Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

Immunogenetics

Volumn 60, Issue 1, 2008, Pages 1-18

  Horton, Roger ^a   Gibson, Richard ^a   Coggill, Penny ^a   Miretti, Marcos ^a   Allcock, Richard J ^c   Almeida, Jeff ^a   Forbes, Simon ^a   Gilbert, James G R ^a   Halls, Karen ^d   Harrow, Jennifer L ^a   Hart, Elizabeth ^a   Howe, Kevin ^b   Jackson, David K ^a   Palmer, Sophie ^a   Roberts, Anne N ⁱ   Sims, Sarah ^a   Stewart, C Andrew ^e   Traherne, James A ^j   Trevanion, Steve ^a   Wilming, Laurens ^a   Rogers, Jane ^a   De Jong, Pieter J ^f   Elliott, John F ^g   Sawcer, Stephen ^h   Todd, John A ⁱ   Trowsdale, John ^j   Beck, Stephan ^a,k   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b CANCER RESEARCH UK CAMBRIDGE RESEARCH INSTITUTE   (United Kingdom)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e NATIONAL CANCER INSTITUTE   (United States)

^f CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^g UNIVERSITY OF ALBERTA   (Canada)

^h UNIVERSITY OF CAMBRIDGE   (United Kingdom)

ⁱ UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^j UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^k UNIVERSITY COLLEGE LONDON   (United Kingdom)

more..

Author keywords

Genetic predisposition to disease; Haplotype; Major histocompatibility complex; Polymorphism; Population genetics; Retroelement

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DQ ANTIGEN; HLA DR ANTIGEN; OCTAMER TRANSCRIPTION FACTOR 4;

ARTICLE; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HOMOZYGOSITY; MAJOR HISTOCOMPATIBILITY COMPLEX; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, HUMAN; HAPLOTYPES; HLA ANTIGENS; HUMANS; TERMINOLOGY AS TOPIC; VARIATION (GENETICS);

EID: 38349100266     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-007-0262-2     Document Type: Article

References (47)

1. Allcock RJ, Atrazhev AM, Beck S, de Jong PJ, Elliott JF, Forbes S, Halls K, Horton R, Osoegawa K, Rogers J, Sawcer S, Todd JA, Trowsdale J, Wang Y, Williams S (2002) The MHC haplotype project: a resource for HLA-linked association studies. Tissue Antigens 59:520-521
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
3. Awdeh ZL, Alper CA (1980) Inherited structural polymorphism of the fourth component of human complement. Proc Natl Acad Sci U S A 77:3576-3580
4. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48
5. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573-580
6. Bentley DR (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16:545-552
7. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14:988-995
8. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78-94
9. Chida S, Hohjoh H, Hirai M, Tokunaga K (2001) Haplotype-specific sequence encoding the protein kinase, interferon-inducible double-stranded RNA-dependent activator in the human leukocyte antigen class II region. Immunogenetics 52:186-194
10. Chung EK, Yang Y, Rennebohm RM, Lokki ML, Higgins GC, Jones KN, Zhou B, Blanchong CA, Yu CY (2002) Genetic sophistication of human complement components C4A and C4B and RP-C4-CYP21-TNX (RCCX) modules in the major histocompatibility complex. Am J Hum Genet 71:823-837
11. Dangel AW, Mendoza AR, Baker BJ, Daniel CM, Carroll MC, Wu LC, Yu CY (1994) The dichotomous size variation of human complement C4 genes is mediated by a novel family of endogenous retroviruses, which also establishes species-specific genomic patterns among Old World primates. Immunogenetics 40:425-436
12. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, Morrison J, Richardson A, Walsh EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C, Vyse TJ, Beck S, Murray SS, Carrington M, Gregory S, Deloukas P, Rioux JD (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 38:1166-1172
13. De Vet EC, Aguado B, Campbell RD (2003) Adaptor signalling proteins Grb2 and Grb7 are recruited by human G6f, a novel member of the immunoglobulin superfamily encoded in the MHC. Biochem J 375:207-213
14. Down TA, Hubbard TJ (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 12:458-461
15. Dunn DS, Naruse T, Inoko H, Kulski JK (2002) The association between HLA-A alleles and young Alu dimorphisms near the HLA-J, -H, and -F genes in workshop cell lines and Japanese and Australian populations. J Mol Evol 55:718-726
16. Dunn DS, Inoko H, Kulski JK (2003) Dimorphic Alu element located between the TFIIH and CDSN genes within the major histocompatibility complex. Electrophoresis 24:2740-2748
17. Ehlers A, Beck S, Forbes SA, Trowsdale J, Volz A, Younger R, Ziegler A (2000) MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes. Genome Res 10:1968-1978
18. Gaudieri S, Kulski JK, Dawkins RL, Gojobori T (1999) Different evolutionary histories in two subgenomic regions of the major histocompatibility complex. Genome Res 9:541-549
19. Geraghty DE, Koller BH, Hansen JA, Orr HT (1992) The HLA class I gene family includes at least six genes and twelve pseudogenes and gene fragments. J Immunol 149:1934-1946
20. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7(Suppl 1):1-9
21. Hoarau JJ, Cesari M, Caillens H, Cadet F, Pabion M (2004) HLA DQA1 genes generate multiple transcripts by alternative splicing and polyadenylation of the 3′ untranslated region. Tissue Antigens 63:58-71
22. Hoarau JJ, Festy F, Cesari M, Pabion M (2005) A new splicing acceptor site and poly(A) +sequence signal within DQA1*0401 and DQA1*0501 mRNA 3¢UTR contribute to increase the extraordinary diversity of mRNA isoforms. Immunogenetics 57:182-188
23. Horton R, Niblett D, Milne S, Palmer S, Tubby B, Trowsdale J, Beck S (1998) Large-scale sequence comparisons reveal unusually high levels of variation in the HLA-DQB1 locus in the class II region of the human MHC. J Mol Biol 282:71-97
24. Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC Jr, Wright MW, Wain HM, Trowsdale J, Ziegler A, Beck S (2004) Gene map of the extended human MHC. Nat Rev Genet 5:889-899
25. Jamain S, Girondot M, Leroy P, Clergue M, Quach H, Fellous M, Bourgeron T (2001) Transduction of the human gene FAM8A1 by endogenous retrovirus during primate evolution. Genomics 78:38-45
26. Ke X, Miretti MM, Broxholme J, Hunt S, Beck S, Bentley DR, Deloukas P, Cardon LR (2005) A comparison of tagging methods and their tagging space. Hum Mol Genet 14:2757-2767
27. Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R (2007) EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35:D16-D20
28. Kulski JK, Dunn DS (2005) Polymorphic Alu insertions within the major histocompatibility complex class I genomic region: a brief review. Cytogenet Genome Res 110:193-202
29. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17(12):1244-1245
30. Lechler R, Warrens A (2000) HLA in health and disease. Academic, 2000
31. Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Geraghty DE, Hansen JA, Hurley CK, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI, Trowsdale J (2005) Nomenclature for factors of the HLA system, 2004. Hum Immunol 66:571-636
32. Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, Hunt S, Morrison J, Whittaker P, Lander ES, Cardon LR, Bentley DR, Rioux JD, Beck S, Deloukas P (2005) A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am J Hum Genet 76:634-646
33. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M et al (2003) The DNA sequence and analysis of human chromosome 6. Nature 425:805-811
34. Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11:1725-1729
35. Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigo R (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 16:37-44
36. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516-522
37. Searle SM, Gilbert J, Iyer V, Clamp M (2004) The otter annotation system. Genome Res 14:963-970
38. Semple JI, Ribas G, Hillyard G, Brown SE, Sanderson CM, Campbell RD (2003) A novel gene encoding a coiled-coil mitochondrial protein located at the telomeric end of the human MHC Class III region. Gene 314:41-54
39. Shaw CJ, Lupski JR (2004) Implications of human genome architecture for rearrangement-based disorders: The genomic basis of disease. Hum Mol Genet Special Issue 13(1):R57-R64
40. Shiina T, Ota M, Shimizu S, Katsuyama Y, Hashimoto N, Takasu M, Anzai T, Kulski JK, Kikkawa E, Naruse T, Kimura N, Yanagiya K, Watanabe A, Hosomichi K, Kohara S, Iwamoto C, Umehara Y, Meyer A, Wanner V, Sano K, Macquin C, Ikeo K, Tokunaga K, Gojobori T, Inoko H, Bahram S (2006) Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. Genetics 173:1555-1570
41. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195-197
42. Smith WP, Vu Q, Li SS, Hansen JA, Zhao LP, Geraghty DE (2006) Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 87:561-571
43. Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res 14:1176-1187
44. The MHC Sequencing Consortium (1999) Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature 401:921-923
45. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661-678
46. Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, Stewart CA, Ashurst JL, Atrazhev AM, Coggill P, Palmer S, Almeida J, Sims S, Wilming LG, Rogers J, de Jong PJ, Carrington M, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2:e9
47. Yeo TW, De Jager PL, Gregory SG, Barcellos LF, Walton A, Goris A, Fenoglio C, Ban M, Taylor CJ, Goodman RS, Walsh E, Wolfish CS, Horton R, Traherne J, Beck S, Trowsdale J, Caillier SJ, Ivinson AJ, Green T, Pobywajlo S, Lander ES, Pericak-Vance MA, Haines JL, Daly MJ, Oksenberg JR, Hauser SL, Compston A, Hafler DA, Rioux JD, Sawcer S (2007) A second major histocompatibility complex susceptibility locus for multiple sclerosis. Ann Neurol 61:228-236