Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT)
Autor: | Annette Fink, Dianne De Santis, Manuela Testi, Marcel G.J. Tilanus, Blanka Vidan-Jeras, Thuong Hien Tran, Gottfried Fischer, Mathijs Groeneweg, Ingrid Fae, Marco Andreani, Ben M. Matern, Christina E.M. Voorter, R. Whidborne, Sendi Montanic |
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Jazyk: | angličtina |
Rok vydání: | 2018 |
Předmět: |
0301 basic medicine
DNA Complementary Genotype Immunology ANTIGEN Peptide binding Human leukocyte antigen Biology 03 medical and health sciences symbols.namesake Polymorphism (computer science) HLA Antigens Immunology and Allergy Humans Typing Allele Gene Alleles Genetics Sanger sequencing Genome Human Histocompatibility Testing Intron High-Throughput Nucleotide Sequencing General Medicine Genomics Sequence Analysis DNA Sanger Sequence Based Typing DNA Full length sequences Introns HLA alleles 030104 developmental biology Allele-specific symbols Hemizygous |
Zdroj: | Human Immunology. 79(11):763-772 |
ISSN: | 0198-8859 |
DOI: | 10.1016/j.humimm.2018.08.004 |
Popis: | The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin. |
Databáze: | OpenAIRE |
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