NEW YORK – A team led by investigators in Canada has demonstrated the wide range of tumor insights that can be obtained by nanopore long-read sequencing, including clues about complex rearrangements and epigenetic features, homologous recombination deficiency (HRD), and the integration of genetic material from the human papillomavirus or other viruses.
"Our initial findings suggest a role for long-read sequencing in personalized cancer medicine through the phasing of somatic mutations, deconvolution of structural variation, identification of tumors driven by HRD, and discovery of allele-specific methylation of tumor suppressors," corresponding and co-first author Kieran O'Neill of Canada's Michael Smith Genome Sciences Centre at BC Cancer and colleagues wrote in Cell Genomics on Monday.
For their analyses, the investigators brought together data from the "Long-Read Personalized OncoGenomics" (POG) project and the Marathon of Hope Cancer Centres Network, which included Oxford Nanopore Technologies PromethIon long reads on 189 metastatic, recurrent, or treatment refractory tumor samples from 181 advanced cancer patients.
The cases, which spanned some 26 cancer types, had also been profiled with short-read whole-genome tumor-matched normal sequencing and tumor RNA-seq. Long-read sequences were also available for 41 matched normal samples.
"As the samples in this cohort have accompanying short-read DNA and RNA sequence data and associated clinical information, our study offers potential for advancing the understanding of [structural variants (SVs)], viral integration, DNA methylation, and allelic information pertinent to cancer pathogenesis and diagnosis," the authors wrote.
Together, the team explained, the approach made it possible to untangle long-read-based variant phasing and related haplotypes, while providing a look at previously unappreciated structural variants, viral integrations, extrachromosomal circular DNA, and allelically differentially methylated regions in the tumor DNA.
For example, the team used long-read sequences to characterize HPV integrations in affected cervical, head and neck, or anogenital cancers. The data also revealed "double hit" alterations affecting tumor suppressor genes such as PTEN or KAT5, as well as recurrent methylation shifts, including HRD-related methylation increases at BRCA1 or RAD51C promoter sites.
"Interestingly, BRCA1 promoter hypermethylation was observed in melanoma and head and neck cancer, in addition to breast and ovarian cancers, where it has been typically described," the authors reported. "This suggests that HRD gene promoter methylation may be involved in a broader spectrum of tumors, a clinically important finding, as deficiency in [homologous recombination] is associated with sensitivity to platinum chemotherapies and PARP inhibitor therapies."
Though they cautioned that the current analytical approaches were not designed to interrogate point mutations or other small somatic variants in the long-read nanopore, the authors noted that small variant calling strategies are expected to improve in the future.
In the meantime, they suggested that "tumor long-read sequencing is warranted as a complement to the established short-read sequencing paradigm to understand its use in biomarker-driven clinical trials and identifying targeted treatment options."