A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity
To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and...
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| Veröffentlicht in: | Human immunology 2020-05, Vol.81 (5), p.202-205 |
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| container_title | Human immunology |
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| creator | Alizadeh, M. Picard, C. Frassati, C. Walencik, A. Gauthier, A. Cesbron Bennasar, F. Verite, F. Semana, G. |
| description | To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described. |
| doi_str_mv | 10.1016/j.humimm.2020.02.003 |
| format | Article |
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Cesbron ; Bennasar, F. ; Verite, F. ; Semana, G.</creator><creatorcontrib>Alizadeh, M. ; Picard, C. ; Frassati, C. ; Walencik, A. ; Gauthier, A. Cesbron ; Bennasar, F. ; Verite, F. ; Semana, G.</creatorcontrib><description>To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.</description><identifier>ISSN: 0198-8859</identifier><identifier>EISSN: 1879-1166</identifier><identifier>DOI: 10.1016/j.humimm.2020.02.003</identifier><identifier>PMID: 32122686</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Alleles ; Bone Marrow - immunology ; Gene Frequency ; Genes, MHC Class I ; Genes, MHC Class II ; Haplotype diversity ; Haplotypes ; High-Throughput Nucleotide Sequencing - methods ; Histocompatibility Antigens Class I - genetics ; Histocompatibility Antigens Class II - genetics ; Histocompatibility Testing - methods ; HLA Antigens - genetics ; HLA genotyping ; Humans ; Indicators and Reagents ; Life Sciences ; Linkage Disequilibrium ; NGS ; Non-classical HLA genes ; Polymerase Chain Reaction - methods ; Polymorphism, Genetic ; Software ; Tissue Donors</subject><ispartof>Human immunology, 2020-05, Vol.81 (5), p.202-205</ispartof><rights>2020 American Society for Histocompatibility and Immunogenetics</rights><rights>Copyright © 2020 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c396t-2eecd6941a71355814d34f90e5e4e96d7812bfff87b17f42559946a9a4b62e383</citedby><cites>FETCH-LOGICAL-c396t-2eecd6941a71355814d34f90e5e4e96d7812bfff87b17f42559946a9a4b62e383</cites><orcidid>0000-0002-3167-7773</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.humimm.2020.02.003$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32122686$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-02612836$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Alizadeh, M.</creatorcontrib><creatorcontrib>Picard, C.</creatorcontrib><creatorcontrib>Frassati, C.</creatorcontrib><creatorcontrib>Walencik, A.</creatorcontrib><creatorcontrib>Gauthier, A. Cesbron</creatorcontrib><creatorcontrib>Bennasar, F.</creatorcontrib><creatorcontrib>Verite, F.</creatorcontrib><creatorcontrib>Semana, G.</creatorcontrib><title>A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity</title><title>Human immunology</title><addtitle>Hum Immunol</addtitle><description>To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.</description><subject>Alleles</subject><subject>Bone Marrow - immunology</subject><subject>Gene Frequency</subject><subject>Genes, MHC Class I</subject><subject>Genes, MHC Class II</subject><subject>Haplotype diversity</subject><subject>Haplotypes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Histocompatibility Antigens Class I - genetics</subject><subject>Histocompatibility Antigens Class II - genetics</subject><subject>Histocompatibility Testing - methods</subject><subject>HLA Antigens - genetics</subject><subject>HLA genotyping</subject><subject>Humans</subject><subject>Indicators and Reagents</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>NGS</subject><subject>Non-classical HLA genes</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism, Genetic</subject><subject>Software</subject><subject>Tissue Donors</subject><issn>0198-8859</issn><issn>1879-1166</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUGP0zAQhSMEYsvCP0DIRzgk2I7jxBekarVskSo4AGfLicetqyQuttOqv4U_i9Msy43T6I2-N0-al2VvCS4IJvzjodhPgx2GgmKKC0wLjMtn2Yo0tcgJ4fx5tsJENHnTVOImexXCAWNc45q9zG5KSijlDV9lv9dohDMKEJEzyIPawRgDUqNOolcRNArOxLPygKaQlHEefX34jlo1q65XIdhO9VfH6Mb832azXaN4Odpxh8LenecJJ6th7OB6RaFdyovgr-ReHXuXcEDansAHGy-vsxdG9QHePM7b7Ofn-x93m3z77eHL3Xqbd6XgMacAneaCEVWTsqoawnTJjMBQAQPBdd0Q2hpjmroltWG0qoRgXAnFWk6hbMrb7MNyd696efR2UP4inbJys97KeYcpJ7Qp-Ykk9v3CHr37NUGIcrChg75XI7gpSFrWmAmKOU8oW9DOuxA8mKfbBMu5QnmQS4VyrjClyFRhsr17TJjaAfST6W9nCfi0AJB-crLgZejs_FVtPXRRamf_n_AH0EKvCg</recordid><startdate>202005</startdate><enddate>202005</enddate><creator>Alizadeh, M.</creator><creator>Picard, C.</creator><creator>Frassati, C.</creator><creator>Walencik, A.</creator><creator>Gauthier, A. Cesbron</creator><creator>Bennasar, F.</creator><creator>Verite, F.</creator><creator>Semana, G.</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0002-3167-7773</orcidid></search><sort><creationdate>202005</creationdate><title>A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity</title><author>Alizadeh, M. ; Picard, C. ; Frassati, C. ; Walencik, A. ; Gauthier, A. 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All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>32122686</pmid><doi>10.1016/j.humimm.2020.02.003</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0002-3167-7773</orcidid></addata></record> |
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| ispartof | Human immunology, 2020-05, Vol.81 (5), p.202-205 |
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| language | eng |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | Alleles Bone Marrow - immunology Gene Frequency Genes, MHC Class I Genes, MHC Class II Haplotype diversity Haplotypes High-Throughput Nucleotide Sequencing - methods Histocompatibility Antigens Class I - genetics Histocompatibility Antigens Class II - genetics Histocompatibility Testing - methods HLA Antigens - genetics HLA genotyping Humans Indicators and Reagents Life Sciences Linkage Disequilibrium NGS Non-classical HLA genes Polymerase Chain Reaction - methods Polymorphism, Genetic Software Tissue Donors |
| title | A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity |
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