Nanopore adaptive sampling accurately detects nucleotide variants and improves the characterisation of large-scale rearrangement for the diagnosis of cancer predisposition
Chevrier et al. used Oxford Nanopore adaptive sampling as an alternative method to multiplex ligation-dependent probe amplification (MLPA) for studying genes associated with cancer predisposition. They detected known and novel variants, even at low coverage, and characterised large-scale rearrangements, noting higher resolution with Oxford Nanopore than MLPA. Therefore, Oxford Nanopore sequencing could potentially be an accurate alternative method for early cancer detection in the future.
Key points:
Adaptive sampling enriched 152 cancer predisposition genes in blood samples from individuals with hereditary solid tumour cancers
Using Oxford Nanopore, Chevrier et al. detected known and novel variants, including a duplication of two exons and a deletion carrying over five different genes
All large-scale rearrangements were detected in the 30 germline samples, matching MLPA results
Oxford Nanopore sequencing characterised the exact start, stop, and size of large-scale rearrangements, offering better resolution than MLPA
The authors identified novel intronic variants that could impact splicing
Oxford Nanopore sequencing offered improved detection of structural variants (SVs) and single nucleotide variants (SNVs) even at low coverage
'[Oxford Nanopore] adaptive sampling sequencing is suitable for the analysis of germline alterations, improves characterisation of large-scale rearrangements, and detects single nucleotide variations even at low coverage'
Watch the lead author, Romain Boidot, discuss this research at London Calling 2023.
Sample type: human blood
