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  1. AU="Gangavarapu, Sridevi"
  2. AU="Hussein, Hazem Abdelwaheb"
  3. AU=Cai Yixin AU=Cai Yixin
  4. AU="Hüls, Anke"
  5. AU="Poondru, Srinivasu"
  6. AU="Coca, Daniel"
  7. AU="Lebeau, Paul"
  8. AU="Dehghani, Sedigheh"
  9. AU="Ishibashi, Kenji"
  10. AU="Xu, Yanhua"
  11. AU="Matera, Katarzyna"
  12. AU="Ait-Ouarab, Slimane"
  13. AU="Nicola, Coppede"
  14. AU="Dewitt, John M"
  15. AU="Sorin M. Dudea"
  16. AU="Tanusha D. Ramdin"
  17. AU="Hao, Zehui"
  18. AU="Chauhan, Aman"

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  1. Artikel ; Online: High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility.

    Osoegawa, Kazutoyo / Creary, Lisa E / Montero-Martín, Gonzalo / Mallempati, Kalyan C / Gangavarapu, Sridevi / Caillier, Stacy J / Santaniello, Adam / Isobe, Noriko / Hollenbach, Jill A / Hauser, Stephen L / Oksenberg, Jorge R / Fernández-Viňa, Marcelo A

    Frontiers in immunology

    2021  Band 12, Seite(n) 644838

    Abstract: Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing ( ... ...

    Abstract Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including
    Mesh-Begriff(e) Adolescent ; Adult ; Alleles ; Case-Control Studies ; Child ; Female ; Genetic Predisposition to Disease ; Genotyping Techniques ; HLA-DP Antigens/genetics ; HLA-DP Antigens/immunology ; Haplotypes ; Humans ; Male ; Middle Aged ; Multiple Sclerosis/genetics ; Multiple Sclerosis/immunology
    Chemische Substanzen HLA-DP Antigens
    Sprache Englisch
    Erscheinungsdatum 2021-05-25
    Erscheinungsland Switzerland
    Dokumenttyp Clinical Trial ; Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2021.644838
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Deconstruction of HLA-DRB1*04:01:01 and HLA-DRB1*15:01:01 class II haplotypes using next-generation sequencing in European-Americans with multiple sclerosis.

    Creary, Lisa E / Mallempati, Kalyan C / Gangavarapu, Sridevi / Caillier, Stacy J / Oksenberg, Jorge R / Fernández-Viňa, Marcelo A

    Multiple sclerosis (Houndmills, Basingstoke, England)

    2018  Band 25, Heft 6, Seite(n) 772–782

    Abstract: Background: The association between HLA-DRB1*15:01 with multiple sclerosis (MS) susceptibility is well established, but the contribution of the tightly associated HLA-DRB5*01:01 allele has not yet been completely ascertained. Similarly, the effects of ... ...

    Abstract Background: The association between HLA-DRB1*15:01 with multiple sclerosis (MS) susceptibility is well established, but the contribution of the tightly associated HLA-DRB5*01:01 allele has not yet been completely ascertained. Similarly, the effects of HLA-DRB1*04:01 alleles and haplotypes, defined at the full-gene resolution level with MS risk remains to be elucidated.
    Objectives: To characterize the molecular architecture of class II HLA-DR15 and HLA-DR4 haplotypes associated with MS.
    Methods: Next-generation sequencing was used to determine HLA-DQB1, HLA-DQA1, and HLA-DRB1/4/5 alleles in 1403 unrelated European-American patients and 1425 healthy unrelated controls. Effect sizes of HLA alleles and haplotypes on MS risk were measured by odds ratio (OR) with 95% confidence intervals.
    Results: HLA-DRB1*15:01:01:01SG (OR = 3.20, p < 2.2E-16), HLA-DRB5*01:01:01 (OR = 2.96, p < 2.2E-16), and HLA-DRB5*01:01:01v1_STR1 (OR = 8.18, p = 4.3E-05) alleles all occurred at significantly higher frequencies in MS patients compared to controls. The most significant predis-posing haplotypes were HLA-DQB1*06:02:01~ HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01 and HLA-DQB1*06:02:01~HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01v1_STR1 (OR = 3.19, p < 2.2E-16; OR = 9.30, p = 9.7E-05, respectively). Analyses of the HLA-DRB1*04 cohort in the absence of HLA-DRB1*15:01 haplotypes revealed that the HLA-DQB1*03:01:01:01~HLA-DQA1*03:03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was protective (OR = 0.64, p = 0.028), whereas the HLA-DQB1*03:02:01~HLA-DQA1*03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was associated with MS susceptibility (OR = 1.66, p = 4.9E-03).
    Conclusion: HLA-DR15 haplotypes, including genomic variants of HLA-DRB5, and HLA-DR4 haplotypes affect MS risk.
    Mesh-Begriff(e) Adult ; European Continental Ancestry Group/genetics ; Female ; HLA-DRB1 Chains/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Multiple Sclerosis/genetics ; Sequence Analysis, DNA
    Chemische Substanzen HLA-DRB1 Chains ; HLA-DRB1*04:01 antigen ; HLA-DRB1*15:01 antigen
    Sprache Englisch
    Erscheinungsdatum 2018-04-23
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1290669-4
    ISSN 1477-0970 ; 1352-4585
    ISSN (online) 1477-0970
    ISSN 1352-4585
    DOI 10.1177/1352458518770019
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations.

    Creary, Lisa E / Gangavarapu, Sridevi / Caillier, Stacy J / Cavalcante, Paola / Frangiamore, Rita / Lie, Benedicte A / Bengtsson, Mats / Harbo, Hanne Flinstad / Brauner, Susanna / Hollenbach, Jill A / Oksenberg, Jorge R / Bernasconi, Pia / Maniaol, Angelina Hatlø / Hammarström, Lennart / Mantegazza, Renato / Fernández-Viña, Marcelo A

    Frontiers in immunology

    2021  Band 12, Seite(n) 667336

    Abstract: Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad ...

    Abstract Genetic susceptibility to myasthenia gravis (MG) associates with specific HLA alleles and haplotypes at the class I and II regions in various populations. Previous studies have only examined alleles at a limited number of HLA loci that defined only broad serotypes or alleles defined at the protein sequence level. Consequently, genetic variants in noncoding and untranslated HLA gene segments have not been fully explored but could also be important determinants for MG. To gain further insight into the role of HLA in MG, we applied next-generation sequencing to analyze sequence variation at eleven HLA genes in early-onset (EO) and late-onset (LO) non-thymomatous MG patients positive for the acetylcholine receptor (AChR) antibodies and ethnically matched controls from Italy, Norway, and Sweden. For all three populations, alleles and haplotype blocks present on the ancestral haplotype AH8.1 were associated with risk in AChR-EOMG patients.
    Mesh-Begriff(e) Adult ; Age of Onset ; Alleles ; Female ; Genetic Predisposition to Disease ; HLA-B Antigens/genetics ; HLA-DR Antigens/genetics ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Italy ; Male ; Middle Aged ; Myasthenia Gravis/epidemiology ; Myasthenia Gravis/genetics ; Myasthenia Gravis/immunology ; Norway ; Sweden
    Chemische Substanzen HLA-B Antigens ; HLA-DR Antigens
    Sprache Englisch
    Erscheinungsdatum 2021-06-07
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2021.667336
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population.

    Creary, Lisa E / Gangavarapu, Sridevi / Mallempati, Kalyan C / Montero-Martín, Gonzalo / Caillier, Stacy J / Santaniello, Adam / Hollenbach, Jill A / Oksenberg, Jorge R / Fernández-Viña, Marcelo A

    Human immunology

    2019  Band 80, Heft 10, Seite(n) 807–822

    Abstract: The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the ... ...

    Abstract The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
    Mesh-Begriff(e) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Alleles ; Cohort Studies ; Europe/ethnology ; European Continental Ancestry Group/ethnology ; European Continental Ancestry Group/genetics ; Female ; Gene Frequency/genetics ; Genetic Loci/genetics ; Genetics, Population/methods ; HLA Antigens/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Histocompatibility Testing ; Humans ; Linkage Disequilibrium/genetics ; Male ; Middle Aged ; United States ; Young Adult
    Chemische Substanzen HLA Antigens
    Sprache Englisch
    Erscheinungsdatum 2019-07-22
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 801524-7
    ISSN 1879-1166 ; 0198-8859
    ISSN (online) 1879-1166
    ISSN 0198-8859
    DOI 10.1016/j.humimm.2019.07.275
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: HLA alleles and haplotypes observed in 263 US families.

    Osoegawa, Kazutoyo / Mallempati, Kalyan C / Gangavarapu, Sridevi / Oki, Arisa / Gendzekhadze, Ketevan / Marino, Susana R / Brown, Nicholas K / Bettinotti, Maria P / Weimer, Eric T / Montero-Martín, Gonzalo / Creary, Lisa E / Vayntrub, Tamara A / Chang, Chia-Jung / Askar, Medhat / Mack, Steven J / Fernández-Viña, Marcelo A

    Human immunology

    2019  Band 80, Heft 9, Seite(n) 644–660

    Abstract: The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical ... ...

    Abstract The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical immunogenetics laboratories, primarily as part of the evaluation of related donor candidates for hematopoietic stem cell and solid organ transplantation. The parents in these families belonged to five broad groups - African (72 parents), Asian (115), European (210), Hispanic (118) and "Other" (11). High-resolution HLA genotypes were generated for each subject using next-generation sequencing (NGS) HLA typing systems. We identified the HLA haplotypes in each family using HaplObserve, software that builds haplotypes in families by reviewing HLA allele segregation from parents to children. We calculated haplotype frequencies within each broad group, by treating the parents in each family as unrelated individuals. We also calculated standard measures of global linkage disequilibrium (LD) and conditional asymmetric LD for each ethnic group, and used untruncated and two-field allele names to investigate LD patterns. Finally we demonstrated the utility of consensus DNA sequences in identifying novel variants, confirming them using HLA allele segregation at the DNA sequence level.
    Mesh-Begriff(e) Alleles ; Base Sequence/genetics ; Child ; Ethnic Groups/genetics ; Exons/genetics ; Gene Frequency/genetics ; HLA Antigens/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Histocompatibility Testing ; Humans ; Introns/genetics ; Linkage Disequilibrium/genetics ; Nuclear Family ; Pedigree ; Software ; United States ; Untranslated Regions/genetics
    Chemische Substanzen HLA Antigens ; Untranslated Regions
    Sprache Englisch
    Erscheinungsdatum 2019-06-27
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 801524-7
    ISSN 1879-1166 ; 0198-8859
    ISSN (online) 1879-1166
    ISSN 0198-8859
    DOI 10.1016/j.humimm.2019.05.018
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  6. Artikel ; Online: High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing.

    Montero-Martín, Gonzalo / Mallempati, Kalyan C / Gangavarapu, Sridevi / Sánchez-Gordo, Francisco / Herrero-Mata, Maria J / Balas, Antonio / Vicario, Jose L / Sánchez-García, Florentino / González-Escribano, Maria F / Muro, Manuel / Moya-Quiles, Maria R / González-Fernández, Rafael / Ocejo-Vinyals, Javier G / Marín, Luis / Creary, Lisa E / Osoegawa, Kazutoyo / Vayntrub, Tamara / Caro-Oleas, Jose L / Vilches, Carlos /
    Planelles, Dolores / Fernández-Viña, Marcelo A

    Human immunology

    2019  Band 80, Heft 7, Seite(n) 429–436

    Abstract: Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing ...

    Abstract Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.
    Mesh-Begriff(e) Cohort Studies ; Exons/genetics ; Gene Frequency/genetics ; Genetic Loci ; Genetic Variation ; Genotype ; HLA Antigens/genetics ; Haplotypes/genetics ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class II/genetics ; Histocompatibility Testing ; Homozygote ; Humans ; Linkage Disequilibrium/genetics ; Sequence Analysis, DNA ; Spain
    Chemische Substanzen HLA Antigens ; Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II
    Sprache Englisch
    Erscheinungsdatum 2019-02-11
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 801524-7
    ISSN 1879-1166 ; 0198-8859
    ISSN (online) 1879-1166
    ISSN 0198-8859
    DOI 10.1016/j.humimm.2019.02.005
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop.

    Creary, Lisa E / Guerra, Sandra G / Chong, Winnie / Brown, Colin J / Turner, Thomas R / Robinson, James / Bultitude, Will P / Mayor, Neema P / Marsh, Steven G E / Saito, Katsuyuki / Lam, Kevin / Duke, Jamie L / Mosbruger, Timothy L / Ferriola, Deborah / Monos, Dimitrios / Willis, Amanda / Askar, Medhat / Fischer, Gottfried / Saw, Chee Loong /
    Ragoussis, Jiannis / Petrek, Martin / Serra-Pagés, Carles / Juan, Manel / Stavropoulos-Giokas, Catherine / Dinou, Amalia / Ameen, Reem / Al Shemmari, Salem / Spierings, Eric / Gendzekhadze, Ketevan / Morris, Gerald P / Zhang, Qiuheng / Kashi, Zahra / Hsu, Susan / Gangavarapu, Sridevi / Mallempati, Kalyan C / Yamamoto, Fumiko / Osoegawa, Kazutoyo / Vayntrub, Tamara / Chang, Chia-Jung / Hansen, John A / Fernández-Viňa, Marcelo A

    Human immunology

    2019  Band 80, Heft 7, Seite(n) 449–460

    Abstract: Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined ... ...

    Abstract Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
    Mesh-Begriff(e) Alleles ; B-Lymphocytes/virology ; Cell Line, Transformed ; Cell Transformation, Viral ; Data Accuracy ; Exons/genetics ; Genetic Loci ; Genetic Variation ; Genotype ; HLA Antigens/genetics ; Haplotypes/genetics ; Herpesvirus 4, Human/immunology ; High-Throughput Nucleotide Sequencing/methods ; Histocompatibility ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class II/genetics ; Histocompatibility Testing/methods ; Homozygote ; Humans ; Sequence Analysis, DNA/methods ; Single-Blind Method
    Chemische Substanzen HLA Antigens ; Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II
    Sprache Englisch
    Erscheinungsdatum 2019-03-04
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 801524-7
    ISSN 1879-1166 ; 0198-8859
    ISSN (online) 1879-1166
    ISSN 0198-8859
    DOI 10.1016/j.humimm.2019.03.001
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  8. Artikel ; Online: Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop.

    Osoegawa, Kazutoyo / Vayntrub, Tamara A / Wenda, Sabine / De Santis, Dianne / Barsakis, Konstantinos / Ivanova, Milena / Hsu, Susan / Barone, Jonathan / Holdsworth, Rhonda / Diviney, Mary / Askar, Medhat / Willis, Amanda / Railton, Dawn / Laflin, Sophie / Gendzekhadze, Ketevan / Oki, Arisa / Sacchi, Nicoletta / Mazzocco, Michela / Andreani, Marco /
    Ameen, Reem / Stavropoulos-Giokas, Catherine / Dinou, Amalia / Torres, Margareth / Dos Santos Francisco, Rodrigo / Serra-Pages, Carles / Goodridge, Damian / Balladares, Sandra / Bettinotti, Maria P / Iglehart, Brian / Kashi, Zahra / Martin, Russell / Saw, Chee Loong / Ragoussis, Jiannis / Downing, Jonathan / Navarrete, Cristina / Chong, Winnie / Saito, Katsuyuki / Petrek, Martin / Tokic, Stana / Padros, Karin / Beatriz Rodriguez, Ma / Zakharova, Viktoria / Shragina, Olga / Marino, Susana R / Brown, Nicholas K / Shiina, Takashi / Suzuki, Shingo / Spierings, Eric / Zhang, Qiuheng / Yin, Yuxin / Morris, Gerald P / Hernandez, Ana / Ruiz, Phillip / Khor, Seik-Soon / Tokunaga, Katsushi / Geretz, Aviva / Thomas, Rasmi / Yamamoto, Fumiko / Mallempati, Kalyan C / Gangavarapu, Sridevi / Kanga, Uma / Tyagi, Shweta / Marsh, Steven G E / Bultitude, Will P / Liu, Xiangjun / Cao, Dajiang / Penning, Maarten / Hurley, Carolyn K / Cesbron, Anne / Mueller, Claudia / Mytilineos, Joannis / Weimer, Eric T / Bengtsson, Mats / Fischer, Gottfried / Hansen, John A / Chang, Chia-Jung / Mack, Steven J / Creary, Lisa E / Fernandez-Viña, Marcelo A

    Human immunology

    2019  Band 80, Heft 4, Seite(n) 228–236

    Abstract: The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and ... ...

    Abstract The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
    Mesh-Begriff(e) Alleles ; Consensus Development Conferences as Topic ; Genotype ; HLA Antigens/genetics ; High-Throughput Nucleotide Sequencing/methods ; Histocompatibility Testing/methods ; Humans ; Immunogenetics ; International Cooperation ; Pilot Projects ; Quality Control ; Software
    Chemische Substanzen HLA Antigens
    Sprache Englisch
    Erscheinungsdatum 2019-02-06
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review
    ZDB-ID 801524-7
    ISSN 1879-1166 ; 0198-8859
    ISSN (online) 1879-1166
    ISSN 0198-8859
    DOI 10.1016/j.humimm.2019.01.009
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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