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

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

Research output: Contribution to journalReview article

3 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)763-772
Number of pages10
JournalHuman Immunology
Volume79
Issue number11
DOIs
Publication statusPublished - Nov 2018
Externally publishedYes

Cite this

Voorter, C. E. M., Matern, B., Thuong Hien Tran, Fink, A., Vidan-Jeras, B., Montanic, S., ... Tilanus, M. G. J. (2018). Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Human Immunology, 79(11), 763-772. https://doi.org/10.1016/j.humimm.2018.08.004
Voorter, Christina E. M. ; Matern, Ben ; Thuong Hien Tran ; Fink, Annette ; Vidan-Jeras, Blanka ; Montanic, Sendi ; Fischer, Gottfried ; Fae, Ingrid ; de Santis, Dianne ; Whidborne, Rebecca ; Andreani, Marco ; Testi, Manuela ; Groeneweg, Mathijs ; Tilanus, Marcel G. J. / Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). In: Human Immunology. 2018 ; Vol. 79, No. 11. pp. 763-772.
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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.",
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Voorter, CEM, Matern, B, Thuong Hien Tran, Fink, A, Vidan-Jeras, B, Montanic, S, Fischer, G, Fae, I, de Santis, D, Whidborne, R, Andreani, M, Testi, M, Groeneweg, M & Tilanus, MGJ 2018, 'Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT)' Human Immunology, vol. 79, no. 11, pp. 763-772. https://doi.org/10.1016/j.humimm.2018.08.004

Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). / Voorter, Christina E. M.; Matern, Ben; Thuong Hien Tran; Fink, Annette; Vidan-Jeras, Blanka; Montanic, Sendi; Fischer, Gottfried; Fae, Ingrid; de Santis, Dianne; Whidborne, Rebecca; Andreani, Marco; Testi, Manuela; Groeneweg, Mathijs; Tilanus, Marcel G. J.

In: Human Immunology, Vol. 79, No. 11, 11.2018, p. 763-772.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT)

AU - Voorter, Christina E. M.

AU - Matern, Ben

AU - Thuong Hien Tran, null

AU - Fink, Annette

AU - Vidan-Jeras, Blanka

AU - Montanic, Sendi

AU - Fischer, Gottfried

AU - Fae, Ingrid

AU - de Santis, Dianne

AU - Whidborne, Rebecca

AU - Andreani, Marco

AU - Testi, Manuela

AU - Groeneweg, Mathijs

AU - Tilanus, Marcel G. J.

PY - 2018/11

Y1 - 2018/11

N2 - 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.

AB - 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.

KW - Full length sequences

KW - HLA alleles

KW - Hemizygous

KW - Allele-specific

KW - Sanger Sequence Based Typing

KW - DNA

KW - ANTIGEN

U2 - 10.1016/j.humimm.2018.08.004

DO - 10.1016/j.humimm.2018.08.004

M3 - Review article

VL - 79

SP - 763

EP - 772

JO - Human Immunology

JF - Human Immunology

SN - 0198-8859

IS - 11

ER -

Voorter CEM, Matern B, Thuong Hien Tran, Fink A, Vidan-Jeras B, Montanic S et al. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Human Immunology. 2018 Nov;79(11):763-772. https://doi.org/10.1016/j.humimm.2018.08.004