Sara Goodwin: Exploring the architecture of organoid genomes with PromethION technology

Lightning talk: Sara Goodwin, of Cold Spring Harbor Laboratory, described how long-read nanopore sequencing can be used to resolve structural changes that occur during the generation of organoids. Organoids are three-dimensional cell cultures, which can be grown from cells taken from tumour biopsies; where biopsies can yield little DNA for long-read sequencing applications, organoids can generate sufficient material. A relatively new technology, they are used in a range of applications including the study of disease genetics & pathology and drug screening, and provide “an important tool in cancer biology.” Sara described how DNA from organoids derived from breast tumour, normal breast tissue and the breast cancer cell line SKBR3 were sequenced via nanopore sequencing, a short-read technology and a long-read technology. Sara displayed structural variant calling for the patient tumour organoid DNA: results were highly concordant between the two long-read technologies, whilst the proportion of data called as structural variants in only the short-reads dataset were shown via PCR validation to mostly comprise false-positives. She went on to show a 62 bp repeat expansion in a BRCA1 intron, which was successfully detected via long reads, but not via short-read sequencing; this was also the case for a ZMYM3 50 bp deletion and an NF1 100 bp insertion. Sara then demonstrated how her team were using nanopore sequencing to investigate methylation: “huge hypermethylation” was seen in the normal sample, whilst correlation of methylation patterns between SKBR3 and the tumour organoid suggested the presence of cancer-specific methylation.