Entries by Richard Casey

How Did We Discover a Novel HLA Allele?

Introduction One of the pleasures of owning a genomics company is assisting client researchers with new discoveries.  Recently, one of our clients completed an 11-loci, 4-field HLA typing project for a clinical trial project.  Using Illumina Next Generation Sequencing (NGS) instruments they multiplexed 48 samples for quick turnaround on a short-deadline schedule.  While most samples […]

HLA Susceptibility in SARS-CoV-2

Intro 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 Multiplexing 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 Fig. 1 shows how (two) samples are multiplexed and demultiplexed in […]

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, […]