Different eplet software programs give discordant and incorrect results: An analysis of <scp>HLAMatchmaker</scp> vs Fusion Matchmaker Eplet calling software

Tassone, Gabriella; Santis, Dianne De; Vuković, Irena; Downing, Jonathan; Martinez, O. P.; D’Orsogna, Lloyd

doi:10.1111/tan.13897

Cited by 14 publications

(13 citation statements)

References 15 publications

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“…It is clear that the compilation of a detailed and accurate list of eplets as well as their calling by software programs are key components for all molecular mismatch scores and the assignment of the immunogenicity of individual eplets 25 . As shown by Kramer et al as well as Tambur et al, the current eplet lists need further refinements and verification 18,21 .…”

Section: Discussionmentioning

confidence: 99%

Development of an immunogenicity score for HLA‐DQ eplets: A conceptual study

Schawalder

Hönger

Kleiser

et al. 2020

HLA

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Eplets are defined as distinct amino acid configurations on the surface of HLA molecules. The aim of this study was to estimate the immunogenicity of HLA-DQ eplets in a cohort of 221 pregnancies with HLA-DQ mismatches. We defined the immunogenicity of an eplet by the frequency of antibody responses against it. Around 90% of all listed DQB1 or DQA1 eplets were at least five times mismatched and thus included for the calculation of their immunogenicity. The DQB1 eplets with the five highest immunogenicity scores were 55PP, 52PR, 52PQ, 85VG and 45EV; 25% of all DQB1 eplets were not reacting. The DQA1 eplets with the five highest immunogenicity scores were 25YS, 47QL, 55RR, 187T and 18S; 17% of all DQA1 eplets were not reacting. The immunogenicity score had a slightly higher area under the curve to predict development of childspecific antibodies than various molecular mismatch scores (eg, eplet mismatch load, amino acid mismatch load). Overlapping eplets were identified as a barrier to unambiguously assign the immunogenicity score based on HLA antibody reaction patterns. In this conceptual study, we explored the immunogenicity of HLA-DQ eplets and created a map of potentially immunogenic regions on HLA-DQ molecules, which requires validation in clinical transplant cohorts.

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Section: Discussionmentioning

confidence: 99%

Development of an immunogenicity score for HLA‐DQ eplets: A conceptual study

Schawalder

Hönger

Kleiser

et al. 2020

HLA

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“…Curiously, eplet 55R was not identified by HLAMatchmaker analysis, while this eplet is present in the HLA Epitope Registry. This issue of inaccuracy in eplet software has been previously addressed by Tassone et al (51). As observed in the SAB data, 55R was also the uniquely shared residue for mAb LB_DQB0601_B, but this mAb demonstrated increased binding strength for eplet 55R with residue 53Q as additional configuration.…”

Section: Discussionmentioning

confidence: 69%

HLA-DQ-Specific Recombinant Human Monoclonal Antibodies Allow for In-Depth Analysis of HLA-DQ Epitopes

et al. 2022

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HLA-DQ donor-specific antibodies (DSA) are the most prevalent type of DSA after renal transplantation and have been associated with eplet mismatches between donor and recipient HLA. Eplets are theoretically defined configurations of surface exposed amino acids on HLA molecules that require verification to confirm that they can be recognized by alloantibodies and are therefore clinically relevant. In this study, we isolated HLA-DQ specific memory B cells from immunized individuals by using biotinylated HLA-DQ monomers to generate 15 recombinant human HLA-DQ specific monoclonal antibodies (mAb) with six distinct specificities. Single antigen bead reactivity patterns were analyzed with HLA-EMMA to identify amino acids that were uniquely shared by the reactive HLA alleles to define functional epitopes which were mapped to known eplets. The HLA-DQB1*03:01-specific mAb LB_DQB0301_A and the HLA-DQB1*03-specific mAb LB_DQB0303_C supported the antibody-verification of eplets 45EV and 55PP respectively, while mAbs LB_DQB0402_A and LB_DQB0602_B verified eplet 55R on HLA-DQB1*04/05/06. For three mAbs, multiple uniquely shared amino acid configurations were identified, warranting further studies to define the inducing functional epitope and corresponding eplet. Our unique set of HLA-DQ specific mAbs will be further expanded and will facilitate the in-depth analysis of HLA-DQ epitopes, which is relevant for further studies of HLA-DQ alloantibody pathogenicity in transplantation.

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“…Accordingly, the use of different definitions for the same eplet and the inclusion of eplet pairs in immunogenicity studies distorts the interpretation and comparability of immunogenicity scores. Furthermore, inconsistencies in eplet definition and antibody-verified status between the HLA Epitope Registry and HLAMatchmaker (60) and the lack of documentation of previous versions of the Registry hamper investigations towards eplet mismatch loads and transplant outcomes.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Evaluation of the Antibody-Verified Status of Eplets Listed in the HLA Epitope Registry

et al. 2022

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Matching strategies based on HLA eplets instead of HLA antigens in solid organ transplantation may not only increase the donor pool for highly sensitized patients, but also decrease the incidence of de novo donor-specific antibody formation. However, since not all eplets are equally capable of inducing an immune response, antibody verification is needed to confirm their ability to be bound by antibodies, such that only clinically relevant eplets are considered. The HLA Epitope Registry has documented all theoretically defined HLA eplets along with their antibody verification status and has been the foundation for many clinical studies investigating eplet mismatch in transplantation. The verification methods for eplets in the Registry range from polyclonal sera from multi- and uni-parous women to murine and human monoclonal antibodies (mAbs), and antibodies purified by adsorption and elution from sera of HLA immunized individuals. The classification of antibody verification based on different methods for validation is problematic, since not all approaches represent the same level of evidence. In this study, we introduce a classification system to evaluate the level of evidence for the antibody-verified status of all eplets in the HLA Epitope Registry. We demonstrate that for a considerable number of eplets, the antibody-verified status is solely based on polyclonal serum reactivity of multiparous women or on reactivity of murine mAbs. Furthermore, we noted that a substantial proportion of patient sera analyses and human mAb data presented in the HLA Epitope Registry Database has never been published in a peer-reviewed journal. Therefore, we tested several unpublished human HLA-specific mAbs by luminex single antigen beads assay to analyze their HLA reactivity for eplet antibody verification. Although the majority of analyzed mAbs indeed verified their assigned eplets, this was not the case for a number of eplets. This comprehensive overview of evidence for antibody verification of eplets in the HLA Epitope Registry is instrumental for future investigations towards eplet immunogenicity and clinical studies considering antibody-verified eplet mismatch in transplantation and warrants further standardization of antibody verification using high quality data.

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Different eplet software programs give discordant and incorrect results: An analysis of HLAMatchmaker vs Fusion Matchmaker Eplet calling software

Cited by 14 publications

References 15 publications

Development of an immunogenicity score for HLA‐DQ eplets: A conceptual study

Development of an immunogenicity score for HLA‐DQ eplets: A conceptual study

HLA-DQ-Specific Recombinant Human Monoclonal Antibodies Allow for In-Depth Analysis of HLA-DQ Epitopes

A Comprehensive Evaluation of the Antibody-Verified Status of Eplets Listed in the HLA Epitope Registry

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