Unravelling the complexity of cancer genomics and predisposition: nanopore sequencing and the potential for personalised care
At the Nanopore Community Meeting 2024, Dr Mathilde Filser from the Curie Institute, France, presented a compelling case for how nanopore sequencing has the potential to transform cancer care. By leveraging the technology, her team has made significant strides in both germline and somatic cancer characterisation, offering new hope for personalised cancer management in the future.
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Unlocking germline insights
Mathilde’s team has focused on germline structural variant (SV) characterisation, where accurate identification of these gross genetic alterations plays a key role in patient and familial cancer management. Using adaptive sampling — a unique feature of nanopore sequencing that offers fast and flexible enrichment of regions of interest — the team successfully identified complex SVs, such as inversions and duplications, that are often missed by legacy short-read sequencing techniques.
Mathilde highlighted the case of a woman presenting with early-onset triple negative ductal carcinoma of the breast with no family history suggestive of hereditary breast-ovarian cancer syndrome (HBOC). Routine tests revealed a heterozygous germline duplication of BRCA1 exons 18–20, subsequently confirmed with multiplex ligation-dependent probe amplification (MLPA), but further characterisation was needed to determine the pathogenicity of the variant.
Adaptive sampling allowed the team to sequence the full long arm of chromosome 17 to discern if the BRCA1 duplication was either: 1) in tandem inducing a premature stop codon or localised within a gene functional domain that would be destabilised, or; 2) if the duplication occurred somewhere else in the genome and would therefore be classified as a variant of unknown significance (VUS).
The team was able to not only confirm the initial BRCA1 duplication with breakpoint-level resolution, but also found that the duplication was in tandem disrupting the reading frame. Mathilde highlighted, ‘Within 10 days in total, we were able to go back to the clinicians and confirm [with] them that she was carrying a pathogenic variant in BRCA1,’ confirming the patient’s surgical eligibility and illustrating how nanopore sequencing can provide critical insights quickly to potentially support clinical decision-making alongside routine testing.
The rapid turnaround and high precision highlight the power of nanopore sequencing to offer a faster and more comprehensive view of patients' genetic predispositions.
Precision in somatic cancer research
Mathilde’s research also demonstrated the role of nanopore sequencing in somatic cancer research, particularly in paediatric brain tumours and sarcomas. As nanopore sequencing generates reads of unrestricted length from native DNA, her team could simultaneously detect copy number variations (CNVs), gene fusions, and methylation modification patterns, providing a multilayered insight into tumour biology.
A notable example was the case of a one-year-old patient with an ependymoma that was initially diagnosed through histological analysis. Using nanopore sequencing, Mathilde’s team found that the methylation profile of the tumour research sample clustered with ependymomas with a YAP fusion, and then leveraging the long nanopore read data confirmed the suspected YAP1 fusion. Therefore, the nanopore data was concordant with the histological analysis and initial diagnosis.
Another example involved a research sample from a six-year-old patient with a tumour that could not be clearly distinguished as either a medulloblastoma or Ewing sarcoma using routine tests. Nanopore sequencing showed that the methylation profile of the tumour research sample was indicative of Ewing sarcoma and further validated this finding by identifying the typical subtype-specific EWSR1 fusion gene.
Mathilde explained how these examples showcase the potential role of nanopore technology in rare and challenging tumour classifications.
‘From our experience, we really think that nanopore sequencing is a really robust three-in-one [research] tool for the classification of brain tumours and sarcomas, because it allows us to obtain simultaneously the copy number profile, the methylation profile, and to detect the fusions of interest in those tumour [classification] entities’
Mathilde Filser, Curie Institute, France
Exploring medulloblastoma grouping and subgrouping
Medulloblastomas, the most common embryonal brain tumour type in the paediatric population, pose a diagnostic challenge because they consist of four main groups (WNT, SHH, Group 3, and Group 4), each resulting in different prognoses and treatments. DNA methylation has had an ‘undeniable impact’ in the classification of medulloblastoma groups. Mathilde’s team utilised whole-genome nanopore sequencing to explore the genome-wide methylation patterns in medulloblastoma research samples and compared performance to the current gold standard, which analyses only ~850,000 CpG sites using a time consuming and complex assay.
Nanopore sequencing not only matched the grouping reliability of the gold standard but offers a simple, more accessible, and faster alternative, which is especially suited for emergency situations. ‘We could imagine loading just one tumour [research sample] on the Flongle Flow Cell and obtaining the results of classification within 24 hours,’ Mathilde explained, highlighting how nanopore sequencing can rapidly assist in providing critical tumour insights.
The team then explored subgrouping within the medulloblastoma groups, an emerging area of research interest that seeks to further refine prognosis and impact treatment. Preliminary results were positive, suggesting that nanopore sequencing could also capture this additional layer of resolution.
‘Our preliminary results are really encouraging because it seems that indeed the nanopore methylation results allow us to obtain the subgrouping of medulloblastomas’
Mathilde Filser, Curie Institute, France
The future of cancer diagnostics
Mathilde and her team’s work underscores the transformative potential of nanopore sequencing across both germline and somatic cancer research. Its ability to provide real-time, multidimensional insights into SVs, methylation profiles, and gene fusions offers a comprehensive view of tumour biology, paving the way for more personalised approaches to cancer care in the future.
Whether through identifying hereditary cancer risks or delivering precise characterisation of somatic tumour variants from paediatric research samples, nanopore sequencing is poised to potentially play a crucial role in advancing oncology diagnostics. As Mathilde remarked, ‘we really believe that nanopore sequencing is a versatile tool with a wide range of applications from the germline side to the somatic level.’
Find out more about cancer research with nanopore sequencing >