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Smith AG, Pereira S, Jaramillo A, Stoll ST, Khan FM, Berka N, Mostafa AA, Pando MJ, Usenko CY, Bettinotti MP, Pyo CW, Nelson WC, Willis A, Askar M, Geraghty DE. Comparison of sequence-specific oligonucleotide probe vs next generation sequencing for HLA-A, B, C, DRB1, DRB3/B4/B5, DQA1, DQB1, DPA1, and DPB1 typing: Toward single-pass high-resolution HLA typing in support of solid organ and hematopoietic cell transplant programs. HLA 2019; 94:296-306. [PMID: 31237117 PMCID: PMC6772026 DOI: 10.1111/tan.13619] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/09/2019] [Accepted: 06/18/2019] [Indexed: 01/18/2023]
Abstract
Many clinical laboratories supporting solid organ transplant programs use multiple HLA genotyping technologies, depending on individual laboratory needs. Sequence‐specific primers and quantitative polymerase chain reaction (qPCR) serve the rapid turnaround necessary for deceased donor workup, while sequence‐specific oligonucleotide probe (SSOP) technology is widely employed for higher volumes. When clinical need mandates high‐resolution data, Sanger sequencing‐based typing (SBT) has been the “gold standard.” However, all those methods commonly yield ambiguous typing results that utilize valuable laboratory resources when resolution is required. In solid organ transplantation, high‐resolution typing may provide critical information for highly sensitized patients with donor‐specific anti‐HLA antibodies (DSA), particularly when DSA involve HLA alleles not discriminated by SSOP typing. Arguments against routine use of SBT include assay complexity, long turnaround times (TAT), and increased costs. Here, we compare a next generation sequencing (NGS) technology with SSOP for accuracy, effort, turnaround time, and level of resolution for genotyping of 11 HLA loci among 289 specimens from five clinical laboratories. Results were concordant except for SSOP misassignments in eight specimens and 21 novel sequences uniquely identified by NGS. With few exceptions, SSOP generated ambiguous results while NGS provided unambiguous three‐field allele assignments. For complete HLA genotyping of up to 24 samples by either SSOP or NGS, bench work was completed on day 1 and typing results were available on day 2. This study provides compelling evidence that, although not viable for STAT typing of deceased donors, a single‐pass NGS HLA typing method has direct application for solid organ transplantation.
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Affiliation(s)
- Anajane G Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shalini Pereira
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Andrés Jaramillo
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona
| | - Scott T Stoll
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona
| | - Faisal M Khan
- Calgary Laboratory Services, Calgary, Alberta Children's Hospital Research Institute, Alberta
| | - Noureddine Berka
- Calgary Laboratory Services, Calgary, Alberta Children's Hospital Research Institute, Alberta
| | - Ahmed A Mostafa
- Calgary Laboratory Services, Calgary, Alberta Children's Hospital Research Institute, Alberta
| | - Marcelo J Pando
- Department of Surgery, Scott & White Medical Center, Temple, Texas
| | - Crystal Y Usenko
- Department of Surgery, Scott & White Medical Center, Temple, Texas
| | - Maria P Bettinotti
- Immunogenetics Laboratory, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wyatt C Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, Texas
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, Texas
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Bouthemy C, Ralazamahaleo M, Jollet I, Filloux M, Visentin J, Guidicelli G. Improvement in HLA-typing by new sequence-specific oligonucleotides kits for HLA-A, -B, and -DRB1 loci. HLA 2018; 92:279-287. [PMID: 30129271 DOI: 10.1111/tan.13382] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022]
Abstract
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.
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Affiliation(s)
- Charlène Bouthemy
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
| | - Isabelle Jollet
- Etablissement Français du Sang Nouvelle Aquitaine, Laboratoire HLA, Poitiers, France
| | - Matthieu Filloux
- CHU de Limoges, Laboratoire d'Immunologie et Immunogénétique, Limoges, France.,Contrôle de la Réponse Immune B et Lymphoproliférations (CRIBL), UMR CNRS 7276-INSERM U 1262, Centre de Biologie et de Recherches en Santé, Limoges, France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France.,Université de Bordeaux, Bordeaux, France.,Immuno ConcEpT, UMR CNRS 5164, Bordeaux, France
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique, Hôpital Pellegrin, Bordeaux, France
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