Tonight, the IPERT summer workshops ended. Sissel Juul & Phill James presented at the Nanopore Community Meeting 2021 about “For want of a nail: investigating somatic and germline variations in cancer.” They are both at Oxford Nanopore Technologies in the Genomics Application Team. In 2021, they spoke about extrachromosomal DNA in cancer. Juul spoke about the impact of cancer and the hereditary and familial cancer incidence. Solid tumor could have biomarkers such as extracellular DNA (ecDNA). ecDNA could be formed by errors in homologous repeat resolution. ecDNA lack telomeres so they are segregated randomly. They also tend to have high expression of genes, Juul noted. ecDNA can be visualized with microscopy stains or analyzed with short read sequencing. Results from their workflow produce circular assemblies of ecDNA. Juul explained that in some cases they had complex bandage plots and the ultra long read protocol could help. They also noted that the Flongle could provide enough data to learn about ecDNA from tumor samples.
Sergey Aganezov created a pipeline to analyze publicly available datasets. Since sequencing with Nanopore offers methylation information, this approach to understanding ecDNA and its variations in cancer can be investigated. James described how adaptive sampling can be used to study somatic or acquired genomic variants in cancer. This technology allows phasing across whole genomes. James and colleagues used this workflow to analyze samples and call pathogenic SNPs. James also shared copy number variation analyses and methylation evaluation of ecDNA. While I don’t work on cancer, I do appreciate the tools available and think there could be ways of studying extracellular/biofilm DNA.
