Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation

Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP

Killer-cell immunoglobulin-like receptors (KIR) control natural killer (NK) cell functions by recognizing HLA molecules and modulating the activity of NK cells. The KIR gene cluster contains polymorphic and highly homologous genes. Diversity of the KIR region is achieved through differences in gene content, allelic polymorphism, and gene copy number, which result in unrelated individuals having different KIR genotypes and individualized immune responses that are relevant to multiple aspects of human health and disease. Therefore, KIR genotyping is increasingly used in epidemiological studies. Here, we developed multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP) to compensate for the shortcomings of the conventional PCR-SSP method, which is most commonly used for KIR analysis. Multiplex PCR-SSP method involves six multiplex reactions that detect 16 KIR genes and distinguish variant types of some KIR genes by adding two reactions. The assay was evaluated in a blind survey using a panel of 40 reference DNA standards from the UCLA KIR Exchange Program. The results are 100% concordant with the genotype determined using Luminex-based reverse sequence-specific oligonucleotide typing systems. Additionally, we investigated the currently known 16 KIR genes and their common variants in 120 unrelated Korean individuals. The results were consistent with the KIR genotype previously reported by Hwang et al. This multiplex PCR-SSP is an efficient method for analyzing KIR genotypes in both small- and large-scale studies with minimal labor, reagents, and DNA. Furthermore, by providing a better definition of KIR polymorphisms it can contribute to developments in immunogenetics.

Challenges in the application of NGS in the clinical laboratory

Next-generation sequencing (NGS), also known as massively parallel sequencing, has revolutionized genomic research. The current advances in NGS technology make it possible to provide high resolution, high throughput HLA typing in clinical laboratories. The focus of this review is on the recent development and implementation of NGS in clinical laboratories. Here, we examine the critical role of NGS technologies in clinical immunology for HLA genotyping. Two major NGS platforms (Illumina and Ion Torrent) are characterized including NGS library preparation, data analysis, and validation. Challenges of NGS implementation in the clinical laboratory are also discussed, including sequencing error rate, bioinformatics, result interpretation, analytic sensitivity, as well as large data storage. This review aims to promote the broader applications of NGS technology in clinical laboratories and advocate for the novel applications of NGS to drive future research.

Accreditation of histocompatibility and immunogenetics laboratories: Achievements and future prospects from the European Federation for Immunogenetics Accreditation Programme

The importance of demonstrating adherence to good practice in the provision of clinical services is well recognised, and there are many legislative and regulatory requirements that aim to ensure that services are appropriately reviewed and certified. Therefore, for regulatory purposes, laboratories must provide assurance of the quality of the services they provide. Additionally in the field of transplantation, where donor organs and stem cells are exchanged across national boundaries, adoption of a common set of standards by laboratories across many different countries is an important factor. The European Federation for Immunogenetics (EFI) Accreditation Programme was established to provide assurance that Histocompatibility & Immunogenetics laboratories providing services for transplantation, transfusion, and disease association testing meet the requirements of the specialty specific EFI standards. The first H&I laboratories achieved EFI accreditation in 1995, and currently there are over 260 EFI accredited laboratories in 36 countries. The programme depends on the voluntary participation of the inspectors, who are all experts in the field of H&I, and who, over the last 22 years, have performed over 1400 onsite inspections of laboratories. Inspection findings show the areas that are most frequently found to be deficient in meeting the requirements of the standards, and this can be used to inform educational and other activities with the aim of improving laboratory compliance with the standards. The EFI standards have been regularly updated to reflect the changes in the field with 19 versions over the last 22 years, and the data from the accreditation programme show how laboratories have changed their practices to incorporate new techniques that support patient care.