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Pascart T, Wasik KA, Preda C, Chune V, Torterat J, Prud'homme N, Nassih M, Martin A, Le Masson J, Rodière V, Frogier S, Canova G, Pescheux JP, Shan Sei Fan C, Jauffret C, Claeys P, von Baeyer SL, Castel SE, Emde AK, Yerges-Armstrong L, Fox K, Leask M, Vitagliano JJ, Graf S, Norberciak L, Raynal J, Dalbeth N, Merriman T, Bardin T, Oehler E. The gout epidemic in French Polynesia: a modelling study of data from the Ma'i u'u epidemiological survey. Lancet Glob Health 2024; 12:e685-e696. [PMID: 38485432 DOI: 10.1016/s2214-109x(24)00012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Gout is the most common cause of inflammatory arthritis worldwide, particularly in Pacific regions. We aimed to establish the prevalence of gout and hyperuricaemia in French Polynesia, their associations with dietary habits, their comorbidities, the prevalence of the HLA-B*58:01 allele, and current management of the disease. METHODS The Ma'i u'u survey was epidemiological, prospective, cross-sectional, and gout-focused and included a random sample of adults from the general adult population of French Polynesia. It was conducted and data were collected between April 13 and Aug 16, 2021. Participants were randomly selected to represent the general adult population of French Polynesia on the basis of housing data collected during the 2017 territorial census. Each selected household was visited by a research nurse from the Ma'i u'u survey who collected data via guided, 1-h interviews with participants. In each household, the participant was the individual older than 18 years with the closest upcoming birthday. To estimate the frequency of HLA-B*58:01, we estimated HLA-B haplotypes on individuals who had whole-genome sequencing to approximately 5× average coverage (mid-pass sequencing). A subset of individuals who self-reported Polynesian ancestry and not European, Chinese, or other ancestry were used to estimate Polynesian-ancestry specific allele frequencies. Bivariate associations were reported for weighted participants; effect sizes were estimated through the odds ratio (OR) of the association calculated on the basis of a logistic model fitted with weighted observations. FINDINGS Among the random sample of 2000 households, 896 participants were included, 140 individuals declined, and 964 households could not be contacted. 22 participants could not be weighted due to missing data, so the final weighted analysis included 874 participants (449 [51·4%] were female and 425 [48·6%] were male) representing the 196 630 adults living in French Polynesia. The estimated prevalence of gout was 14·5% (95% CI 9·9-19·2), representing 28 561 French Polynesian adults, that is 25·5% (18·2-32·8) of male individuals and 3·5% (1·0-6·0) of female individuals. The prevalence of hyperuricaemia was estimated at 71·6% (66·7-76·6), representing 128 687 French Polynesian adults. In multivariable analysis, age (OR 1·5, 95% CI 1·2-1·8 per year), male sex (10·3, 1·8-60·7), serum urate (1·6, 1·3-2·0 per 1 mg/dL), uraturia (0·8, 0·8-0·8 per 100 mg/L), type 2 diabetes (2·1, 1·4-3·1), BMI more than 30 kg/m2 (1·1, 1·0-1·2 per unit), and percentage of visceral fat (1·7, 1·1-2·7 per 1% increase) were associated with gout. There were seven heterozygous HLA-B*58:01 carriers in the full cohort of 833 individuals (seven [0·4%] of 1666 total alleles) and two heterozygous carriers in a subset of 696 individuals of Polynesian ancestry (two [0·1%]). INTERPRETATION French Polynesia has an estimated high prevalence of gout and hyperuricaemia, with gout affecting almost 15% of adults. Territorial measures that focus on increasing access to effective urate-lowering therapies are warranted to control this major public health problem. FUNDING Variant Bio, the French Polynesian Health Administration, Lille Catholic University Hospitals, French Society of Rheumatology, and Novartis.
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Affiliation(s)
- Tristan Pascart
- Service de Rhumatologie, Hôpital Saint-Philibert, Lille, France.
| | | | - Cristian Preda
- Department of Methodology and Biostatistics, Hôpital Saint-Philibert, Lille, France
| | - Valérie Chune
- Department of Biology, Centre Hospitalier de Polynésie Française, Pape'ete, Tahiti, French Polynesia
| | - Jérémie Torterat
- Institut de la Statistique de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Nicolas Prud'homme
- Institut de la Statistique de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Maryline Nassih
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France
| | - Agathe Martin
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France
| | - Julien Le Masson
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France
| | - Vahinetua Rodière
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France; Direction de la Santé de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Sylvain Frogier
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France; Direction de la Santé de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Georges Canova
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France; Direction de la Santé de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Jean-Paul Pescheux
- Lille Catholic University and Research Department, Hôpital Saint-Philibert, Lille, France; Direction de la Santé de Polynésie Française, Papeete, Tahiti, French Polynesia
| | | | | | - Patrick Claeys
- Department of Biology, Centre Hospitalier de Polynésie Française, Pape'ete, Tahiti, French Polynesia
| | | | | | | | | | - Keolu Fox
- Global Health Program, Department of Anthropology and Indigenous Futures Institute, Division of Design and Innovation, University of California San Diego, San Diego, CA, USA; Native BioData Consortium, Eagle Butte, SD, USA
| | - Megan Leask
- Division of Clinical Rheumatology and Immunology, University of Alabama, Birmingham, AL, USA; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Sahara Graf
- Department of Methodology and Biostatistics, Hôpital Saint-Philibert, Lille, France
| | - Laurène Norberciak
- Department of Methodology and Biostatistics, Hôpital Saint-Philibert, Lille, France
| | - Jacques Raynal
- Ministère de la Santé de Polynésie Française, Papeete, Tahiti, French Polynesia
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Tony Merriman
- Division of Clinical Rheumatology and Immunology, University of Alabama, Birmingham, AL, USA; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Thomas Bardin
- National Institute of Health and Medical Research U1132, Université Paris-Cité, Hôpital Lariboisière, Paris, France
| | - Erwan Oehler
- Department of Internal Medicine and Infectious Diseases, Centre Hospitalier de Polynésie Française, Pape'ete, Tahiti, French Polynesia
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Anukul N, Jenjaroenpun P, Sirikul C, Wankaew N, Nimsamer P, Roothumnong E, Pithukpakorn M, Leetrakool N, Wongsurawat T. Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing. Front Genet 2023; 14:1213457. [PMID: 37424729 PMCID: PMC10326273 DOI: 10.3389/fgene.2023.1213457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Nanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, which requires several enzymatic reactions and remains relatively expensive, even when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid Barcoding kit, which is transposase-based, with library preparation taking less than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different ethnicity and nine were from Thai individuals. Two primer sets, a commercial set and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing tools that used different algorithms were applied and compared. We found that without using several third-party reagents, the transposase-based method reduced the hands-on time from approximately 9 h to 4 h, making this a viable approach for obtaining same-day results from 2 to 24 samples. However, an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost.
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Affiliation(s)
- Nampeung Anukul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chonticha Sirikul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Natnicha Wankaew
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pattaraporn Nimsamer
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ekkapong Roothumnong
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nipapan Leetrakool
- Blood Bank Section, Maharaj Nakorn Chiang Mai Hospital, Faculty of Medicines, Chiang Mai University, Chiang Mai, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research and Innovation Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
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Chmel M, Bartoš O, Beran O, Pajer P, Dresler J, Čurdová M, Holub M. Salmonella Paratyphi Infection: Use of Nanopore Sequencing as a Vivid Alternative for the Identification of Invading Bacteria. Prague Med Rep 2021; 122:96-105. [PMID: 34137685 DOI: 10.14712/23362936.2021.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In our study we present an overview of the use of Oxford Nanopore Technologies (ONT) sequencing technology on the background of Enteric fever. Unlike traditional methods (e.g., qPCR, serological tests), the nanopore sequencing technology enables virtually real-time data generation and highly accurate pathogen identification and characterization. Blood cultures were obtained from a 48-year-old female patient suffering from a high fever, headache and diarrhea. Nevertheless, both the initial serological tests and stool culture appeared to be negative. Therefore, the bacterial isolate from blood culture was used for nanopore sequencing (ONT). This technique in combination with subsequent bioinformatic analyses allowed for prompt identification of the disease-causative agent as Salmonella enterica subsp. enterica serovar Paratyphi A. The National Reference Laboratory for Salmonella (NIPH) independently reported this isolate also as serovar Paratyphi A on the basis of results of biochemical and agglutination tests. Therefore, our results are in concordance with certified standards. Furthermore, the data enabled us to assess some basic questions concerning the comparative genomics, i.e., to describe whether the isolated strain differs from the formerly published ones or not. Quite surprisingly, these results indicate that we have detected a novel and so far, unknown variety of this bacteria.
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Affiliation(s)
- Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic. .,Military Health Institute, Military Medical Agency, Prague, Czech Republic.
| | - Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic.,Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Ondřej Beran
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Martina Čurdová
- Department of Clinical Microbiology, Military University Hospital Prague, Prague, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic
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5
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Johansson T, Koskela S, Yohannes DA, Partanen J, Saavalainen P. Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes. Front Genet 2021; 12:635601. [PMID: 33763116 PMCID: PMC7982845 DOI: 10.3389/fgene.2021.635601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/11/2021] [Indexed: 01/29/2023] Open
Abstract
Identification of human leukocyte antigen (HLA) alleles from next-generation sequencing (NGS) data is challenging because of the high polymorphism and mosaic nature of HLA genes. Owing to the complex nature of HLA genes and consequent challenges in allele assignment, Oxford Nanopore Technologies' (ONT) single-molecule sequencing technology has been of great interest due to its fitness for sequencing long reads. In addition to the read length, ONT's advantages are its portability and possibility for a rapid real-time sequencing, which enables a simultaneous data analysis. Here, we describe a targeted RNA-based method for HLA typing using ONT sequencing and SeqNext-HLA SeqPilot software (JSI Medical Systems GmbH). Twelve classical HLA genes were enriched from cDNA of 50 individuals, barcoded, pooled, and sequenced in 10 MinION R9.4 SpotON flow cell runs producing over 30,000 reads per sample. Using barcoded 2D reads, SeqPilot assigned HLA alleles to two-field typing resolution or higher with the average read depth of 1750x. Sequence analysis resulted in 99-100% accuracy at low-resolution level (one-field) and in 74-100% accuracy at high-resolution level (two-field) with the expected alleles. There are still some limitations with ONT RNA sequencing, such as noisy reads, homopolymer errors, and the lack of robust algorithms, which interfere with confident allele assignment. These issues need to be inspected carefully in the future to improve the allele call rates. Nevertheless, here we show that sequencing of multiplexed cDNA amplicon libraries on ONT MinION can produce accurate high-resolution typing results of 12 classical HLA loci. For HLA research, ONT RNA sequencing is a promising method due to its capability to sequence full-length HLA transcripts. In addition to HLA genotyping, the technique could also be applied for simultaneous expression analysis.
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Affiliation(s)
- Tiira Johansson
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Dawit A Yohannes
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Päivi Saavalainen
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
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Liu C, Yang X, Duffy BF, Hoisington-Lopez J, Crosby M, Porche-Sorbet R, Saito K, Berry R, Swamidass V, Mitra RD. High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells. Hum Immunol 2021; 82:288-295. [PMID: 33612390 DOI: 10.1016/j.humimm.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/12/2023]
Abstract
Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Xiao Yang
- GeneGenieDx, 160 E Tasman Dr Ste 109, San Jose, CA, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jessica Hoisington-Lopez
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - MariaLynn Crosby
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhonda Porche-Sorbet
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Rick Berry
- PlatformSTL, 4340 Duncan Ave. St. Louis, MO, USA
| | | | - Robi D Mitra
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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7
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Jan A, Saeed M, Afridi MH, Khuda F, Shabbir M, Khan H, Ali S, Hassan M, Akbar R. Association of HLA-B Gene Polymorphisms with Type 2 Diabetes in Pashtun Ethnic Population of Khyber Pakhtunkhwa, Pakistan. J Diabetes Res 2021; 2021:6669731. [PMID: 34258292 PMCID: PMC8254654 DOI: 10.1155/2021/6669731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/20/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022] Open
Abstract
Human leukocyte antigen (HLA) system is the most polymorphic and gene dense region of human DNA that has shown many disease associations. It has been further divided into HLA classes I, II, and III. Polymorphism in HLA class II genes has been reported to play an important role in the pathogenesis of type 1 diabetes (T1D). It also showed association with T2D in different ethnic populations. However, a little is known about the relationship of HLA class I gene polymorphism and T2D. This study has evaluated the association of HLA-B (class I gene) variants with T2D in Pashtun ethnic population of Khyber Pakhtunkhwa. In the first phase of the study, whole exome sequencing (WES) of 2 pooled DNA samples was carried out, and DNA pools used were constructed from 100 diabetic cases and 100 control subjects. WES results identified a total of n = 17 SNPs in HLA-B gene. In the next phase, first 5 out of n = 17 reported SNPs were genotyped using MassARRAY® system in order to validate WES results and to confirm association of selected SNPs with T2D. Minor allele frequencies (MAFs) and selected SNPs×T2D association were determined using chi-square test and logistic regression analysis. The frequency of minor C allele was significantly higher in the T2D group as compared to control group (45.0% vs. 13.0%) (p = 0.006) for rs2308655 in HLA-B gene. No significant difference in MAF distribution between cases and controls was observed for rs1051488, rs1131500, rs1050341, and rs1131285 (p > 0.05). Binary logistic regression analyses showed significant results for SNP rs2308655 (OR = 2.233, CI (95%) = 1.223-4.077, and p = 0.009), while no considerable association was observed for the other 4 SNPs. However, when adjusted for these variants, the association of rs2308655 further strengthened significantly (adjusted OR = 7.485, CI (95%) = 2.353-23.812, and p = 0.001), except for rs1131500, which has no additive effect. In conclusion, the finding of this study suggests rs2308655 variant in HLA-B gene as risk variant for T2D susceptibility in Pashtun population.
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Affiliation(s)
- Asif Jan
- Department of Pharmacy, University of Peshawar, Pakistan
| | - Muhammad Saeed
- Department of Pharmacy, University of Peshawar, Pakistan
| | | | - Fazli Khuda
- Department of Pharmacy, University of Peshawar, Pakistan
| | - Muhammad Shabbir
- Internal Medicine, College of Medicine, Shaqra University, Saudi Arabia
| | - Hamayun Khan
- Department of Pharmacy, University of Peshawar, Pakistan
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | | | - Rani Akbar
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
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Liu C. A long road/read to rapid high-resolution HLA typing: The nanopore perspective. Hum Immunol 2020; 82:488-495. [PMID: 32386782 DOI: 10.1016/j.humimm.2020.04.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches. Current methodologies still face challenges in resolving cis-trans ambiguity involving distant variant positions, and the turnaround time is affected by testing volume and batching. Nanopore sequencing may become a promising addition to the existing options for HLA typing. The technology delivered by the MinION sequencer of Oxford Nanopore Technologies (ONT) can record the ionic current changes during the translocation of DNA/RNA strands through transmembrane pores and translate the signals to sequence reads. It features simple and flexible library preparations, long sequencing reads, portable and affordable sequencing devices, and rapid, real-time sequencing. However, the error rate of the sequencing reads is high and remains a hurdle for its broad application. This review article will provide a brief overview of this technology and then focus on the opportunities and challenges of using nanopore sequencing for high-resolution HLA typing and immunogenetics research.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63105, United States.
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9
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Russell LE, Schwarz UI. Variant discovery using next-generation sequencing and its future role in pharmacogenetics. Pharmacogenomics 2020; 21:471-486. [DOI: 10.2217/pgs-2019-0190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) has enabled the discovery of a multitude of novel and mostly rare variants in pharmacogenes that may alter a patient’s therapeutic response to drugs. In addition to single nucleotide variants, structural variation affecting the number of copies of whole genes or parts of genes can be detected. While current guidelines concerning clinical implementation mostly act upon well-documented, common single nucleotide variants to guide dosing or drug selection, in silico and large-scale functional assessment of rare variant effects on protein function are at the forefront of pharmacogenetic research to facilitate their clinical integration. Here, we discuss the role of NGS in variant discovery, paving the way for more comprehensive genotype-guided pharmacotherapy that can translate to improved clinical care.
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Affiliation(s)
- Laura E Russell
- Department of Physiology & Pharmacology, Western University, Medical Sciences Building, London, ON, N6A 5C1, Canada
| | - Ute I Schwarz
- Department of Physiology & Pharmacology, Western University, Medical Sciences Building, London, ON, N6A 5C1, Canada
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre – University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada
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10
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Liu C, Duffy BF, Weimer ET, Montgomery MC, Jennemann JE, Hill R, Phelan D, Lay L, Parikh BA. Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing. PLoS One 2020; 15:e0232050. [PMID: 32324777 PMCID: PMC7179861 DOI: 10.1371/journal.pone.0232050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplant-relevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. METHODS Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. RESULTS The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. CONCLUSION The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian F. Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Eric T. Weimer
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Jo-Ellen Jennemann
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Rachel Hill
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Donna Phelan
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Lindsay Lay
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Bijal A. Parikh
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
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11
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Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results. J Mol Diagn 2020; 22:101-110. [DOI: 10.1016/j.jmoldx.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 01/07/2023] Open
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12
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Cargou M, Ralazamahaleo M, Blouin L, Top I, Elsermans V, Andreani M, Guidicelli G, Visentin J. Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform. HLA 2019; 95:30-39. [DOI: 10.1111/tan.13708] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Laura Blouin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Isabelle Top
- CHRU de Lille, Institut d'Immunologie‐HLA Lille France
| | | | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti IRCCS Ospedale Pediatrico Bambino Gesù Roma Italy
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
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13
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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.
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14
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15
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Ring N, Abrahams JS, Jain M, Olsen H, Preston A, Bagby S. Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. Microb Genom 2018; 4:e000234. [PMID: 30461375 PMCID: PMC6321869 DOI: 10.1099/mgen.0.000234] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/12/2018] [Indexed: 11/30/2022] Open
Abstract
The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run. We then trialled combinations of the many nanopore user community-built long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis genome sequences. This pipeline produced closed genome sequences for four strains, allowing visualization of inter-strain genomic rearrangement. Read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (almost 200 kbp), which was not resolved by our pipeline; further investigation also revealed that a second strain that was seemingly resolved by our pipeline may contain an even longer duplication, albeit in a small subset of cells. We have therefore demonstrated the ability to resolve the structure of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterization, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.
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Affiliation(s)
- Natalie Ring
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jonathan S. Abrahams
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Miten Jain
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hugh Olsen
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Andrew Preston
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
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