James is currently a Senior Postdoctoral Associate in SMART-CAMP working on microbial T-cell spike generation, NGS library preparation, metagenome sequencing analysis and machine learning modelling. He holds a Ph.D. from Ph.D. from University of Manchester and A*STAR, MSc from University of Nottingham, BSc from Imperial College, London.

‍

His current projects include,

‍

(a) Extracting sources of sequencing variance in low biomass samples: Multiple patient autologous samples increase the risk of contamination events in cell therapies.Sterility release testing is necessary for patient safety. Current methods are not able to meet the current demands in a timely manner. We used Nanopore amplicon sequencing to increase contaminant signal relative to background.Computational analyses were used to remove noise. Limit of detection improved from 1000 CFU / mL to at least 10 CFU / mL. Host noise is reduced both during library prep and from sequenced data.Genuine contaminant reads can be separated from misclassified reads. We can now detect contaminants to 10 CFU / mL in less than 24 hours from low sample volumes. Replicating each sample with 3-fold PCR increases the confidence that an event was captured.

‍

(b) Low concentration agnostic viral detection: Viruses do not share a conserved genetic region that can be exploited for amplicon based detection. We combine Nanopore long read sequencing with concentration techniques and SISPA-seq to amplify RNA/DNA single and double-stranded viruses and detect them using metagenome classification in spiked T-cell samples. We can detect to 10⁵viral genome copies consistently pre-concentration and this will allow for more sensitive agnostic viral detection in less than 48 hours.