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Medulloblastoma Long-Read Sequences Reveal Complex Rearrangements, Methylation Changes

NEW YORK – With long-read genome sequencing on pre- and post-treatment samples from a childhood brain tumor type called medulloblastoma, a research team from the European Molecular Biology Laboratory (EMBL), the German Cancer Research Center (DFKZ), and elsewhere tracked down new tumor rearrangement and epigenetic patterns that subsequently turned up in other cancer types.

"[N]anopore sequencing enabled us to discover a complex pattern of DNA rearrangement 'missed' by short-read sequencing and such patterns may prove to be potentially relevant for precision medicine in the future," co-senior and co-corresponding author Jan Korbel, a genome biology researcher affiliated with EMBL, EMBL's European Bioinformatics Institute, and DKFZ, and head of data science at EMBL, explained in an email.­­

As they reported in Cell Genomics on Wednesday, the researchers used Oxford Nanopore Technologies long-read whole-genome sequencing to assess a diagnostic primary sample from one medulloblastoma case occurring in an individual with Li-Fraumeni syndrome, a cancer susceptibility condition marked by risky mutations in TP53. They also did long-read genome sequencing on a corresponding post-treatment relapse tumor sample, as well as a matched normal blood sample from the same individual.

With these long-read medulloblastoma sequences, the team uncovered complex structural variant and methylation signatures that were subsequently assessed in thousands more cancer genomes spanning other cancer types characterized with short-read sequencing by members of the Pan-Cancer Analysis of Whole Genomes consortium.

On the DNA methylation side, the authors noted that the long-read sequencing strategy highlighted features ranging from allele-specific methylation to methylation shifts found at cancer driver gene promoter sequences or at specific complex rearrangement events.

Combining the new long-read sequences with available Illumina short-reads, the team mapped nearly 700 deletion, duplication, inversion, rearrangement, or other structural variants across the medulloblastoma primary tumor.

The researchers took a closer look at some of these structural changes, including a 1.55-megabase chromothripsis event involving stretches of chromosomes 11 and 17 that they characterized more fully with the help of fluorescence in situ hybridization experiments.

They also found so-called "templated insertion (TI) threads" marked by self-linked and cross-linked insertions that each spanned no more than 1,000 bases, making up larger amplified structures — rearrangements assessed further by long-read sequencing on a patient-derived xenograft model.

"Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements," Korbel and his coauthors wrote, adding that "[w]e associate a subset of the somatic DNA rearrangements, including TI threads, with functional consequences, and demonstrate the ability to explain aberrant gene expression patterns, such as allele-specific expression and gene fusions, by integrating genomic and epigenetic long-read data."

When they used patterns found in the long-read sequenced medulloblastoma tumors to re-analyze almost 2,600 short-read cancer genomes, for example, the investigators tracked down TI thread rearrangements in 3 percent of the tumors considered overall, with Ti threads often occurring in tumors marked by chromothripsis more generally.

But the alterations were more common in certain cancer types, the team reported, turning up in 14 percent of melanomas, 22 percent of osteosarcomas, 24 percent of glioblastoma tumors, and nearly three-quarters of the liposarcoma tumors profiled.

Moreover, at least some of the TI thread rearrangements turned up in or around cancer-promoting oncogenes that are found at higher-than-usual levels in some tumors, the researchers reported, noting that such structural variants may provide a boost to tumor evolution in some cases.

"While our study did not have a clinical focus — the primary focus was to show feasibility of long-read nanopore sequencing with respect to cancer genome and epigenome characterization — there are some potential implications for future clinical use," Korbel said.

"Nanopore sequencing has a very rapid turnaround, and reveals both genetic changes and epigenetic changes in tumors," he explained. "Therefore, it is likely to contribute to accelerated diagnosis and clinical decision making in the future."