HLA genotyping by next‐generation sequencing is now widely performed. We aimed at evaluating the performance of the One Lambda AllType kit using Thermo Fisher Scientific reagents on the Ion S5 XL platform. Reads were analyzed using the TypeStream Visual software. We performed 15 runs between April and September 2018 to type DNA at the HLA‐A/B/C/DRB1/3/4/5/DQA1/DQB1/DPA1/DPB1 loci from 340 samples and 15 positive controls. We observed only seven (0.1%) critical mistakes among the 6009 alleles typed, corresponding to two allele dropouts, one false heterozygous typing assignment, and four phasing abnormalities. Among the 1793 presumably new alleles detected by the analysis software, 11 displayed exon mismatches, of which nine were confirmed as new alleles and two had been described previously. Intron mismatches were observed among the remaining presumably new alleles, of which 371 were considered as probably new, and 1411 were rejected for at least one sequence feature such as homopolymers (n = 1206), nucleotide doublet repeats (n = 26), low read depth (<200 reads, n = 93), high background (>20%, n = 79), or phasing abnormalities (n = 7). A comparison of the AllType results with those obtained using other methods at the second‐field resolution level showed 99.5% (1497/1504) concordance for the HLA‐A/B/C/DRB1/DQB1/DPB1 loci. Similar agreement was observed between the HLA‐C or HLA‐DRB3/4/5 results and common linkage disequilibrium, with 96.6% (657/680) and 97.2% (530/545) concordance, respectively. Therefore, the AllType kit used with the Ion S5 XL platform displayed satisfactory performance for HLA typing in current clinical practice.

Polymerase chain reaction sequence-specific oligonucleotide is commonly used for HLA-typing. We replaced our LabType SSO HD (HD) kits with LabType SSO XR (XR) kits (One Lambda, Inc., Canoga Park, California) for HLA-A, -B, and -DRB1 following acquisition of a LABScan3D analyzer. The XR kits have more bead regions than the HD kits, allowing for an extended number of probes and exon coverage. They are claimed to improve typing resolution and to diminish the number of allele ambiguities, including common and well-documented (CWD) and null alleles to be resolved. We retrospectively selected patients who had their first HLA-typing performed with the HD kits and their second determination with the XR kits between 2015 and 2016. Forty-two patients were selected for HLA-A typing comparison, and 48 for HLA-B and 41 for HLA-DRB1. XR kits significantly decreased the number of allele ambiguities for HLA-A and -B. On the other hand, the improvement was limited for the HLA-DRB1 locus. The XR kits did not resolve all the CWD HLA allele ambiguities, which may be important for organ and/or hematopoietic stem cell transplantations. The XR kits eliminated 88%, 62%, and 27% of null allele ambiguities for HLA-A, -B, and -DRB1 loci, respectively. In conclusion, the XR kits allow for a significant improvement of HLA-typing resolution for HLA-A and -B loci in comparison with HD kits. In contrast, the number of oligonucleotides in the XR HLA-DRB1 kit should be extended to include exon 3 at the very least. It could also be interesting to include oligonucleotides allowing HLA-DRB3, 4, and 5 typing.

Abbreviations: +LR, positive likelihood ratio; AMR, antibody-mediated rejection; anti-dHLA, anti-denatured HLA antibodies; anti-nHLA, anti-native HLA antibodies; AUC, area under curve; B-FCXM, B-lymphocyte flow cytometry crossmatch; DSA, donor-specific antibodies; EDTA, ethylenediaminetetraacetic acid; FCXM, flow cytometry crossmatch; −LR, negative likelihood ratio; MFI, mean fluorescence intensity; NPV, negative predictive value; PPV, positive predictive value; ROC, receiver operating characteristic; SAFB, single antigen flow bead(s); T-FCXM, T-lymphocyte flow cytometry crossmatch.Anti-denatured HLA-Cw antibodies are highly prevalent, whereas anti-native HLA-Cw antibodies seem to lead to random flow cytometry crossmatch results. We aimed to reassess crossmatch prediction for anti-HLA-Cw using 2 types of single antigen flow beads (classical beads and beads with diminished expression of denatured HLA), and to compare the pathogenicity of preformed anti-denatured and anti-native HLA-Cw antibodies in kidney transplantation. We performed 135 crossmatches with sera reacting against donor HLA-Cw (classical beads fluorescence ≥500); only 20.6% were positive. Forty-three (31.6%) were anti-denatured HLA antibodies (beads with diminished expression of denatured HLA fluorescence <300); all were crossmatch negative.The correlation between classical beads fluorescence and the crossmatch ratio was low (ρ = 0.178), and slightly higher with beads with diminished expression of denatured HLA (ρ = 0.289). We studied 52 kidney recipients with preformed anti-HLA-Cw

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PCR‐sequence‐specific oligonucleotide (PCR‐SSO) is commonly used for HLA‐typing. We recently replaced LabType SSO HD kit for HLA‐C typing with the XR kit (OneLambda, Inc.). We used 137 patients' samples representing unique most likely HLA‐C allele combinations to compare these kits' performance. The XR kit decreased the number of allele ambiguities with a median of 26.1% (first to third quartiles 20% to 36.2%, range 0% to 96.1%). The XR kit did not resolve all the common, intermediate and well‐documented HLA allele ambiguities, which may be important in the clinical setting. The XR kit eliminated 23.6% of null allele ambiguities. In conclusion, the HLA‐C XR kit provides a moderate yet valuable improvement of HLA‐typing resolution in comparison with the HLA‐C HD kit.

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HLA‐C*07:639 differs from HLA‐C*07:19 by one nucleotide substitution at codon 324 in exon 6.

HLA‐DRB1*03:147 differs from HLA‐DRB1*03:01:01:01 by one nucleotide substitution at codon 233 in exon 5.