Martin Smith from the Garvan Institute of Medical Research in Australia was mentioned in the London Calling 2019 session I watched yesterday. Today, I watched the recording of the 2019 London Calling session that Smith did on “Leveraging long reads for high-throughput multiomic analyses of cellular diversity in human tumours.” Smith wasn’t able to travel, and someone else from the research group presented. They spoke about immunotherapies for cancer treatment. However, these therapies sometimes do not work… even for similar cancers. The group has been using single-cell sequencing. Smith calls it the “Wholly Tri-munity” comparing tumor, blood, and draining lymph nodes. T-cell and B-cell receptor variety results from V(D)J recombination. The variety can be effectively used as a barcode. The limitation of droplet-based scRNA-seq is that the enrichment process may result in the loss of sequence ends. Long reads are promising. RAGE-seq: repertoire and gene expression sequencing was developed by the group to focus on regions of interest with hybridization capture and Nanopore sequencing. Short-read sequencing is used to determine the barcodes, and assembly helps determine the single-nucleotide accuracy of isoforms across thousands of cells. Using the unique V(D)J sequences, individual cells can be tracked! CITE-seq can be used with RAGE-seq for multi-omic analysis of tumors. The status of cells and memory can be determined. Total RNA sequencing on PromethION flow cells helps obtain isoform information, though the group is working to improve single-cell barcode recovery. While this information is several years old now, I learned about the approaches and got ideas for how these techniques can be used with bacteria and metagenomes.
