Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT)

• Verfasst von: Voorter, Christina E. M. [VerfasserIn]
• Verfasst von: Tran, Thuong Hien [VerfasserIn]
• Verfasst von: Fink, Annette [VerfasserIn]
• Titel: Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT)
• Verf.angabe: Christina E.M. Voorter, Ben Matern, Thuong Hien Tran, Annette Fink, Blanka Vidan-Jeras, Sendi Montanic, Gottfried Fischer, Ingrid Fae, Dianne de Santis, Rebecca Whidborne, Marco Andreani, Manuela Testi, Mathijs Groeneweg, Marcel G.J. Tilanus
• E-Jahr: 2018
• Jahr: 11 August 2018
• Umfang: 10 S.
• Fussnoten: Gesehen am 09.04.2019
• Titel Quelle: Enthalten in: Human immunology
• Ort Quelle: Amsterdam [u.a.] : Elsevier Science, 1980
• Jahr Quelle: 2018
• Band/Heft Quelle: 79(2018), 11, Seite 763-772
• ISSN Quelle: 1879-1166
• DOI: doi:10.1016/j.humimm.2018.08.004
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: Allele-specific
• Sach-SW: Alleles
• Sach-SW: DNA, Complementary
• Sach-SW: Full length sequences
• Sach-SW: Genome, Human
• Sach-SW: Genomics
• Sach-SW: Genotype
• Sach-SW: Hemizygous
• Sach-SW: High-Throughput Nucleotide Sequencing
• Sach-SW: Histocompatibility Testing
• Sach-SW: HLA alleles
• Sach-SW: HLA Antigens
• Sach-SW: Humans
• Sach-SW: Introns
• Sach-SW: Sanger Sequence Based Typing
• Sach-SW: Sequence Analysis, DNA
• K10plus-PPN: 166300630X

Abstract

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.