Thread by @NanoporeConf

10 minute reminder: @VanessaPorter will be on stage in the auditorium shortly with her talk: 'Identification of novel #genomic structures and regulation patterns at #HPV integration events in cervical #cancer'. #nanoporeconf

VP: HPV is a necessary driver of cervical cancer. HPV integration is present 70% of cervical cancers. Often disrupts E2 gene & causes structural rearrangements. #nanoporeconf

VP: HPV integration often upregulated neighbouring genes. #nanoporeconf

VP: We used nanopore sequencing to characterise 44 cervical cancer clinical research samples. We looked at SNPs, SVs, methylation & phasing. #nanoporeconf

VP: To call HPV breakpoints we called SVs and identified translocations. The benefits of long reads - we can identify integration events that "span multiple chromosomes". #nanoporeconf

VP: identified three common resolutions of two breakpoint integration events. Deletions, duplications and extrachromosomal DNA (ecDNA) #nanoporeconf

VP: we were able to identify both simple (2 breakpoints) & complex ecDNA integration (multiple breakpoints) #nanoporeconf

VP: Multi-breakpoint events: Example 20 breakpoints & cross chromosomal translocations. #nanoporeconf

VP: Integration detected in both #telomeric and #centromeric regions. #nanoporeconf

VP: Most common integration event = multi integration, followed by ecDNA. Preverlance of integration events is different for HPV subtypes. #nanoporeconf

VP: Major advantage of #nanopore sequencing is the ability to detect and phase #methylation. We were able to identify of #HPV methylation across broad regions of the genome. #nanoporeconf

VP: Genic regions more #methylated than in episomal #HPV. #nanoporeconf

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