in heterozygosity (CN-LOH) and translocations, which usually lead to fusion transcripts. We detect them at the same time with the transcriptome analysis, the two methods providing us with an internal confirmation. For smaller alterations, such as mutations in individual genes, we study a gene set relevant for hematological neoplasia, which lets us factor in all of the mutation information necessary for the diagnostics and risk stratification. In addition to the detection of fusion genes and overexpressions of the genes involved, the transcriptome analysis also allows for the generation of an expression profile.

Depending on the subtype, this produces a different pattern, particularly for ALL, making classification into specific groups possible. From our research projects, we know that a larger proportion of patients can be assigned to a specific group than is possible using traditional diagnostic methods. If you, the treating doctor, are interested in participating in our study, please send a declaration of consent signed by your patient at the time when you explained AML or ALL, after which the patient can be included and tested using WGS/WTS along with the current gold standard diagnostic method.

In this case, of course, you will also receive a corresponding supplementary report on the results of the WGS/WTS analysis. Naturally, we will cover the costs for the WGS/WTS analysis ourselves.