1
|
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.
Collapse
|
2
|
Osoegawa K, Creary LE, Montero-Martín G, Mallempati KC, Gangavarapu S, Caillier SJ, Santaniello A, Isobe N, Hollenbach JA, Hauser SL, Oksenberg JR, Fernández-Viňa MA. High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. Front Immunol 2021; 12:644838. [PMID: 34211458 PMCID: PMC8240666 DOI: 10.3389/fimmu.2021.644838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from ‘hitchhiking’ alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.
Collapse
Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Lisa E Creary
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kalyan C Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Marcelo A Fernández-Viňa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| |
Collapse
|
4
|
Tu B, Masaberg C, Hou L, Behm D, Brescia P, Cha N, Kariyawasam K, Lee JH, Nong T, Sells J, Tausch P, Yang R, Ng J, Hurley CK. Combining one-step Sanger sequencing with phasing probe hybridization for HLA class I typing yields rapid, G-group resolution predicting 99% of unique full length protein sequences. HLA 2017; 89:90-97. [PMID: 28102036 DOI: 10.1111/tan.12951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 11/25/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry. Next generation DNA sequencing (NGS) was applied to over 1000 of these samples to identify the alleles present within the G group designations. RESULTS Single genotypes at G level resolution were obtained for over 95% of the loci without additional assays. The vast majority of alleles identified (>99%) were the primary allele giving the G groups their name. Only 0.7% of the alleles identified encoded protein variants that were not detected by a focus on the antigen recognition domain (ARD)-encoding exons. CONCLUSION Our combined method routinely provides biologically relevant typing resolution at the level of the ARD. It can be applied to both single samples or to large volume typing supporting either bone marrow or solid organ transplantation using technologies currently available in many HLA laboratories.
Collapse
Affiliation(s)
- Bin Tu
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Carly Masaberg
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Lihua Hou
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | | | - Peter Brescia
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Nuri Cha
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Kanthi Kariyawasam
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Jar How Lee
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Thoa Nong
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | | | - Paul Tausch
- One Lambda Inc. (Thermo Fisher Scientific), Canoga Park, California
| | - Ruyan Yang
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Jennifer Ng
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| | - Carolyn Katovich Hurley
- Departments of Oncology and Pediatrics, Georgetown University, Washington, District of Columbia
| |
Collapse
|
6
|
Voorter CE, Groeneweg M, Groeneveld L, Tilanus MG. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue. Hum Immunol 2016; 77:184-90. [DOI: 10.1016/j.humimm.2015.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 10/23/2015] [Accepted: 11/19/2015] [Indexed: 01/24/2023]
|
7
|
Crivello P, Zito L, Sizzano F, Zino E, Maiers M, Mulder A, Toffalori C, Naldini L, Ciceri F, Vago L, Fleischhauer K. The Impact of Amino Acid Variability on Alloreactivity Defines a Functional Distance Predictive of Permissive HLA-DPB1 Mismatches in Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2015; 21:233-41. [DOI: 10.1016/j.bbmt.2014.10.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/19/2014] [Indexed: 01/11/2023]
|
8
|
Vidan-Jeras B, Buhler S, Dubois V, Grubic Z, Ivanova M, Jaatinen T, Ligeiro D, Lokki ML, Papasteriades C, Poli F, Spyropoulou-Vlachou M, Tordai A, Viken M, Wenda S, Nunes J, Sanchez-Mazas A, Tiercy JM. Resolution ofHLA-B*44:02:01G, -DRB1*14:01:01Gand -DQB1*03:01:01Greveals a high allelic variability among 12 European populations. ACTA ACUST UNITED AC 2014; 84:459-64. [DOI: 10.1111/tan.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- B. Vidan-Jeras
- Tissue Typing Center; Blood Transfusion Center of Slovenia; Ljubljana Slovenia
| | - S. Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3); University of Geneva; Geneva Switzerland
| | - V. Dubois
- Etablissement Français du Sang (EFS) Rhône-Alpes; Laboratoire HLA; Lyon France
| | - Z. Grubic
- Tissue Typing Centre; University Hospital Centre Zagreb; Zagreb Croatia
| | - M. Ivanova
- Department of Clinical Immunology; University Hospital Alexandrovska; Sofia Bulgaria
| | - T. Jaatinen
- Finnish Red Cross Blood Service; Clinical Laboratory; Helsinki Finland
| | - D. Ligeiro
- Centro de Histocompatibilidad do Sul; Instituto Português de Sangue e Transplantaçâo; Lisbon Portugal
| | - M.-L. Lokki
- Transplantation Laboratory, Haartman Institute; University of Helsinki; Helsinki Finland
| | - C. Papasteriades
- Department of Immunology and Histocompatibility; Evangelismos Hospital; Athens Greece
| | - F. Poli
- Organ and Tissue Transplantation Immunology, Regenerative Medicine Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico; Milan Italy
| | - M. Spyropoulou-Vlachou
- Immunology Department - Tissue Typing Laboratory; General University Hospital of Athens Alexandra; Athens Greece
| | - A. Tordai
- Hungarian National Blood Transfusion Center; Transplantation Immunogenetics Laboratory; Budapest Hungary
| | - M.K. Viken
- Department of Immunology; Oslo University Hospital and University of Oslo; Oslo Norway
| | - S. Wenda
- Department for Blood Group Serology; Medical University Vienna; Wien Austria
| | - J.M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3); University of Geneva; Geneva Switzerland
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3); University of Geneva; Geneva Switzerland
| | - J.-M. Tiercy
- National Reference Laboratory for Histocompatibility; University Hospital Geneva; Geneva Switzerland
| |
Collapse
|