Study Validates Noninvasive Urinary Cell-Free DNA Assay for Urothelial Bladder Cancer

European Journal of Human Genetics, has shown that extracting cell-free DNA from urine is a highly effective technique for analyzing the genetic profile of urothelial bladder cancers (UBCs).¹

“This is truly noninvasive. All we need is some urine from the patient, which they can provide themselves,” said lead author Fiona Togneri, a researcher at West Midland Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, in Birmingham, England. “It means we can look more frequently and without patients being subjected to uncomfortable medical procedures."

To assess the accuracy of the cell-free DNA urinary assay at detecting genomic aberrations, the researchers compared test results with those obtained using a cell-based DNA assay that isolates exfoliated cells from urine. The genomic profile generated with each urinary assay was compared with the genomic profile obtained with an assay that analyzed multiple slices from a matched formalin-fixed-paraffin-embedded (FFPE) tumor sample (OncoScan FFPE Assay Kit, Affymetrix, Santa Clara, CA). The OncoScan assay detects copy number alterations, loss of heterozygosity, and somatic mutations.

The authors also examined all the genomic profiles from the urinary and FPPE assays for “tumor alterations relevant for genomics-driven therapy (TARGET)” that are listed in the Van Allen database to determine how sensitive the different techniques were at detecting these. Whenever possible, polymerase chain reaction and next-generation sequencing were used to confirm somatic mutations identified by OncoScan.

The urine and FFPE samples analyzed in the study came from 23 patients with UBC who had previously contributed to a biospecimen repository. The investigators also tested samples from a control group of 12 patients who had UBC symptoms but did not have UBC.

Results showed a high degree of concordance between the 3 assays for the UBC patients and the controls, with consistent detection of certain genomic aberrations in UBC patients. At the same time, differences between the 3 assays in the genomic profile for a single patient confirmed that UBC is a very heterogeneous disease. For example, some somatic mutations detected in cell-free urine samples were present in FFPE slices obtained from deep within the tumor but were not found in more peripheral FPPE slices.

In urine samples from the UBC group, the cell-free DNA contained significantly more tumor material than the exfoliated cellular DNA and was more sensitive at detecting the genetic biomarkers revealed through FFPE testing. The cell-free DNA assay identified 90% of the key genomic biomarkers compared with 61% for the cellular DNA assay (P<.04).

In addition, the FFPE and cell-free assays revealed approximately 2.3 TARGET aberrations, compared with 1.3 for the cellular DNA assay. Dr Togneri said cell-free DNA contains a greater tumor genomic burden because &ldquo;cell-free DNA is being produced at an increased rate from the tumor as a result of the chaotic tumor development,&rdquo; which she characterized as one of rapid cell growth and death.

&ldquo;In contrast, the cellular DNA represents all of the urothelium, and the tumor will make up only a small percentage of this,&rdquo; she explained.

Of the 12 control group patients, the cell-free assay showed 1 patient harbored a genetic aberration consistent with malignancy, and this patient was subsequently found to have a type of cancer other than UBC. The authors said this finding suggests that although urinary cell-free DNA is highly effective at detecting malignancy, it is not UBC-specific.

Dr Togneri said the previous work her team did to validate the OncoScan platform,²as well as the results of confirmatory tests using next-generation sequencing, lends confidence to the authors&rsquo; conclusion that cell-free DNA from urine is a promising resource for genomic profiling in UBC.

&ldquo;It allows easier, and potentially more accurate, noninvasive monitoring of patients with bladder cancer,&rdquo; she said. Dr Togneri predicted that cell-free urinary DNA assays may someday have even greater practical application for managing UBC patients. &ldquo;Genome-wide copy number detection with a panel of clinically actionable somatic mutations offers a considerable improvement for intelligent treatment stratification of patients as biomarkers and treatments become approved in the clinic,&rdquo; she said.

References

1. Togneri FS, Ward DG, Foster JM, et al. Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA. Eur J Hum Genet. 2016. doi: 10.1308/ejhg.2015.281. [Epub ahead of print]
2. Foster JM, Oumie A, Togneri FS, et al. Cross-laboratory validation of the OncoScan FFPE Assay, a multiplex tool for whole genome tumour profiling. BMC Medical Genomics. 2015;8:5: doi: 10.1186/s12920-015-0079-z.