Entries by Richard Casey

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Leveraging AI and ML in HLA Typing: A New Frontier in Health Science

Our understanding of human health is constantly evolving, and at the cutting edge of this expansion is the increasingly critical role of Human Leukocyte Antigen (HLA) typing. This method, key in immunogenetic research, involves identifying specific variations in the human genome that can influence immune response. A dauntingly complex task, HLA typing is being streamlined […]

HLA Typing the HLA-DRB Allele Paralogues

As we navigate the fascinating world of human genetics, we’re consistently astounded by the complexity and diversity of our gene networks. Our journey today brings us to a family of genes that share a remarkable history and function – the paralogues HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5. Positioned within the Major Histocompatibility Complex (MHC) on human […]

Harnessing Long-Read Sequencing in HLA Typing

The Human Leukocyte Antigen (HLA) system holds a significant role in the world of genomics, driving research in areas as diverse as organ transplantation, disease association studies, and immune response. HLA Typing, a method used to identify specific variations of the HLA gene complex in individuals, has historically posed numerous challenges due to the highly […]

Mastering the Art of HLA Typing

For those who TL;DR, here’s a summary.   The paper titled “The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside” by Lee Ann Baxter-Lowe1 provides an in-depth overview of the Human Leukocyte Antigen (HLA) system and its significant impact on clinical and […]

HLA Typing: Unlocking the Secrets of the Human Immune System

HLA Typing, or Human Leukocyte Antigen typing, is a powerful tool in the world of medical research and clinical applications. As the cornerstone of understanding the human immune system, HLA Typing has become increasingly essential for successful organ transplantation, disease susceptibility research, and pharmacogenomics. In this blog post, we will delve into the role of […]

The HLA-DRB5 Gene

The HLA-DRB5 gene is a human leukocyte antigen gene located on chromosome 6. It is a part of the major histocompatibility complex (MHC) family, which helps the immune system recognize and respond to foreign substances. HLA-DRB5 is involved in presenting peptide antigens to T-cells for recognition. HLA-DRB5 is a polymorphic gene, meaning that it has […]

The HLA-G Gene

HLA-G is a Major Histocompatibility Complex (MHC) gene located on human chromosome 6. The gene is a member of the HLA-A, -B, -C, -E, -F, and -G family of molecules, which are involved in the regulation of the immune system and other cellular functions. HLA-G is expressed at the surface of cells in a variety […]

The HLA-DQB1 Gene

The HLA-DQB1 gene is an important component of the human leukocyte antigen (HLA) system, a group of genes that regulate the immune system. It is located on chromosome 6 in humans and encodes a class II major histocompatibility complex (MHC) molecule, known as the HLA-DQB1 molecule. The HLA-DQB1 gene plays a key role in antigen […]

The HLA-DQA1 Gene

The HLA-DQA1 gene is a member of the HLA gene family, which is located on the short arm of chromosome 6. The gene encodes proteins that are involved in the immune response and are part of the major histocompatibility complex (MHC). HLA-DQA1 proteins are primarily expressed on the surface of antigen-presenting cells, such as macrophages, […]

The HLA-DPB1 Gene

The HLA-DPB1 gene is a gene located on the short arm of the sixth chromosome (6p21.3) and is part of the human leukocyte antigen (HLA) major histocompatibility complex (MHC) locus. The HLA-DPB1 gene is important for the immune system as it is involved in the recognition of foreign antigens. Specifically, the HLA-DPB1 gene encodes for […]

The HLA-DPA1 Gene

The HLA-DPA1 gene belongs to the human leukocyte antigen (HLA) family and is located on chromosome 6. It plays a key role in the immune system by helping the body to recognize and respond to foreign antigens. The gene provides instructions for making a protein that is a component of the major histocompatibility complex (MHC) […]

The HLA-DRB4 Gene

The HLA-DRB4 gene is a member of the human leukocyte antigen (HLA) family, which is responsible for coding proteins that help the body’s immune system recognize and fight off foreign substances, such as viruses and bacteria. The HLA-DRB4 gene, located on the short arm of human chromosome 6, encodes a transmembrane glycoprotein that antigen-presenting cells […]

The HLA-DRB3 Gene

HLA-DRB3 is a human leukocyte antigen (HLA) gene located on chromosome 6. It codes for a polymorphic cell surface glycoprotein known as the DRB3 molecule. This molecule is a member of the MHC class II family of immune-related proteins and is expressed on the surface of antigen presenting cells. HLA-DRB3 is involved in the recognition […]

The HLA-DRB1 Gene

The HLA-DRB1 gene is a major histocompatibility complex (MHC) gene located on human chromosome 6. It is a polymorphic gene, meaning that it has many different forms that vary from person to person. The HLA-DRB1 gene encodes for the HLA-DRB1 protein, which is a type of MHC class II molecule. MHC molecules play an important […]

The HLA-C Gene

The HLA-C gene is a major histocompatibility complex (MHC) class I gene located on human chromosome 6. It is a member of the MHC Class I family of genes, which are responsible for the recognition and presentation of antigens to the immune system. The HLA-C gene is composed of two exons, which encode the heavy […]

Nanopore Long-Reads Coming to HLA

GenDx announced NGS-Turbo, a long-read HLA sequencing product for Nanopore instruments. Although we will have to see the actual protocol in practice, HLA sequencing with Nanopore long-reads should offer significant benefits in relation to short-read technologies, including: 1) Dramatic improvement in turnaround time. Nanopore long-read protocols for lib prep and sequencing often require just hours, […]

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Novel HLA Allele Identified

In May 2020, we reported on the likely discovery of a novel HLA-B allele, a finding that would later unfold into a captivating tale of scientific collaboration and the importance of data archiving. During our initial analysis, we performed HLA typing and sequence alignments against the then-current version of the IMGT/HLA database, v.3.38.0. The sample […]

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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. What We […]

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 […]

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How Did We Discover a Novel HLA Allele?

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 yielded […]