IMGT/HLA and the immuno polymorphism database

Methods in Molecular Biology

Volumn 1184, Issue , 2014, Pages 109-121

  Robinson, James ^a,b   Halliwell, Jason A ^a   Marsh, Steven G E ^a,b  

^a ROYAL FREE HOSPITAL   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Allele; Database; HLA; Immunogenetics; KIR; MHC; Polymorphism; Sequence; Variation

Indexed keywords

ALLOANTIGEN; HLA ANTIGEN; HLA DPB1 ANTIGEN; KILLER CELL IMMUNOGLOBULIN LIKE RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; CANCER SURVIVAL; EPITOPE MAPPING; GENE FUNCTION; GENE SEQUENCE; GENETIC CODE; GENETIC DATABASE; HEMATOPOIETIC STEM CELL; HLA SYSTEM; HUMAN; HUMAN CHROMOSOME; IMMUNO POLYMORPHISM DATABASE; IMMUNOGENICITY; MAJOR HISTOCOMPATIBILITY COMPLEX; MELANOMA CELL LINE; NONHUMAN; NUCLEOTIDE SEQUENCE; OUTCOME ASSESSMENT; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SURVIVAL PREDICTION; ALLELE; ANIMAL; BIOLOGY; GENETIC POLYMORPHISM; GENETICS; IMMUNOGENETICS; INTERNET; TUMOR CELL LINE;

ALLELES; ANIMALS; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HLA ANTIGENS; HUMANS; IMMUNOGENETICS; INTERNET; MAJOR HISTOCOMPATIBILITY COMPLEX; POLYMORPHISM, GENETIC; RECEPTORS, KIR;

EID: 84925884566     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1115-8_5     Document Type: Article

References (79)

1. Robinson J, Halliwell JA, McWilliam H et al (2013) IPD-The Immuno-Polymorphism Database. Nucleic Acids Res 41:D1234-D1240
2. Robinson J, Halliwell JA, McWilliam H et al (2013) The IMGT/HLA Database. Nucleic Acids Res 41:D1222-D1227
3. Horton R, Wilming L, Rand V et al (2004) Gene map of the extended human MHC. Nat Rev Genet 5:889-899
4. Shaw BE, Arguello R, Garcia-Sepulveda CA et al (2010) The impact of HLA genotyping on survival following unrelated donor haematopoietic stem cell transplantation. Br J Haematol 150: 251-258
5. Robinson J, Bodmer JG, Malik A et al (1998) Development of the international immunogenetics HLA database. Hum Immunol 59:17
6. WHO Nomenclature Committee (1968) Nomenclature for factors of the HL-A system. Bull World Health Organ 39:483-486
7. WHO Nomenclature Committee (1970) WHO Terminology Report. In: Terasaki PI (ed) Histocompatibility testing. Munksgaard, Copenhagen. p 49
8. WHO Nomenclature Committee (1972) Nomenclature for factors of the HL-A system. Bull World Health Organ 47:659-662
9. WHO IUIS Terminology-Committee (1975) Nomenclature for factors of the HLA system. Bull World Health Organ 52:261-265
10. WHO Nomenclature Committee (1978) Nomenclature for factors of the HLA system, 1977. Tissue Antigens 11:81-86
11. WHO Nomenclature Committee (1980) Nomenclature for Factors of the HLA System. In: Terasaki PI, (ed). Histocompatibility Testing, 1980 . UCLA Tissue Typing Laboratory, Los Angeles: pp 18-20
12. WHO Nomenclature Committee (1984) Nomenclature for factors of the HLA system 1984. Tissue Antigens 24:73-80
13. WHO Nomenclature Committee (1988) Nomenclature for factors of the HLA system, 1987. Tissue Antigens 32:177-187
14. Bodmer JG, Marsh SGE, Parham P et al (1990) Nomenclature for factors of the HLA system, 1989. Tissue Antigens 35:1-8
15. Bodmer JG, Marsh SGE, Albert ED et al (1991) Nomenclature for factors of the HLA system, 1990. Tissue Antigens 37:97-104
16. Bodmer JG, Marsh SGE, Albert ED et al (1992) Nomenclature for factors of the HLA system, 1991. Hum Immunol 34:4-18
17. Bodmer JG, Marsh SGE, Albert ED et al (1994) Nomenclature for factors of the HLA system, 1994. Tissue Antigens 44:1-18
18. Bodmer JG, Marsh SGE, Albert ED et al (1995) Nomenclature for factors of the HLA system, 1995. Tissue Antigens 46:1-18
19. Bodmer JG, Marsh SGE, Albert ED et al (1997) Nomenclature for factors of the HLA system, 1996. Tissue Antigens 49:297-321
20. Bodmer JG, Marsh SGE, Albert ED et al (1999) Nomenclature for factors of the HLA system, 1998. Tissue Antigens 53:407-446
21. Marsh SGE, Bodmer JG, Albert ED et al (2001) Nomenclature for factors of the HLA system, 2000. Tissue Antigens 57:236-283
22. Marsh SGE, Albert ED, Bodmer WF et al (2002) Nomenclature for factors of the HLA system, 2002. Tissue Antigens 60:407-464
23. Marsh SGE, Albert ED, Bodmer WF et al (2005) Nomenclature for factors of the HLA system, 2004. Tissue Antigens 65:301-369
24. Marsh SGE, Albert ED, Bodmer WF et al (2010) Nomenclature for factors of the HLA system, 2010. Tissue Antigens 75:291-455
25. Lee SJ, Klein J, Haagenson M et al (2007) Highresolution donor-recipient HLA matching contributes to the success of unrelated donor marrow transplantation. Blood 110:4576-4583
26. Shaw BE, Mayor NP, Russell NH et al (2010) Diverging effects of HLA-DPB1 matching status on outcome following unrelated donor transplantation depending on disease stage and the degree of matching for other HLA alleles. Leukemia 24:58-65
27. Orr HT, Lopez de Castro JA, Lancet D et al (1979) Complete amino acid sequence of a papain-solubilized human histocompatibility antigen, HLA-B7. 2. Sequence determination and search for homologies. Biochemistry 18: 5711-5720
28. Lee JS, Trowsdale J, Travers PJ et al (1982) Sequence of an HLA-DR alpha-chain cDNA clone and intron-exon organization of the corresponding gene. Nature 299:750-752
29. Wake CT, Long EO, Strubin M et al (1982) Isolation of cDNA clones encoding HLA-DR alpha chains. Proc Natl Acad Sci U S A 79: 6979-6983
30. Yang C, Kratzin H, Gotz H et al (1982) Primary structure of class II human histocompatibility antigens. 2nd Communication. Amino acid sequence of the N-Terminal 179 residues of the alpha-chain of an HLA-Dw2/ DR2 alloantigen (authors transl). Hoppe Seylers Z Physiol Chem 363:671-676
31. Longenecker BM, Mosmann TR (1981) Nomenclature for chicken MHC (B) antigens defined by monoclonal antibodies. Immunogenetics 13:25-28
32. Briles WE, Bumstead N, Ewert DL et al (1982) Nomenclature for chicken major histocompatibility (B) complex. Immunogenetics 15: 441-447
33. 1991 Leukocyte antigens in cattle, sheep and goats. Nomenclature. Vet Immunol Immunopathol. 27:15-16
34. Davies CJ, Andersson L, Joosten I et al (1992) Characterization of bovine MHC class II polymorphism using three typing methods: serology, RFLP and IEF. Eur J Immunogenet 19:253-262
35. Naessens J (1993) Leukocyte antigens of cattle and sheep. Nomenclature. Vet Immunol Immuno pathol 39:11-12
36. Kennedy LJ, Altet L, Angles JM et al (2000) Nomenclature for factors of the dog major histocompatibility system (DLA), 1998: fi rst report of the ISAG DLA Nomenclature Committee. Anim Genet 31:52-61
37. Kennedy LJ, Angles JM, Barnes A et al (2001) Nomenclature for factors of the dog major histocompatibility system (DLA), 2000: second report of the ISAG DLA Nomenclature Committee. Anim Genet 32:193-199
38. Miller MM, Bacon LD, Hala K et al (2004) 2004 Nomenclature for the chicken major histocompatibility (B and Y) complex. Immunogenetics 56:261-279
39. Smith DM, Lunney JK, Ho CS et al (2005) Nomenclature for factors of the swine leukocyte antigen class II system, 2005. Tissue Antigens 66:623-639
40. Ballingall KT, Herrmann-Hoesing L, Robinson J et al (2011) A single nomenclature and associated database for alleles at the major histocompatibility complex class II DRB1 locus of sheep. Tissue Antigens 77:546-553
41. de Groot NG, Otting N, Robinson J et al (2012) Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species. Immunogenetics 64:615-631
42. Hammond JA, Marsh SGE, Robinson J et al (2012) Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes? Immunogenetics 64:475-480
43. Klein J, Bontrop RE, Dawkins RL et al (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31:217-219
44. Robinson J, Halliwell JA, McWilliam H et al (2013) The IMGT/HLA Database. Nucleic Acids Res 41:D1222-D1227
45. Rodgers JR, Levitt JM, Cresswell P et al (1999) A nomenclature solution to mouse MHC confusion. J Immunol 162:6294
46. Eppig JT, Blake JA, Bult CJ et al (2012) The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40: D881-D886
47. Ellis SA, Bontrop RE, Antczak DF et al (2006) ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report, 2005. Immuno genetics 57:953-958
48. Ballingall KT (2012) Progress of the Comparative MHC Committee and a summary of the Comparative MHC Workshops held at the 32nd ISAG, Edinburgh and the 9th IVIS, Tokyo, 2010. Vet Immunol Immunopathol 148:202-208
49. Parham P (1999) Virtual reality in the MHC. Immunol Rev 167:5-15
50. Robinson J, Waller MJ, Parham P et al (2003) IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 31: 311-314
51. Drake GJ, Kennedy LJ, Auty HK et al (2004) The use of reference strand-mediated conformational analysis for the study of cheetah (Acinonyx jubatus) feline leucocyte antigen class II DRB polymorphisms. Mol Ecol 13: 221-229
52. Lukacs MF, Harstad H, Bakke HG et al (2010) Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon. BMC Genomics 11:154
53. Fujii H, Kakinuma M, Yoshiki T et al (1991) Polymorphism of the class II gene of rat major histocompatibility complex, RT1: partial sequence comparison of the fi rst domain of the RT1.B beta 1 alleles. Immunogenetics 33: 399-403
54. Ho CS, Lunney JK, Ando A et al (2009) Nomenclature for factors of the SLA system, update 2008. Tissue Antigens 73:307-315
55. Garcia CA, Robinson J, Guethlein LA et al (2003) Human KIR sequences 2003. Immunogenetics 55:227-239
56. Marsh SGE, Parham P, Dupont B et al (2003) Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002. Tissue Antigens 62:79-86
57. Mungall AJ, Palmer SA, Sims SK et al (2003) The DNA sequence and analysis of human chromosome 6. Nature 425:805-811
58. Karsch-Mizrachi I, Nakamura Y, Cochrane G (2012) The international nucleotide sequence database collaboration. Nucleic Acids Res 40:D33-D37
59. Kodama Y, Mashima J, Kaminuma E et al (2012) The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Res 40:D38-D42
60. Amid C, Birney E, Bower L et al (2012) Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res 40: D43-D47
61. Benson DA, Karsch-Mizrachi I, Clark K et al (2012) GenBank. Nucleic Acids Res 40: D48-D53
62. Flicek P, Amode MR, Barrell D et al (2012) Ensembl 2012. Nucleic Acids Res 40:D84-D90
63. Wilming LG, Gilbert JG, Howe K et al (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36:D753-D760
64. Goujon M, McWilliam H, Li W et al (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38: W695-W699
65. McWilliam H, Valentin F, Goujon M et al (2009) Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res 37:W6-W10
66. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85:2444-2448
67. Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
68. Santamaria P, Lindstrom AL, Boyce-Jacino MT et al (1993) HLA class I sequence-based typing. Hum Immunol 37:39-50
69. Rozemuller EH, Bouwens AG, van Oort E et al (1995) Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism. Tissue Antigens 45:57-62
70. Ruggeri L, Capanni M, Casucci M et al (1999) Role of natural killer cell alloreactivity in HLAmismatched hematopoietic stem cell transplantation. Blood 94:333-339
71. Cooley S, Weisdorf DJ, Guethlein LA et al (2010) Donor selection for natural killer cell receptor genes leads to superior survival after unrelated transplantation for acute myelogenous leukemia. Blood 116: 2411-2419
72. Kawase T, Morishima Y, Matsuo K et al (2007) High-risk HLA allele mismatch combinations responsible for severe acute graft-versus-host disease and implication for its molecular mechanism. Blood 110:2235-2241
73. Fleischhauer K, Shaw BE, Gooley T et al (2012) Effect of T-cell-epitope matching at HLADPB1 in recipients of unrelated-donor haemopoietic-cell transplantation: a retrospective study. Lancet Oncol 13:366-374
74. Crocchiolo R, Zino E, Vago L et al (2009) Nonpermissive HLA-DPB1 disparity is a signifi cant independent risk factor for mortality after unrelated hematopoietic stem cell transplantation. Blood 114:1437-1444
75. Zino E, Frumento G, Marktel S et al (2004) A T-cell epitope encoded by a subset of HLA- DPB1 alleles determines nonpermissive mismatches for hematologic stem cell transplantation. Blood 103:1417-1424
76. Zino E, Vago L, Di Terlizzi S et al (2007) Frequency and targeted detection of HLADPB1 T cell epitope disparities relevant in unrelated hematopoietic stem cell transplantation. Biol Blood Marrow Transplant 13:1031-1040
77. Shaw BE, Robinson J, Fleischhauer K et al (2013) Translating the HLA-DPB1 T-cell epitope matching algorithm into clinical practice. Bone Marrow Transplant 48(12): 1510-1512
78. Robinson J, Malik A, Parham P et al (2000) IMGT/HLA database-A sequence database for the human major histocompatibility complex. Tissue Antigens 55:280-287
79. Robinson J, Waller MJ, Fail SC et al (2009) The IMGT/HLA database. Nucleic Acids Res 37:D1013-D1017