NEW YORK (GenomeWeb) – Targeted sequencing can provide insights into the effectiveness of myelodysplastic syndrome treatment (MDS) and the likelihood that the cancer-related conditions will recur, according to new research published online today in the New England Journal of Medicine.
"A genetic analysis is a much more precise method of measuring how many blood cells are cancerous," senior author Matthew Walter, a researcher at the Washington University School of Medicine, said in a statement. "It also lets us find abnormal cells at earlier time points after a stem cell transplant, when there are fewer cancerous cells to find. The earlier we can detect that the cancer is coming back, the more time we may have to intervene."
Walter and his colleagues used enhanced exome sequencing on matched bone marrow and normal skin samples to identify pre-treatment mutations in MDS in 90 individuals treated at Washington University over more than a decade, from 2002 to 2015. When they searched for the characteristic mutations with error-corrected sequencing a month after allogeneic hematopoietic stem cell transplantation, the investigators saw one or more suspicious somatic mutations in more than one-third of the patients.
The team noted that the risk of post-treatment MDS progression tended to edge up with increasing mutant allele frequencies in the samples collected 30 days after stem cell transplantation — rising from a 13 percent risk of progression in individuals with mutant allele frequencies below 0.5 percent to more than 53 percent progression risk in those with greater than 0.5 percent mutant allele frequencies. Conversely, progression-free survival was lower at the one year mark when mutant alleles were more common.
"Using our sequencing method, we're identifying residual tumor cells before a pathologist could see them under the microscope and before a patient develops symptoms," Walter said. "At that moment, there may be time to intervene in ways that could delay the cancer from coming back or potentially prevent it completely."
The researchers used the Illumina HiSeq 2500 instrument to do enhanced exome sequencing on matched bone marrow and normal skin samples from 90 adults with MDS, secondary acute myeloid leukemia, or MDS stemming from prior cancer treatment.
In the exomes — which spanned protein-coding sequences captured with a Roche Nimblegen hybrid capture method, along with 285 genes previously implicated in MDS or AML — they tracked down pre-treatment somatic mutations in all but four of the MDS patients. That mutation set included more than 2,500 validated single nucleotide changes.
At 30 days and 100 days post-treatment, the team collected samples to test for mutations identified in the original exome sequences. The group applied error-corrected targeted sequencing at average depths exceeding 30,000-fold, and used its analytical pipeline to find one or more residual somatic mutations — present in at least 0.5 percent allele frequency — in samples from 32 of the patients.
All told, the researchers identified 35 patients who had post-treatment MDS progression over a median of nearly five months. Disease progression rose, and progression-free survival at one year dipped from more than 59 percent to 31.3 percent, on average, in individuals with mutant alleles present at frequencies beyond 0.5 percent in 30-day post-treatment samples.
"Although this exploratory study has limitations, our results suggest that sequencing-based detection of tumor cells and measurable residual disease after allogeneic hematopoietic stem cell transplantation has prognostic significance for patients with MDS," the authors wrote.
The researchers saw particularly lower decreased progression-free survival times in patients with mutant allele frequencies beyond 0.5 percent who had received reduced-intensity treatment.
The team subsequently demonstrated that it could identify pre-treatment mutations in 79 percent of the patients by profiling a smaller set of 40 genes with panel sequencing. And post-treatment samples tested with that panel sequencing method again picked out individuals more prone to disease progression after one year, using 0.5 percent mutant allele frequency as a cutoff.
Despite the association with progression-free survival, mutant allele frequencies exceeding 0.5 percent in the 30 or 100 days after treatment did not show ties to overall survival, the researchers reported, noting that "this effect may be due to biologic characteristics of the disease or to the nature of response to salvage therapy in patient with MDS."