Nomenclature for factors of the hla system, 2000

Nomenclature for Factors of the HLASystem, 2000

Steven G. E. Marsh, Julia G. Bodmer,Ekkehard D. Albert, Walter F. Bodmer,Ronald E. Bontrop, Bo Dupont, Henry A. Erlich,John A. Hansen, Bernard Mach, Wolfgang R. Mayr,Peter Parham, Effie W. Petersdorf, Takehiko Sasazuki,Geziena M. Th. Schreuder, Jack L. Strominger,Arne Svejgaard, and Paul I. Terasaki

Following the decision to hold their next full meetingafter the 13th International Histocompatibility Work-shop in 2002, the WHO Nomenclature Committee forFactors of the HLA System has decided to publish aninterim report listing updated tables of alleles includingthose assigned since the publication of the last full reportin 1999 [1]. The alleles named during the period followthe principles established in previous reports [1–15].

NAMING OF NEW ALLELES1. Conditions for acceptance of new allele sequencesAs emphasized in previous reports, there are requiredconditions for acceptance of new sequences for officialnames.

1. Where a sequence is obtained from cDNA or wherePCR products are subcloned prior to sequencing,several clones should have been sequenced.

2. Sequencing should always be performed in bothdirections.

3. If direct sequencing of PCR amplified material isperformed, products from at least two separate PCRreactions should have been sequenced.

4. In individuals who are heterozygous for a locus,where one of the alleles is novel, the novel allele

must be sequenced in isolation from the secondallele. Thus an allele sequence which is derivedusing a sequence based typing (SBT) methodology,where both alleles of a heterozygous individual aresequenced together, is insufficient evidence for as-signment of an official designation.

5. Sequence derived solely from the primers used toamplify an allele should not be included in thesequence that is submitted.

6. Where possible, a novel sequence should be con-firmed by a DNA typing method such as PCR-SSOP or PCR-SSP. Newly-defined sequence motifsmust be confirmed by a DNA typing techniqueusing appropriately designed probes or primerswhere necessary.

7. An accession number in a databank should havebeen obtained. Sequences may be submitted tothe databases online at the following addresses:EMBL: www.ebi.ac.uk/Submissions/index.htmlGenBank: www.ncbi.nlm.nih.gov/Genbank/index.htmlDDBJ: www.ddbj.nig.ac.jp/sub-e.html

8. Full length sequences are preferable though notessential; the minimum requirements are exons 2and 3 for an HLA class I sequence and exon 2 for anHLA class II sequence.

9. Where possible, a paper should have been submittedfor publication.

10. DNA or other material, in particular cell lines,should, wherever possible, be made available in apublicly accessible repository or alternatively, atleast in the originating laboratory. Documentation

Address reprint requests to: Dr. Steven G. E. Marsh, Anthony NolanResearch Institute, Royal Free Hospital, Pond Street, Hampstead, LondonNW3 2QG, United Kingdom

New sequences should be communicated to Steven Marsh via the sequencesubmission tool of the IMGT/HLA Database to receive official names. Pleasego to www.ebi.ac.uk/imgt/hla

Human Immunology 62, 419–468 (2001)0198-8859/01/$–see front matter© American Society for Histocompatibility and Immunogenetics, 2001

Published by Elsevier Science Inc. PII S0198-8859(01)00229-4

on this will be maintained by the WHO Nomen-clature Committee.

11. Submission of a sequence to the WHO Nomencla-ture Committee should be performed using the on-line submission tool available at www.ebi.ac.uk/imgt/hla/subs/submit.html. Researchers will beexpected to complete a questionnaire relating to thesequence and provide a comparison of their newsequence with known related alleles. If the sequencecannot be submitted using the online web tools,researchers should contact [email protected] directlyfor details of alternative submission methods.

It should be noted with some caution that cells fromwhich only partial sequences have been obtained maylater be shown to represent different or novel alleleswhen further sequencing is performed. This is of par-ticular importance in cases where several different cellshave been partially sequenced for an allele. In suchcases, all cells have been listed in this report.

Official designations are currently being assigned tonew alleles in the period between Nomenclature Com-mittee meetings, provided they meet the criteria out-lined above. Details of the newly reported alleles arepublished in monthly nomenclature updates in the jour-nals Tissue Antigens, Human Immunology and the Eu-ropean Journal of Immunogenetics. The listing of refer-ences to new sequences does not imply priority ofpublication. The use of numbers or names for alleles,genes or specificities which pre-empt formal designationssuch as “HLA-M,” “A*0109,” “DRB5*0301” or “HLA-DL” before consideration by the Nomenclature Commit-tee is strongly discouraged. The list of genes in the HLAregion is given in Table 1.

2. New AllelesOver 370 HLA alleles have been named since the 1998report. The newly-named alleles are shown in bold type-face in Tables 2–10. A total of 85 alleles at the HLA-Alocus, 156 at HLA-B, 28 at HLA-C, 1 at HLA-E, 1 atHLA-F and 1 at HLA-G were named, making a total of746 Class I alleles with official names. At the HLA-DRBloci 68 alleles were named, 2 at DQA1, 6 at DQB1, 4 atDPA1, 9 at DPB1, 8 at DOB and 1 at DMB making atotal of 542 Class II alleles named. An allele for each ofthe HLA-F, -DRB2, -DRB8 and -DRB9 loci have alsobeen named as these had previously only been listedunder their locus names.

Following previous discussion for the MIC loci, it hasbeen decided to use the fourth and fifth digits to indicatesynonymous polymorphisms within the coding sequence.A total of 36 MICA alleles have been named, six of whichdiffer from previously defined alleles by synonymousmutations, see Table 11.

The total number of alleles assigned with officialnames at each locus by December 2000 is given in Table12. A comprehensive list of all the allele names whichhave been deleted is given in Table 13.

As discussed previously, with the continuing discov-ery of new HLA allele sequences, it is becoming increas-ingly difficult to maintain the link given by the allelename between the sequence and the serological profile ofthe antigen associated with it. In many cases, with re-searchers relying heavily on DNA technology, they areunable to provide a serological definition, and where thisis available, they often cannot place the newly definedantigen within a known serological grouping. This isespecially true of the DRB1*03, *11, *13, *14 and *08family of alleles and the description of new alleles withinthis group illustrates that this is in fact a continuum ofallelic diversity. We would like to stress that, althoughit is our goal wherever possible to indicate the serologicalgrouping into which an allele will fall, this is not alwayspossible, and that most importantly the allele nameshould be seen as no more than a unique designation.

SEROLOGICAL SPECIFICITIES ASSOCIATEDWITH ALLELESColumn 2 of Tables 2–6 lists the serological specificitiesor antigens, associated with the alleles, where this infor-mation is known. The data given in the tables has beenpreviously based solely on the serological typing ob-tained for the cells which were sequenced for the indi-vidual alleles and from the information submitted to theCommittee. In many cases no serological information isavailable and the entry in the table has been left blank.This is also true for cases when the serological patternassociated with an expressed allele does not correspond toa single defined specificity. A comprehensive dictionaryof antigen and allele equivalents has twice been pub-lished by World Marrow Donor Association (WMDA)Quality Assurance Working Group on HLA Serology toDNA Equivalents [16, 17] and an up-to-date version iscurrently in preparation (I. Schreuder, personal commu-nication). Where additional or superior data is availablefrom the dictionary this has now been included in col-umn 2 of Tables 2–6 and the source of this informationindicated.

THE IMGT/HLA DATABASEThe IMGT/HLA Database came on-line in December1998 [18, 19] and is the official repository for HLAsequences named by the WHO Nomenclature Commit-tee for Factors of the HLA System. The database containssequences for all HLA alleles officially recognized by theWHO Nomenclature Committee for Factors of the HLA

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System and provides users with online tools and facilitiesfor their retrieval and analysis. These include allele re-ports, alignment tools, and detailed descriptions of thesource cells. The online IMGT/HLA submission toolallows both new and confirmatory sequences to be sub-mitted directly to the WHO Nomenclature Committee.New releases of the database are made quarterly with thelatest version (release 1.9.0 January 2001) containing1340 HLA alleles derived from over 3028 componentsequences from the EMBL/GenBank/DDBJ databases.The database may be accessed via the World Wide Webat www.ebi.ac.uk/imgt/hla.

The IMGT/HLA Database is supported by the follow-ing organizations: the American Society for Histocom-patibility and Immunogenetics (ASHI), the AnthonyNolan Bone Marrow Trust (ANBMT), Dynal, Genovi-sion, Lifecodes Corporation, the National Marrow DonorProgram (NMDP), PE Applied Biosystems, Visible Ge-netics and the German National Bone Marrow Registry(ZKRD). This funding has been coordinated by JanetHegland at the NMDP, to whom we are greatly in-debted. It is hoped that it will be possible to continuesuch funding for the foreseeable future. Initial supportfor the IMGT/HLA database project was from the Im-perial Cancer Research Fund and an EU Biotech grant(BIO4CT960037).

ACKNOWLEDGMENTS

The Committee would like to thank James Robinson andMatthew Waller for their work with the IMGT/HLA Sequencedatabase. We would also like to thank Dr. Peter Stoehr and thestaff at the European Bioinformatics Institute for their contin-ued support of the IMGT/HLA Database.

LIST OF COMMITTEE MEMBERS INVOLVEDIN PREPARING THIS REPORTE. D. Albert, Policlinic for Children, University of Mu-nich, Germany, (Chairman)

J. G. Bodmer, Imperial Cancer Research Fund, Ox-ford, UK (Rapporteur)

S. G. E. Marsh, Anthony Nolan Research Institute,London, UK (Rapporteur and Data Coordinator)

W. F. Bodmer, Imperial Cancer Research Fund, Ox-ford, UK

B. Dupont, Sloan-Kettering Institute for Cancer Re-search, New York, USA

H. A. Erlich, Roche Molecular Systems, Alameda, USAB. Mach, University of Geneva, Geneva, SwitzerlandW. R. Mayr, University of Vienna, Vienna, AustriaP. Parham, Stanford University School of Medicine,

Stanford, USAT. Sasasuki, Kyushu University, Fukuoka, JapanG. M. Th. Schreuder, Leiden University Medical Cen-

ter, Leiden, The Netherlands

J. L. Strominger, Harvard University, Cambridge,USA

A. Svejgaard, State University Hospital, Copenhagen,Denmark

P. I. Terasaki, Los Angeles, USA

CO-OPTED MEMBERSR. E. Bontrop, Biomedical Primate Research Centre,Rijswijk, The Netherlands

J. A. Hansen, Fred Hutchinson Cancer Center, Seattle,USA

E. Petersdorf, Fred Hutchinson Cancer Center, Seat-tle, USA

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37. Ramon D, Scott I, Cox ST, Pesoa S, Vullo C, Little A-M,Madrigal JA: HLA-A*6817, identified in the Kolla Am-erindians of North-West Argentina possesses a novelnucleotide substitution. Tissue Antigens 55(5):453,2000.

38. Voorter CE, van der Vlies S, Kik M, van den Berg-Loonen EM: Unexpected Bw4 and Bw6 reactivity pat-terns in new alleles. Tissue Antigens 56(4):363, 2000.

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40. Steiner NK, Jones P, Kosman C, Edson S, Rizzuto G,Gans CP, Mitton W, Koester R, Rodriguez-Marino SG,Ng J, Hartzman RJ, Hurley CK: Novel HLA-B allelesassociated with antigens in the 7C CREG. Tissue Anti-gens 57:in press, 2001.

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53. Hoddinott MA, Cox ST, McWhinnie AJ, Marsh SGE,Ogilvie H, Madrigal JA, Little A-M: A new allele,HLA-B*1555, identified in an African patient awaitingbone marrow transplantation. Tissue Antigens 55(5):463, 2000.

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58. Williams F, Curran MD, Leheny WA, Daar AS, Middle-ton D: Characterization of HLA-B*3921 and confirma-tion of HLA-B*4415, two variant HLA-B alleles iden-tified in the Omani population. Tissue Antigens 56(4):376, 2000.

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63. Turner DM, Vlachos G, Cavanna SL, Brown J, NavarreteCV: A novel HLA allele, B*4104, identified in a cordblood donor. Tissue Antigens 57:83, 2001.

64. Steiner NK, Gans CP, Kosman C, Bradshaw D, KoesterR, Menchaca EM, Mitton W, Ng J, Hartzman RJ,Hurley CK: New alleles in the B44 family includingB*44022, B*44032, B*4411, B*4420, B*4421,B*4424, and B*8301. Tissue Antigens 57:in press,2001.

65. Cox ST, McWhinnie A, Prokupek B, Madrigal JA, LittleA-M: HLA-B*4413 identified in a UK Caucasoid po-tential bone marrow donor. Tissue Antigens 55(2):185,2000.

66. Elsner HA, Schmits G, Ballas M, Lenhard V, Blasczyk R:Charaterization of the novel allele HLA-B*4417: Impli-cations for bone marrow transplantation. Tissue Anti-gens 56:463, 2000.

67. Bettens F, Tiercy J-M: Sequence of a new class I nullallele within the HLA-B44 specificity. Tissue Antigens56:441, 2000.

68. Akesaka T, Kashiwase K, Shimamura M, Ishikawa Y,Tanaka H, Fujii M, Akaza T, Hando K, Yuasa S, Taka-hashi T, Juji T: Identification of a novel HLA-B46 allele,B*4602, in Japanese. Tissue Antigens 55(5):460, 2000.

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70. Voorter CEM, Hepkema BG, Mulkers EMT, Lems SPM,van den Berg-Loonen EM: Identification of two newHLA-B22 variants, HLA-B*5509 and B*5606. TissueAntigens 57:in press, 2001.

71. Gaidulis L, Krausa P, Schaub B, Senitzer D: Identifica-tion of a new HLA-B*78 allele in a Hispanic family.Tissue Antigens 56(2):184, 2000.

72. Cox ST, Hossain E, McWhinnie A, Prokupek B, Mad-rigal JA, Little A-M: HLA-B*8202 identified in a Cau-casoid potential bone marrow donor. Tissue Antigens56(2):188, 2000.

73. van der Vlies SA, Voorter CE, van den Berg-Loonen EM:There is more to HLA-C than exons 2 and 3: sequencingexons 1, 4 and 5. Tissue Antigens 54(2):169, 1999.

74. Huang LQ, Boon T, Van Pel A: Identification of a novel

HLA-Cw*05 allele, Cw*0503. Tissue Antigens 55(5):473, 2000.

75. Santos S, Vicario JL, Garcia-Sanchez F, Aviles MJ, BalasA: Sequencing based typing for HLA-C. Identification ofthree new alleles: Cw*0307, Cw*0502 and Cw*0504.Tissue Antigens 57:in press, 2001.

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87. Longhi E, Frison S, Poli F, Scalamogna M, Sirchia G:

424

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88. Martinetti M, Pizzochero C, Asti M, Salvaneschi L: NewHLA-DRB1* nucleotide sequence of Italian origin:HLA-DRB1*13022. Tissue Antigens 56(2):192, 2000.

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90. Vincek V, Klein D, Figueroa F, Hauptfeld V, KasaharaM, O’HUigin C, Mach B, Klein J: The evolutionaryorigin of the HLA-DR3 haplotype. Immunogenetics35(4):263, 1992.

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425

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TABLE 1. Names for genes in the HLA region

Name Previous equivalents Molecular characteristics

HLA-A — Class I a-chainHLA-B — Class I a-chainHLA-C — Class I a-chainHLA-E E, 96.29 Associated with class I 6.2-kB Hind III fragmentHLA-F F, 95.49 Associated with class I 5.4-kB Hind III fragmentHLA-G G, 96.09 Associated with class I 6.0-kB Hind III fragmentHLA-H H, AR, 912.49 Class I pseudogene associated with 5.4-kB Hind III fragmentHLA-J cda12 Class I pseudogene associated with 5.9-kB Hind III fragmentHLA-K HLA-70 Class I pseudogene associated with 7.0-kB Hind III fragmentHLA-L HLA-92 Class I pseudogene associated with 9.2-kB Hind III fragmentHLA-DRA DRa DR a chainHLA-DRB1 DRbI, DR1B DR b1 chain determining specificities DR1, DR2, DR3, DR4, DR5 etc.HLA-DRB2 DRbII Pseudogene with DR b-like sequencesHLA-DRB3 DRbIII, DR3B DR b3 chain determining DR52 and Dw24, Dw25, Dw26 specificitiesHLA-DRB4 DRbIV, DR4B DR b4 chain determining DR53HLA-DRB5 DRbIII DR b5 chain determining DR51HLA-DRB6 DRBX, DRBs DRB pseudogene found on DR1, DR2 and DR10 haplotypesHLA-DRB7 DRBi1 DRB pseudogene found on DR4, DR7 and DR9 haplotypesHLA-DRB8 DRBi2 DRB pseudogene found on DR4, DR7 and DR9 haplotypesHLA-DRB9 M4.2 b exon DRB pseudogene, isolated fragmentHLA-DQA1 DQa1, DQ1A DQ a chain as expressedHLA-DQB1 DQb1, DQ1B DQ b chain as expressedHLA-DQA2 DXa, DQ2A DQ a-chain-related sequence, not known to be expressedHLA-DQB2 DXb, DQ2B DQ b-chain-related sequence, not known to be expressedHLA-DQB3 DVb, DQB3 DQ b-chain-related sequence, not known to be expressedHLA-DOA DNA, DZa, DOa DO a chainHLA-DOB DOb DO b chainHLA-DMA RING6 DM a chainHLA-DMB RING7 DM b chainHLA-DPA1 DPa1, DP1A DP a chain as expressedHLA-DPB1 DPb1, DP1B DP b chain as expressedHLA-DPA2 DPa2, DP2A DP a-chain-related pseudogeneHLA-DPB2 DPb2, DP2B DP b-chain-related pseudogene

TAP1 RING4, Y3, PSF1 ABC (ATP Binding Cassette) transporterTAP2 RING11, Y1, PSF2 ABC (ATP Binding Cassette) transporterLMP2 RING12 Proteasome-related sequenceLMP7 RING10 Proteasome-related sequenceMICA MICA, PERB11.1 Class I chain-related geneMICB MICB, PERB11.2 Class I chain-related geneMICC MICC, PERB11.3 Class I chain-related pseudogeneMICD MICD, PERB11.4 Class I chain-related pseudogeneMICE MICE, PERB11.5 Class I chain-related pseudogene

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463

TABLE 9 Designations of HLA-DM alleles

HLAallelesa

Previousequivalents

Individual or cell line from whichthe sequence was derived Accession number

References or submittingauthor(s)

DMA*0101 RING6 JY, MANN X62744DMA*0102 DMA-Ile 140 AZL Z24753DMA*0103 DMA3.2 HOM-2 U04878DMA*0104 DMA3.4 BM21 U04877

DMB*0101 RING7 JY, MANN Z23139DMB*0102 DMB-Glu 143 YAR Z24750DMB*0103 DMB-Thr 179 BM16 Z24751DMB*0104 DMB3.4 CEPH 23-01 U00700DMB*0105 HY595, DMB*KV1 HY595, H.S.K. D32055, U16762DMB*0106 DMB*PERR CC44 AF134890, AF072680 [112]

a Allele names given in bold type have been assigned since the 1998 Nomenclature report.

TABLE 10 Designations of TAP alleles

TAP alleles Previous equivalentsIndividual or cell line from which

the sequence was derived Accession number

TAP1*0101 RING4, PSF(Y3), TAP1A U937, LCL721.45, HB00028, HB00032 X57522, X57521, L21204TAP1*0102N TAP1*0101Null KMW AB012644, AB012645TAP1*02011 TAP1B CK L21206TAP1*02012 TAP1E HEH L21205TAP1*0301 TAP1C JT L21208TAP1*0401 TAP1D HB00031 L21207

TAP2*0101 RING11A, TAP2A CEM-CCRF M84748TAP2*0102 TAP2E JY Z22936TAP2*0103 TAP2F S-2 U07844TAP2*0201 RING11B, TAP2B DX3 Z22935

TABLE 8 Designations of HLA-DOA, -DOB alleles

HLAallelesa

Previousequivalents

Individual or cell line from whichthe sequence was derived Accession number

References or submittingauthor(s)

DOA*01011 DZa, DNA1.2a JG, MANN, DBB X02882, Z81310, AB005994DOA*0101201 pII-a-6, DNA1.1b SPL, TOK M26039, AB005992DOA*0101202 PGDZ1, DNA1.1a PGF, SA M31525, AB005991DOA*0101203 DNA1.1c SPO101 AB005993DOA*01013 DNA1.2b DKB AB005995DOA*0101401 DNA1.3a U937 AB005996DOA*0101402 DNA1.3b U937 AB005997DOA*01015 DNA1.4 COX AB005998

DOB*0101101 DO, pII-b-9 45.1, SPL, SA, LCL721 X03066, M26040, AB035249 [108, 109], H. InokoDOB*0101102 — WT100BIS, LCL721 AB035250 H. InokoDOB*01012 DOB1.6 SR117 AB035254 H. InokoDOB*01021 DOB BOLETH L29472 [110]DOB*01022 DOB1.3 AKIBA AB035251 H. InokoDOB*0103 HA14 MANN X87344 [111]DOB*0104101 DOB1.4 PEA AB035252 H. InokoDOB*0104102 DOB1.5 SPO010 AB035253 H. Inoko

a Allele names given in bold type have been assigned since the 1998 Nomenclature report.

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466

TABLE 12 Numbers of alleles with official names ateach locus by 31st December 2000

Locus Number of alleles

HLA-A 209HLA-B 414HLA-C 101HLA-E 6HLA-F 1HLA-G 15HLA-DRA 2HLA-DRB1 273HLA-DRB2 1HLA-DRB3 30HLA-DRB4 10HLA-DRB5 15HLA-DRB6 3HLA-DRB7 2HLA-DRB8 1HLA-DRB9 1HLA-DQA1 21HLA-DQB1 45HLA-DPA1 19HLA-DPB1 93HLA-DOA 8HLA-DOB 8HLA-DMA 4HLA-DMB 6

TAP1 6TAP2 4

MICA 51

467

TABLE 13 List of allele names which have been deleted

Old namenow deleted New name Reason for change

A*0223 A*0222 Sequence named in errorA*2401 — Sequence shown to be in errorA*2412 A*2408 Sequence shown to be in error

A*3005 A*3004 Sequence shown to be in errorA*31011 A*31012 Sequence shown to be in errorA*3302 A*3303 Sequence shown to be in errorB*0701 — Sequence shown to be in errorB*1305 B*1304 Sequence submitted with errorsB*1541 B*1539 Sequence named in errorB*27051 B*27052 Sequence shown to be in errorB*39012 B*39011 Sequence shown to be in errorB*3921 B*3924 Sequence submitted with errorsB*4017 B*4016 Sequence named in errorB*4203 B*4202 Name never officially assignedB*4401 B*4402 Sequence shown to be in errorB*5003 B*5002 Sequence named in errorB*5125 B*5122 Sequence named in errorB*5506 B*5504 Sequence submitted with errorsB*5803 — Name never officially assignedB*7901 B*1518 Sequence renamedCw*0101 Cw*0102 Sequence shown to be in errorCw*0201 Cw*02022 Sequence shown to be in errorCw*0301 Cw*0304 Sequence shown to be in errorCw*0402 Cw*04011 Sequence shown to be in errorCw*0601 Cw*0602 Sequence shown to be in errorCw*1101 — Sequencing artefactCw*1201 Cw*12022 Sequence shown to be in errorCw*1401 Cw*1402 Sequence shown to be in errorCw*1501 Cw*1502 Sequence shown to be in errorCw*1603 Cw*1403 Sequence shown to be in errorCw*16042 Cw*16041 Sequence submitted with errorsCw*1605 Cw*16041 Sequence submitted with errorsDRB1*0702 DRB1*0701 Sequence shown to be in errorDRB1*08031 DRB1*08032 Sequence shown to be in errorDRB1*09011 DRB1*09012 Sequence shown to be in errorDRB1*12031 DRB1*1201 Sequence shown to be in errorDRB1*1606 DRB1*1605 Sequence shown to be in errorDRB4*0101102N DRB4*0103102N Sequence named in errorDRB5*0201 DRB5*0202 Sequence shown to be in errorDQA1*03012 DQA1*0302 Sequence shown to be in errorDQA1*05013 DQA1*0505 Additional coding polymorphism detectedDQB1*03031 DQB1*03032 Sequence shown to be in errorDPA1*0101 DPA1*0103 Sequence shown to be in errorDPA1*0102 DPA1*0103 Sequence shown to be in errorDPB1*02011 DPB1*02012 Sequence shown to be in errorDPB1*0701 — Name never assignedDPB1*1201 — Name never assignedDPB1*4201 DPB1*3101 Sequence shown to be in errorDPB1*4301 DPB1*2801 Sequence shown to be in errorMICA*003 — Name never assigned

468

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Nomenclature for factors of the hla system, 2000

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