1
|
Mack SJ, Schefzyk D, Millius RP, Maiers M, Hollenbach JA, Pollack J, Heuer ML, Gragert L, Spellman SR, Guethlein LA, Schneider J, Bochtler W, Eberhard HP, Robinson J, Marsh SGE, Schmidt AH, Hofmann JA, Sauter J. Genotype List String 1.1: Extending the Genotype List String grammar for describing HLA and Killer-cell Immunoglobulin-like Receptor genotypes. HLA 2023; 102:206-212. [PMID: 37286192 PMCID: PMC10524834 DOI: 10.1111/tan.15126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/09/2023]
Abstract
The Genotype List (GL) String grammar for reporting HLA and Killer-cell Immunoglobulin-like Receptor (KIR) genotypes in a text string was described in 2013. Since this initial description, GL Strings have been used to describe HLA and KIR genotypes for more than 40 million subjects, allowing these data to be recorded, stored and transmitted in an easily parsed, text-based format. After a decade of working with HLA and KIR data in GL String format, with advances in HLA and KIR genotyping technologies that have fostered the generation of full-gene sequence data, the need for an extension of the GL String system has become clear. Here, we introduce the new GL String delimiter "?," which addresses the need to describe ambiguity in assigning a gene sequence to gene paralogs. GL Strings that do not include a "?" delimiter continue to be interpreted as originally described. This extension represents version 1.1 of the GL String grammar.
Collapse
Affiliation(s)
- Steven J. Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | | | | | | | - Jill A. Hollenbach
- Department of Neurology and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jane Pollack
- National Marrow Donor Program, Minneapolis, MN, USA
| | | | - Loren Gragert
- School of Medicine, Tulane University, New Orleans, LA, USA
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | | | - Werner Bochtler
- Zentrales Knochenmarkspender-Register für Deutschland (ZKRD), Ulm, Germany
| | | | - James Robinson
- Anthony Nolan Research Institute, Royal Free Campus, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Campus, London, UK
- UCL Cancer Institute, Royal Free Campus, London, UK
| | | | | | | |
Collapse
|
2
|
Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
Collapse
Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
| |
Collapse
|
3
|
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
|
4
|
Ahmad-Nejad P, Ashavaid T, Vacaflores Salinas A, Huggett J, Harris K, Linder MW, Baluchova K, Steimer W, Payne DA. Current and future challenges in quality assurance in molecular diagnostics. Clin Chim Acta 2021; 519:239-246. [PMID: 33971158 DOI: 10.1016/j.cca.2021.05.004] [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: 10/30/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The development and performance of molecular genetic assays has required increasingly complex quality assurance in recent years and continues to pose new challenges. Quality management officers, as well as academic and technical personnel are confronted with new molecular genetic parameters, methods, changing regulatory environments, questions regarding appropriate validation, and quality control for these innovative assays that are increasingly applying quantification and/or multiplex formats. Yet, quality assurance and quality control guidelines are still not widely available or in some circumstances have become outdated. For these reasons, the need for solutions to provide test confidence continues to grow. In order to integrate new test procedures into existing quality assurance measures, the ISO 15189 guideline can serve as an orientation. The ISO 15189 guideline describes requirements for medical laboratories and thus includes those performing molecular diagnostics. This article gives an overview of the possibilities and challenges in quality assurance of molecular parameters and shows possible solutions.
Collapse
Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Medicine Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS University Hospital, Wuppertal, Witten/Herdecke University, Germany.
| | - Tester Ashavaid
- Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Center, Mumbai, India
| | | | - Jim Huggett
- National Measurement Laboratory (NML) at LGC, Queens Rd, Teddington, TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Kathryn Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katarina Baluchova
- OncoLab Diagnostics GmbH Technologie- und Forschungszentrum, Viktor-Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Werner Steimer
- Institute for Clinical Chemistry and Pathobiochemistry, Munich University of Technology, Klinikum rechts der Isar, D-81675 Munich, Germany
| | | | | |
Collapse
|
5
|
Hurley CK. Naming HLA diversity: A review of HLA nomenclature. Hum Immunol 2020; 82:457-465. [PMID: 32307125 DOI: 10.1016/j.humimm.2020.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/06/2020] [Accepted: 03/22/2020] [Indexed: 11/29/2022]
Abstract
The development of a standardized HLA nomenclature has been critical in our understanding of the HLA system and in facilitating the clinical applications of HLA. The Nomenclature Committee for Factors of the HLA System, established in 1968, has overseen the development and usage of nomenclature based on serologic specificities, cellular responses, and DNA sequences. Their decisions have been guided by community consensus reached through 17 international workshops beginning in 1964 and continuing today. Two websites provide a curated database of the sequences of over 26,000 HLA alleles and a reference site for the current nomenclature. This review covers the major steps in the development of the HLA nomenclature as well as the efforts of other groups to extend its usefulness for research and clinical applications.
Collapse
|
6
|
Klasberg S, Surendranath V, Lange V, Schöfl G. Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping. Transfus Med Hemother 2019; 46:312-325. [PMID: 31832057 PMCID: PMC6876610 DOI: 10.1159/000502487] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
The advent of next generation sequencing (NGS) has altered the face of genotyping the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, and research contexts. NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies. This has led to a broader and deeper profiling of the key genes in the human immunogenetic make-up. The rapid evolution of sequencing technologies is evidenced by the development of varied short-read sequencing platforms with differing read lengths and sequencing capacities to long-read sequencing platforms capable of profiling full genes without fragmentation. Concomitantly, there has been development of a diverse set of computational analyses and software tools developed to deal with the various strengths and limitations of the sequencing data generated by the different sequencing platforms. This review surveys the different modalities involved in generating NGS HLA profiling sequence data. It systematically describes various computational approaches that have been developed to achieve HLA genotyping to different degrees of resolution. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.
Collapse
|
7
|
|
8
|
Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
Collapse
Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| |
Collapse
|
9
|
Wagner I, Schefzyk D, Pruschke J, Schöfl G, Schöne B, Gruber N, Lang K, Hofmann J, Gnahm C, Heyn B, Marin WM, Dandekar R, Hollenbach JA, Schetelig J, Pingel J, Norman PJ, Sauter J, Schmidt AH, Lange V. Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations. Front Immunol 2018; 9:2843. [PMID: 30564239 PMCID: PMC6288436 DOI: 10.3389/fimmu.2018.02843] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) genes regulate natural killer cell activity, influencing predisposition to immune mediated disease, and affecting hematopoietic stem cell transplantation (HSCT) outcome. Owing to the complexity of the KIR locus, with extensive gene copy number variation (CNV) and allelic diversity, high-resolution characterization of KIR has so far been applied only to relatively small cohorts. Here, we present a comprehensive high-throughput KIR genotyping approach based on next generation sequencing. Through PCR amplification of specific exons, our approach delivers both copy numbers of the individual genes and allelic information for every KIR gene. Ten-fold replicate analysis of a set of 190 samples revealed a precision of 99.9%. Genotyping of an independent set of 360 samples resulted in an accuracy of more than 99% taking into account consistent copy number prediction. We applied the workflow to genotype 1.8 million stem cell donor registry samples. We report on the observed KIR allele diversity and relative abundance of alleles based on a subset of more than 300,000 samples. Furthermore, we identified more than 2,000 previously unreported KIR variants repeatedly in independent samples, underscoring the large diversity of the KIR region that awaits discovery. This cost-efficient high-resolution KIR genotyping approach is now applied to samples of volunteers registering as potential donors for HSCT. This will facilitate the utilization of KIR as additional selection criterion to improve unrelated donor stem cell transplantation outcome. In addition, the approach may serve studies requiring high-resolution KIR genotyping, like population genetics and disease association studies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wesley M. Marin
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Ravi Dandekar
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Johannes Schetelig
- DKMS, Tübingen, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado Anschutz Medical, Aurora, CO, United States
| | | | | | | |
Collapse
|
10
|
Valenzuela NM, Askar M, Heidt S, Jindra P, Madbouly A, Pinelli D, Jackson A, Hidalgo LG. Minimal data reporting standards for serological testing for histocompatibility. Hum Immunol 2018; 79:865-868. [DOI: 10.1016/j.humimm.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/15/2018] [Indexed: 12/30/2022]
|
11
|
Profaizer T, Kumánovics A. Human Leukocyte Antigen Typing by Next-Generation Sequencing. Clin Lab Med 2018; 38:565-578. [DOI: 10.1016/j.cll.2018.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
12
|
Chang CJ, Osoegawa K, Milius RP, Maiers M, Xiao W, Fernandez-Viňa M, Mack SJ. Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2018; 79:77-86. [PMID: 29247682 PMCID: PMC5805642 DOI: 10.1016/j.humimm.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/12/2017] [Accepted: 12/08/2017] [Indexed: 01/06/2023]
Abstract
For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17th IHIW adopted a centralized approach to these issues, and we developed the tools, services and systems to create an effective system for capturing and managing these NGS data. We worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applied our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We have created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications.
Collapse
Affiliation(s)
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Robert P Milius
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Palo Alto, CA, USA; Massachusetts General Hospital and Shriners Hospital for Children, Boston, MA, USA
| | - Marcelo Fernandez-Viňa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| |
Collapse
|
13
|
Wiener HW, Shrestha S, Lu H, Karita E, Kilembe W, Allen S, Hunter E, Goepfert PA, Tang J. Immunogenetic factors in early immune control of human immunodeficiency virus type 1 (HIV-1) infection: Evaluation of HLA class I amino acid variants in two African populations. Hum Immunol 2017; 79:166-171. [PMID: 29289742 DOI: 10.1016/j.humimm.2017.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023]
Abstract
Immune control of HIV-1 infection depends heavily on cytotoxic T-lymphocyte responses restricted by diverse HLA class I molecules. Recent work has uncovered specific amino acid residues (AARs) that seem to dictate the extent of immune control in African Americans, which prompted us to test these emerging hypotheses in seroconverters (SCs) from southern and eastern Africa. Based on data from 196 Zambians and 76 Rwandans with fully resolved HLA alleles and pre-therapy HIV-1 viral loads (VL) in the first 3- to 36-month of infection (>2300 person-visits), four AARs of primary interest (positions 63, 97, 116 and 245 in the mature HLA-B protein) were found to explain 8.1% and 15.8% of variance in set-point VL for these cohorts (P = .024 and 7.5 × 10-6, respectively). Two AARs not reported previously (167S in HLA-B and 116F in HLA-C) also showed relatively consistent associations with VL (adjusted P = .009-.069), while many population-specific associations were also noted (false discovery rate <0.05). Extensive and often strong linkage disequilibrium among neighboring AAR variants called for more extensive analyses of AAR haplotypes in diverse cohorts before the structural basis of antigen presentation can be fully comprehended.
Collapse
Affiliation(s)
- Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hailin Lu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
14
|
Agbor-Enoh S, Tunc I, De Vlaminck I, Fideli U, Davis A, Cuttin K, Bhatti K, Marishta A, Solomon MA, Jackson A, Graninger G, Harper B, Luikart H, Wylie J, Wang X, Berry G, Marboe C, Khush K, Zhu J, Valantine H. Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation. J Heart Lung Transplant 2017. [PMID: 28624139 DOI: 10.1016/j.healun.2017.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Use of new genomic techniques in clinical settings requires that such methods are rigorous and reproducible. Previous studies have shown that quantitation of donor-derived cell-free DNA (%ddcfDNA) by unbiased shotgun sequencing is a sensitive, non-invasive marker of acute rejection after heart transplantation. The primary goal of this study was to assess the reproducibility of %ddcfDNA measurements across technical replicates, manual vs automated platforms, and rejection phenotypes in distinct patient cohorts. METHODS After developing and validating the %ddcfDNA assay, we subjected the method to a rigorous test of its reproducibility. We measured %ddcfDNA in technical replicates performed by 2 independent laboratories and verified the reproducibility of %ddcfDNA patterns of 2 rejection phenotypes: acute cellular rejection and antibody-mediated rejection in distinct patient cohorts. RESULTS We observed strong concordance of technical-replicate %ddcfDNA measurements across 2 independent laboratories (slope = 1.02, R2 > 0.99, p < 10-6), as well as across manual and automated platforms (slope = 0.80, R2 = 0.92, p < 0.001). The %ddcfDNA measurements in distinct heart transplant cohorts had similar baselines and error rates. The %ddcfDNA temporal patterns associated with rejection phenotypes were similar in both patient cohorts; however, the quantity of ddcfDNA was significantly higher in samples with severe vs mild histologic rejection grade (2.73% vs 0.14%, respectively; p < 0.001). CONCLUSIONS The %ddcfDNA assay is precise and reproducible across laboratories and in samples from 2 distinct types of heart transplant rejection. These findings pave the way for larger studies to assess the clinical utility of %ddcfDNA as a marker of acute rejection after heart transplantation.
Collapse
Affiliation(s)
- Sean Agbor-Enoh
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Ilker Tunc
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Iwijn De Vlaminck
- Department of Bioengineering, Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Ulgen Fideli
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Andrew Davis
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Karen Cuttin
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Kenneth Bhatti
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Argit Marishta
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Michael A Solomon
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Annette Jackson
- Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Grace Graninger
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Bonnie Harper
- Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Helen Luikart
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Jennifer Wylie
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Xujing Wang
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Gerald Berry
- Department of Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Charles Marboe
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Kiran Khush
- Department of Medicine, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Jun Zhu
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Hannah Valantine
- Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland; Laboratory of Transplantation Genomics, National Heart, Lung, and Blood Institute, Bethesda, Maryland.
| |
Collapse
|
15
|
Siniard RC, Harada S. Immunogenomics: using genomics to personalize cancer immunotherapy. Virchows Arch 2017; 471:209-219. [DOI: 10.1007/s00428-017-2140-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 01/06/2023]
|
16
|
Gandhi MJ, Ferriola D, Huang Y, Duke JL, Monos D. Targeted Next-Generation Sequencing for Human Leukocyte Antigen Typing in a Clinical Laboratory: Metrics of Relevance and Considerations for Its Successful Implementation. Arch Pathol Lab Med 2017; 141:806-812. [PMID: 28234015 DOI: 10.5858/arpa.2016-0537-ra] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Numerous feasibility studies to type human leukocyte antigens (HLAs) by next-generation sequencing (NGS) have led to the development of vendor-supported kits for HLA typing by NGS. Some clinical laboratories have introduced HLA-NGS, and many are investigating the introduction. Standards from accrediting agencies form the regulatory framework for introducing this test into clinical laboratories. OBJECTIVES - To provide an assessment of metrics and considerations relevant to the successful implementation of clinical HLA-NGS typing, and to provide as a reference a validated HLA-NGS protocol used clinically since December 2013 at the Children's Hospital of Philadelphia (Philadelphia, Pennsylvania). DATA SOURCES - The HLA-NGS has been performed on 2532 samples. The initial 1046 and all homozygous samples were also typed by an alternate method. The HLA-NGS demonstrated 99.7% concordance with the alternate method. Ambiguous results were most common at the DPB1 locus because of a lack of phasing between exons 2 and 3 or the unsequenced exon 1 (533 of 2954 alleles; 18.04%) and the DRB1 locus because of not sequencing exon 1 (75 of 3972 alleles; 1.89%). No ambiguities were detected among the other loci. Except for 2 false homozygous samples, all homozygous samples (1891) demonstrated concordance with the alternate method. The article is organized to address the critical elements in the preanalytic, analytic, and postanalytic phases of introducing this assay into the clinical laboratory. CONCLUSIONS - The results demonstrate that HLA typing by NGS is a highly accurate, reproducible, efficient method that provides more-complete sequencing information for the length of the HLA gene and can be the single methodology for HLA typing in clinical immunogenetics laboratories.
Collapse
Affiliation(s)
| | | | | | | | - Dimitri Monos
- From the Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Dr Gandhi); the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Ms Ferriola and Drs Huang, Duke, and Monos); and the Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Dr Monos)
| |
Collapse
|
17
|
Yin Y, Lan JH, Nguyen D, Valenzuela N, Takemura P, Bolon YT, Springer B, Saito K, Zheng Y, Hague T, Pasztor A, Horvath G, Rigo K, Reed EF, Zhang Q. Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples. PLoS One 2016; 11:e0165810. [PMID: 27798706 PMCID: PMC5087893 DOI: 10.1371/journal.pone.0165810] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022] Open
Abstract
Background Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Methods Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3’ UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Results Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Conclusion Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.
Collapse
Affiliation(s)
- Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - James H. Lan
- University of British Columbia Clinician Investigator Program, Vancouver, BC, Canada
| | - David Nguyen
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Nicole Valenzuela
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Ping Takemura
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Yung-Tsi Bolon
- National Marrow Donor Program, Minneapolis, MN, United States of America
| | - Brianna Springer
- National Marrow Donor Program, Minneapolis, MN, United States of America
| | - Katsuyuki Saito
- One Lambda, Thermo Fisher Scientific, Canoga Park, CA, United States of America
| | - Ying Zheng
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | | | | | | | | | - Elaine F. Reed
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
18
|
Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C. The impact of Docker containers on the performance of genomic pipelines. PeerJ 2015; 3:e1273. [PMID: 26421241 PMCID: PMC4586803 DOI: 10.7717/peerj.1273] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/05/2015] [Indexed: 12/01/2022] Open
Abstract
Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.
Collapse
Affiliation(s)
- Paolo Di Tommaso
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Emilio Palumbo
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Maria Chatzou
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Pablo Prieto
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Michael L Heuer
- Department of Bioinformatics Research, National Marrow Donor Program , Minneapolis, MN , United States
| | - Cedric Notredame
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) , Barcelona , Spain ; Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| |
Collapse
|
19
|
Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping. Hum Immunol 2015; 76:963-74. [PMID: 26319908 DOI: 10.1016/j.humimm.2015.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/30/2015] [Accepted: 08/06/2015] [Indexed: 11/22/2022]
Abstract
We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS.
Collapse
|