ASH 2025 | Ultra-deep WGS of cell-free DNA to detect bone marrow-derived mutations in multiple myeloma

So a question that we have is how we can recapitulate the bone marrow, find all of the relevant bone marrow mutations in cell-free DNA to reduce the reliance on an invasive bone marrow aspirate. Previously, we were using Illumina sequencing, about 30 to 40x whole genome sequencing, to span all the variants we’re interested in for tracking minimal residual disease and longitudinal time points. But because of cost, we could only sequence around 30 to 40x. With new Ultima sequencing, we can get comparable cost for 150 to 200x sequencing. And what we’re curious to establish is, can we find the mutations that we’re interested in in the bone marrow and how similar are the two technologies? 

And what we found is with Ultima sequencing, we can find 88% median of all the mutations from the bone marrow, which we were interested in for tracking MRD. And we see the biggest gain in mutation recovery in samples with low circulating tumor DNA fraction of about 6% or below, which is about half of all of the samples in our cohort. This increased gain in the low circulating tumor DNA tumor fraction cases, primarily since we have so few fragments coming from the tumor, the extra depth, extra reads really helps us. And using that, we can find an additional one to three OncoKB hits so likely oncogenic clinically validated annotated mutations in our patients which are useful for risk stratification. 

Lastly we were interested in understanding what copy number profiles look like with this new Ultima genomics technology and we find highly concordant profiles across both our Illumina and matched Ultima cases, and the circulating tumor DNA fraction estimates are very comparable between them as well. And finally, the variant allele fraction estimates that we get from both technologies, Illumina 30 to 40X and Ultima 150 to 200X are also highly concordant. So in summary, Ultima sequencing gives us comparable cost, significantly deeper sequencing, which uncovers a median of 88% of all bone marrow-derived variants. We see a large increase in mutation recovery in primarily our low ctDNA fraction cases, and we’re hoping that this will help us push towards a much lower need for bone marrow aspirates for profiling myeloma in the future.

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