Ana Peres from UNC-Chapel Hill presented at the Nanopore Community Meeting on “Unraveling gene expression patterns in pediatric germ cell tumors: a nanopore sequencing approach.” They spoke about how rare pediatric tumors are and the differentiation stages. Germ cell tumors can occur in the gonads and along the midline of the body. Peres and team studied forty-seven pediatric germ-cell tumors. The team used the SQK-PCB109 multiplexing 4-10 samples per run. Basecalling was performed with Dorado with the Super High Accuracy mode. Alignment was performed with minimap2. They generated Principal Component Analysis and generated separation based on storage. PCA also revealed higher expression of different genes based on the type of tumor. The data was then used to train a classifier. The samples were correctly classified with 72.9% accuracy. To improve this, teratomas were grouped, and mixed tumors were added as a subtype. This improved accuracy to 90.4%. Peres concluded that nanopore sequencing “represents a potential globally-accessible technology for characterization of pediatric germ cell tumors.” The classifier is able to classify major subtypes with shallow data. The team continues working to improve the classifier and create new ones. Peres noted they were working with the Barretos Cancer Hospital. I wonder how this collaboration is happening!
