NEW YORK – Researchers at St. Jude Children's Research Hospital have developed a non-invasive comprehensive genomic profiling assay designed specifically for pediatric cancers, publishing results of an initial validation study in Nature Leukemia earlier this month.
The test, which they dubbed PeCan-seq, relies on deep sequencing across 357 genes using a DNA capture panel for de novo detection of chromosomal copy number aberrations and single-gene variants.
Analyzing results in 233 children with hematologic, solid tumor, and brain cancers, researchers concluded that the method shows promise as a non-invasive augmentation of tumor tissue-based diagnostics, as well as a platform for disease monitoring.
Charles Mullighan, the study's senior author and deputy director of St. Jude's Comprehensive Cancer Center, said that pediatric cancers tend to have lower mutational burden and more heterogeneous genomic features than adult tumors. As such, genomic diagnoses require methods and tools specifically tailored to address these challenges.
Despite this, the larger field of genomic diagnostics has not seen significant investment, at least commercially, in advancing targeted sequencing tests specific to childhood cancers.
Mullighan said that part of the reason for that is that pediatric cancers make up a much smaller group than other disease areas, and are thus a less-attractive commercial target. The above-mentioned biological complications could also play a role.
He and his colleagues view PeCan-seq as having several unique and valuable features, including a small sample requirement of only 1 ml of plasma, the ability to detect diverse classes of genomic alteration, including structural variants, and relative cost-effectiveness compared to whole-genome or exome sequencing, which have been St. Jude's standard in recent years, but aren't standard practice across the community.
In their study the St. Jude team set out to test the approach across hematologic cancers, solid tumors, and brain cancers, aiming to evaluate PeCan-seq both for its ability to detect relevant mutations in cell-free DNA at a similar rate to tissue sequencing, and as a way to monitor hematologic cancers in kids.
"Moving more and more towards less-invasive procedures is really attractive for all three tumor types," Mullighan said.
In solid and brain tumors, sampling a tumor can be difficult and resulting tissue specimens can be scarce. Even in blood cancers there is often a need to acquire primary tissue from the bone marrow, which involves invasive procedures under anesthesia and associated complications, from which it would be nice to spare children.
"Going into this, we were very interested to see whether a cell-free assay would capture the diversity that we see in pediatric cancer," Mullighan said.
What they found in the study was that PeCan-seq could detect circulating tumor DNA most sensitively in blood cancers. It picked up alterations in all 144 patients with hematologic cancers, with the resulting genomic profiling showing high concordance with patients' matched tumor samples.
Overall, the capture panel covered 81 percent of clinically important variants present in the tumor samples, authors wrote.
The test was not nearly as effective in solid tumors, where it only picked up somatic mutations in half of a group of 38 kids. For brain cancer, the test only picked up mutated DNA in 1 of 18 children.
Solid tumor successes included children with EWSR1 fusion-positive Ewing sarcoma, liver tumors, osteosarcomas, neuroblastoma, Wilms tumors, and alveolar rhabdomyosarcoma.
PeCan-seq was also able to identify several variants in cell-free DNA not presenting in matched tumor tissue.
Mullighan said that the results weren't surprising to his team, considering that other studies have had similar outcomes in pediatric solid tumors, and because of the biological reality of the blood-brain barrier, which prevents tumor DNA from entering the blood.
"We simply didn't know going into this study how well it would perform," Mullighan said, but the hope was that a pan-cancer panel could serve patients across all tumor types, so this was the first step.
In addition to identifying relevant mutations, the St. Jude's team also tested whether PeCan-seq as a monitoring tool could match or exceed the performance of current methods including flow cytometry and bone marrow biopsies.
The assay successfully detected cancer mutations in 14 B-ALL patients with varying levels of residual disease, suggesting it could complement existing methods, but further study will be needed, the authors wrote.
As they move forward, Mullighan said he and his team are experimenting with adapting PeCan-seq to work better for solid tumor and brain cancer patients, as well as to optimize the ability to monitor disease in blood cancers.
"There are other approaches for brain tumors that perform much better for cell-free DNA analysis, such as sampling the cerebral spinal fluid, so as we go, we may break it down to incorporate other techniques to improve efficiencies, costs, and potentially sensitivity, as well," said Mullighan.
Other areas the group is exploring include RNA and cell-free methylation profiling. "Tissue-based methylation sequencing has been adopted clinically for some brain tumors, and it's showing great promise for solid tumors in children, so we're looking to expand this toolbox and evaluate these other modalities," he added.