Entries by Richard Casey

HLA Susceptibility in SARS-CoV-2

Nguyen et al. recently published a paper “Human leukocyte antigen susceptibili8ty map for SARS-CoV-2” in the Journal of Virology. Using in-silico methods, they assessed the binding affinities of MHC Class I alleles (HLA-A, HLA-B, HLA-C) with all known SARS-CoV-2 8-12mer peptides from the full SARS-CoV-2 proteome.  Presumably, the binding affinities of MHC Class I molecules to […]

Cost Savings with Multiplex Samples

Multiplex sequencing, or multiplexing for short, is a method of combining two or more samples (pooling samples) in a single sequencing run. Multiplexing can increase the throughput of sequencing runs and save money at the same time. Conceptually, multiplexing is a fairly straightforward process.   Fig. 1 shows how (two) samples are multiplexed and demultiplexed […]

Bacteriophage DNA Extraction Protocol

We routinely perform bacteriophage whole genome sequencing.  However, we do not currently offer phage DNA extraction services.  Instead, researchers perform phage DNA extraction at their own facilities and then ship purified gDNA to our sequencing Lab.  Apparently, DNA extraction for some phage species can be challenging.  Therefore, we present the following option. Jakociune and Moodley, […]