Entries by Richard Casey

Illumina Announces Long Reads

Illumina recently announced the upcoming availability of long-read technology at the 40th Annual J.P. Morgan Healthcare Conference, in a press release and on Illumina’s Genomics Research Hub.  The new long-read sequencing assay is code-named Infinity and is predicted to launch in the second-half of 2022.  However, no firm release date has been set.   Illumina […]

On an HLA Null Allele Case Study

A recent case study report describes the discovery of a novel HLA null allele and its effect on protein synthesis and gene expression (Rozar, 2021).  We occasionally deliver HLA reports that include null alleles.  This case study highlights the potential importance of null alleles for donor-recipient HLA matching in acute myeloid leukemia (AML). HLA null […]

How Did We Discover a Novel HLA Allele?

Intro 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 susceptibility 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 SARS-CoV-2 […]

Cost Savings with Multiplex Samples

Multiplex Sequencing Multiplexing is a method of combining two or more 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 a sequencing […]