Novel Approaches and Technologies in Molecular HLA Typing

Dunn, P. P. J.

doi:10.1007/978-1-4939-2690-9_18

Cited by 10 publications

(3 citation statements)

References 48 publications

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“…Although HLA typing by serology can give a rough result in a short time, it cannot identify rare or new HLA alleles [ 10 ]. Currently, polymerase chain reaction (PCR) is the most widely used HLA typing method [ 11 ], and it can be further divided into polymerase chain reaction sequence-specific primer (PCR-SSP), polymerase chain reaction sequence-specific oligonucleotide probes (PCR-SSO) and polymerase chain reaction sequenced based typing (PCR-SBT). Among them, PCR-SBT with the highest typing accuracy is the only technique that can directly detect the nucleotide sequence of each allele.…”

Section: Introductionmentioning

confidence: 99%

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Yi¹,

Chen²,

Xiao³

et al. 2020

Briefings in Bioinformatics

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Human leukocyte antigen (HLA) can encode the human major histocompatibility complex (MHC) proteins and play a key role in adaptive and innate immunity. Emerging clinical evidences suggest that the presentation of tumor neoantigens and neoantigen-specific T cell response associated with MHC class I molecules are of key importance to activate the adaptive immune systemin cancer immunotherapy. Therefore, accurate HLA typing is very essential for the clinical application of immunotherapy. In this study, we conducted performance evaluations of 4 widely used HLA typing tools (OptiType, Phlat, Polysolver and seq2hla) for predicting HLA class Ia genes from WES and RNA-seq data of 28 cancer patients. HLA genotyping data using PCR-SBT method was firstly obtained as the golden standard and was subsequently compared with HLA typing data by using NGS techniques. For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions can present a probably superior performance for HLA-Ia typing, enabling its application in cancer immunotherapy.

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Section: Introductionmentioning

confidence: 99%

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Yi¹,

Chen²,

Xiao³

et al. 2020

Briefings in Bioinformatics

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“…This is primarily because the majority of commercially accessible HLA primers lack the capability to differentiate between closely related alleles, consequently preventing them from achieving two-field resolution. Additionally, the use of fluorescent probes adds to the overall cost of the technique, making it less suitable for routine applications [ 40 ].…”

Section: Real-time Pcrmentioning

confidence: 99%

Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine

Geo,

Ameen,

Al Shemmari

et al. 2024

Med Princ Pract

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HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.

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“…The expanse of polymorphism in the HLA genes continues to be revealed and this polymorphism represents a significant barrier for successful allogeneic transplantation of an organ or stem cells (Tiercy, ; Tait, ). The extent of polymorphism discovery will accelerate with the adoption of next‐generation sequencing technology (Dunn, ) especially for donors for stem cell transplantation in which allelic HLA matching is vital. We have been using group‐specific amplification of HLA class I alleles since 2003 to ensure unambiguous allele‐level HLA typing by sequencing the isolated alleles.…”

Section: Introductionmentioning

confidence: 99%

Identification of seven novel HLA class I alleles in New Zealand

Lamb¹,

Choi²,

Selwyn³

et al. 2015

Int J Immunogenetics

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Seven new HLA class I alleles have been identified in the New Zealand population in the process of routine HLA typing and they are described here. Unusual bead positivity in Luminex typing identified potential new alleles in a bone marrow registry donor (B*40:285) and two HIV patients prior to abacavir prescription (B*14:02:09, B*41:29). In addition, four new class I alleles were identified through class I sequencing-based typing (SBT) outside of exons 2 and 3. One mutation was identified in exon 4 (new allele C*12:125) and three have been found in exon 5, an exon rarely sequenced. Two stem cell transplant recipients (B*07:02:45, C*03:279) had novel mutations in exon 5 and one was found in exon 5 of a potentially matched unrelated donor from DKMS, previously thought to be B*40:02:01 (B*40:303).

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Novel Approaches and Technologies in Molecular HLA Typing

Cited by 10 publications

References 48 publications

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine

Identification of seven novel HLA class I alleles in New Zealand

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