• Je něco špatně v tomto záznamu ?

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

LE. Creary, SG. Guerra, W. Chong, CJ. Brown, TR. Turner, J. Robinson, WP. Bultitude, NP. Mayor, SGE. Marsh, K. Saito, K. Lam, JL. Duke, TL. Mosbruger, D. Ferriola, D. Monos, A. Willis, M. Askar, G. Fischer, CL. Saw, J. Ragoussis, M. Petrek, C....

. 2019 ; 80 (7) : 449-460. [pub] 20190304

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc19044951

Grantová podpora
U19 NS095774 NINDS NIH HHS - United States

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.

Anthony Nolan Research Institute Royal Free Hospital London UK

Biomedical Research Foundation Academy of Athens Hellenic Cord Blood Bank Athens Greece

Department for Blood Group Serology and Transfusion Medicine Medical University of Vienna Vienna Austria

Department of Histocompatibility and Immunogenetics NHS Blood and Transplant London UK

Department of Human Genetics McGill University and McGill University and Genome Quèbec Innovation Centre Montreal Canada

Department of Pathological Physiology and Immunogenomics IMTM Faculty of Medicine and Dentistry Palacky University Olomouc Czech Republic

Department of Pathology and Lab Medicine University of Pennsylvania Philadelphia PA USA

Department of Pathology and Laboratory Medicine Baylor University Medical Center Dallas USA

Department of Pathology and Laboratory Medicine UCLA Immunogenetics Center Los Angeles CA USA

Department of Pathology Stanford University School of Medicine Palo Alto CA USA

Department of Pathology University of California San Diego La Jolla CA USA

Fred Hutchinson Cancer Research Center Seattle WA USA

Health Sciences Center Kuwait University Kuwait

Histocompatibility and Immunogenetics Service Development Laboratory NHS Blood and Transplant London UK

Histocompatibility Immunogenetics and Disease Profiling Laboratory Stanford Blood Center Palo Alto CA USA

HLA Department Kashi Clinical Laboratories Inc Portland OR USA

HLA Laboratory American Red Cross Philadelphia PA USA

HLA Laboratory City of Hope Duarte CA USA

HLA Laboratory Division of Haematology McGill University Health Centre Montreal Canada

Immunogenetics Laboratory The Children's Hospital of Philadelphia Philadelphia PA USA

Immunology Department Hospital Clinic de Barcelona University of Barcelona IDIBAPS Barcelona Spain

Laboratory of Translational Immunology UMC Utrecht Utrecht Netherlands

Molecular Biology Research Department One Lambda Thermo Fisher Scientific Canoga Park CA USA

Stanford Genome Technology Center Palo Alto CA USA

UCL Cancer Institute Royal Free Campus London UK

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc19044951
003      
CZ-PrNML
005      
20200114085659.0
007      
ta
008      
200109s2019 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1016/j.humimm.2019.03.001 $2 doi
035    __
$a (PubMed)30844424
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Creary, Lisa E $u Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA. Electronic address: lcreary@stanford.edu.
245    10
$a Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop / $c LE. Creary, SG. Guerra, W. Chong, CJ. Brown, TR. Turner, J. Robinson, WP. Bultitude, NP. Mayor, SGE. Marsh, K. Saito, K. Lam, JL. Duke, TL. Mosbruger, D. Ferriola, D. Monos, A. Willis, M. Askar, G. Fischer, CL. Saw, J. Ragoussis, M. Petrek, C. Serra-Pagés, M. Juan, C. Stavropoulos-Giokas, A. Dinou, R. Ameen, S. Al Shemmari, E. Spierings, K. Gendzekhadze, GP. Morris, Q. Zhang, Z. Kashi, S. Hsu, S. Gangavarapu, KC. Mallempati, F. Yamamoto, K. Osoegawa, T. Vayntrub, CJ. Chang, JA. Hansen, MA. Fernández-Viňa,
520    9_
$a 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.
650    _2
$a alely $7 D000483
650    _2
$a B-lymfocyty $x virologie $7 D001402
650    _2
$a transformované buněčné linie $7 D002461
650    _2
$a virová transformace buněk $7 D002472
650    _2
$a správnost dat $7 D000068598
650    _2
$a exony $x genetika $7 D005091
650    _2
$a genetické lokusy $7 D056426
650    _2
$a genetická variace $7 D014644
650    _2
$a genotyp $7 D005838
650    _2
$a HLA antigeny $x genetika $7 D006680
650    _2
$a haplotypy $x genetika $7 D006239
650    _2
$a virus Epsteinův-Barrové $x imunologie $7 D004854
650    _2
$a vysoce účinné nukleotidové sekvenování $x metody $7 D059014
650    _2
$a histokompatibilita $7 D006648
650    _2
$a histokompatibilita - antigeny třídy I $x genetika $7 D015395
650    _2
$a histokompatibilita - antigeny třídy II $x genetika $7 D000949
650    _2
$a testování histokompatibility $x metody $7 D006650
650    _2
$a homozygot $7 D006720
650    _2
$a lidé $7 D006801
650    _2
$a sekvenční analýza DNA $x metody $7 D017422
650    _2
$a jednoduchá slepá metoda $7 D016037
655    _2
$a časopisecké články $7 D016428
700    1_
$a Guerra, Sandra G $u Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK.
700    1_
$a Chong, Winnie $u Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK.
700    1_
$a Brown, Colin J $u Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK.
700    1_
$a Turner, Thomas R $u Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
700    1_
$a Robinson, James $u Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
700    1_
$a Bultitude, Will P $u Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
700    1_
$a Mayor, Neema P $u Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
700    1_
$a Marsh, Steven G E $u Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
700    1_
$a Saito, Katsuyuki $u Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
700    1_
$a Lam, Kevin $u Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
700    1_
$a Duke, Jamie L $u Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
700    1_
$a Mosbruger, Timothy L $u Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
700    1_
$a Ferriola, Deborah $u Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
700    1_
$a Monos, Dimitrios $u Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA.
700    1_
$a Willis, Amanda $u Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA.
700    1_
$a Askar, Medhat $u Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA.
700    1_
$a Fischer, Gottfried $u Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
700    1_
$a Saw, Chee Loong $u HLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada.
700    1_
$a Ragoussis, Jiannis $u Department of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada.
700    1_
$a Petrek, Martin $u Department of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
700    1_
$a Serra-Pagés, Carles $u Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain.
700    1_
$a Juan, Manel $u Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain.
700    1_
$a Stavropoulos-Giokas, Catherine $u Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece.
700    1_
$a Dinou, Amalia $u Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece.
700    1_
$a Ameen, Reem $u Health Sciences Center, Kuwait University, Kuwait.
700    1_
$a Al Shemmari, Salem $u Health Sciences Center, Kuwait University, Kuwait.
700    1_
$a Spierings, Eric $u Laboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands.
700    1_
$a Gendzekhadze, Ketevan $u HLA Laboratory, City of Hope, Duarte, CA, USA.
700    1_
$a Morris, Gerald P $u Department of Pathology, University of California San Diego, La Jolla, CA, USA.
700    1_
$a Zhang, Qiuheng $u Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA.
700    1_
$a Kashi, Zahra $u HLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA.
700    1_
$a Hsu, Susan $u HLA Laboratory, American Red Cross, Philadelphia, PA, USA.
700    1_
$a Gangavarapu, Sridevi $u Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
700    1_
$a Mallempati, Kalyan C $u Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
700    1_
$a Yamamoto, Fumiko $u Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
700    1_
$a Osoegawa, Kazutoyo $u Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
700    1_
$a Vayntrub, Tamara $u Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
700    1_
$a Chang, Chia-Jung $u Stanford Genome Technology Center, Palo Alto, CA, USA.
700    1_
$a Hansen, John A $u Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
700    1_
$a Fernández-Viňa, Marcelo A $u Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
773    0_
$w MED00002076 $t Human immunology $x 1879-1166 $g Roč. 80, č. 7 (2019), s. 449-460
856    41
$u https://pubmed.ncbi.nlm.nih.gov/30844424 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20200109 $b ABA008
991    __
$a 20200114090032 $b ABA008
999    __
$a ok $b bmc $g 1483220 $s 1083624
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2019 $b 80 $c 7 $d 449-460 $e 20190304 $i 1879-1166 $m Human immunology $n Hum Immunol $x MED00002076
GRA    __
$a U19 NS095774 $p NINDS NIH HHS $2 United States
LZP    __
$a Pubmed-20200109

Najít záznam

Citační ukazatele

Možnosti archivace