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Hod‐Dvorai R, Schiller JJ, Riddick MC, Gallay B. Identification of a
DRB1*04:07
–
DRB4*01:03:01:02N
haplotype in a native
American
individual. HLA 2022; 100:500-504. [DOI: 10.1111/tan.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Reut Hod‐Dvorai
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | | | - Mary C. Riddick
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | - Brian Gallay
- Department of Medicine SUNY Upstate Medical University Syracuse New York USA
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2
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Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories. Hum Immunol 2021; 82:820-828. [PMID: 34479742 DOI: 10.1016/j.humimm.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022]
Abstract
Next generation sequencing (NGS) is being applied for HLA typing in research and clinical settings. NGS HLA typing has made it feasible to sequence exons, introns and untranslated regions simultaneously, with significantly reduced labor and reagent cost per sample, rapid turnaround time, and improved HLA genotype accuracy. NGS technologies bring challenges for cost-effective computation, data processing and exchange of NGS-based HLA data. To address these challenges, guidelines and specifications such as Genotype List (GL) String, Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING), and Histoimmunogenetics Markup Language (HML) were proposed to streamline and standardize reporting of HLA genotypes. As part of the 17th International HLA and Immunogenetics Workshop (IHIW), we implemented standards and systems for HLA genotype reporting that included GL String, MIRING and HML, and found that misunderstanding or misinterpretations of these standards led to inconsistencies in the reporting of NGS HLA genotyping results. This may be due in part to a historical lack of centralized data reporting standards in the histocompatibility and immunogenetics community. We have worked with software and database developers, clinicians and scientists to address these issues in a collaborative fashion as part of the Data Standard Hackathons (DaSH) for NGS. Here we report several categories of challenges to the consistent exchange of NGS HLA genotyping data we have observed. We hope to address these challenges in future DaSH for NGS efforts.
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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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5
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Marsh SG. Nomenclature for factors of the HLA system, update October, November, and December 2018. Int J Immunogenet 2019; 46:88-137. [DOI: 10.1111/iji.12419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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