Defining multiple common "completely" conserved major histocompatibility complex SNP haplotypes

Clinical Immunology

Volumn 132, Issue 2, 2009, Pages 203-214

  Baschal, Erin E ^a   Aly, Theresa A ^a   Jasinski, Jean M ^a   Steck, Andrea K ^a   Noble, Janelle A ^b   Erlich, Henry A ^c   Eisenbarth, George S ^a  

^a UNIVERSITY OF COLORADO DENVER   (United States)

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

^c ROCHE MOLECULAR SYSTEMS   (United States)

Author keywords

8.1; DR8; Extended haplotypes; HLA; MHC; SNP; Type 1 diabetes

Indexed keywords

HLA A ANTIGEN; HLA DR ANTIGEN;

ARTICLE; CHROMOSOME; CONTROLLED STUDY; DISEASE PREDISPOSITION; GENE FREQUENCY; HAPLOTYPE; HLA SYSTEM; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; COHORT STUDIES; DIABETES MELLITUS, TYPE 1; GENE FREQUENCY; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HLA-A ANTIGENS; HLA-B ANTIGENS; HLA-DR ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; MAJOR HISTOCOMPATIBILITY COMPLEX; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 67649979852     PISSN: 15216616     EISSN: 15217035     Source Type: Journal    
DOI: 10.1016/j.clim.2009.03.530     Document Type: Article

References (34)

1. Gibson J., Morton N.E., and Collins A. Extended tracts of homozygosity in outbred human populations. Hum. Mol. Genet. 15 (2006) 789-795
2. Simon-Sanchez J., Scholz S., Fung H.C., Matarin M., Hernandez D., Gibbs J.R., Britton A., de Vrieze F.W., Peckham E., Gwinn-Hardy K., Crawley A., Keen J.C., Nash J., Borgaonkar D., Hardy J., and Singleton A. Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals. Hum. Mol. Genet. 16 (2007) 1-14
3. International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861
4. Curtis D., Vine A.E., and Knight J. Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations. Ann. Hum. Genet. 72 (2008) 261-278
5. Bersaglieri T., Sabeti P.C., Patterson N., Vanderploeg T., Schaffner S.F., Drake J.A., Rhodes M., Reich D.E., and Hirschhorn J.N. Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74 (2004) 1111-1120
6. Saunders M.A., Slatkin M., Garner C., Hammer M.F., and Nachman M.W. The extent of linkage disequilibrium caused by selection on G6PD in humans. Genetics 171 (2005) 1219-1229
7. International HapMap Consortium. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
8. Awdeh Z.L., Raum D., Yunis E.J., and Alper C.A. Extended HLA/complement allele haplotypes: evidence for T/t-like complex in man. Proc. Natl Acad. Sci. U. S. A. 80 (1983) 259-263
9. Yunis E.J. 1987 Philip Levine award lecture. MHC haplotypes in biology and medicine. Am. J. Clin. Pathol. 89 (1988) 268-280
10. Degli-Esposti M.A., Leaver A.L., Christiansen F.T., Witt C.S., Abraham L.J., and Dawkins R.L. Ancestral haplotypes: conserved population MHC haplotypes. Hum. Immunol. 34 (1992) 242-252
11. Yunis E.J., Larsen C.E., Fernandez-Vina M., Awdeh Z.L., Romero T., Hansen J.A., and Alper C.A. Inheritable variable sizes of DNA stretches in the human MHC: conserved extended haplotypes and their fragments or blocks. Tissue Antigens 62 (2003) 1-20
12. Alper C.A., Larsen C.E., Dubey D.P., Awdeh Z.L., Fici D.A., and Yunis E.J. The haplotype structure of the human major histocompatibility complex. Hum. Immunol. 67 (2006) 73-84
13. Aly T.A., Eller E., Ide A., Gowan K., Babu S.R., Erlich H.A., Rewers M.J., Eisenbarth G.S., and Fain P.R. Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 55 (2006) 1265-1269
14. Bilbao J.R., Calvo B., Aransay A.M., Martin-Pagola A., Perez d.N., Aly T.A., Rica I., Vitoria J.C., Gaztambide S., Noble J., Fain P.R., Awdeh Z.L., Alper C.A., and Castano L. Conserved extended haplotypes discriminate HLA-DR3-homozygous Basque patients with type 1 diabetes mellitus and celiac disease. Genes Immun. 7 (2006) 550-554
15. Romero V., Larsen C.E., Duke-Cohan J.S., Fox E.A., Romero T., Clavijo O.P., Fici D.A., Husain Z., Almeciga I., Alford D.R., Awdeh Z.L., Zuniga J., El Dahdah L., Alper C.A., and Yunis E.J. Genetic fixity in the human major histocompatibility complex and block size diversity in the class I region including HLA-E. BMC Genet. 8 (2007) 14
16. Aly T.A., Baschal E.E., Jahromi M.M., Fernando M.S., Babu S.R., Fingerlin T.E., Kretowski A., Erlich H.A., Fain P.R., Rewers M.J., and Eisenbarth G.S. Analysis of single nucleotide polymorphisms identifies major type 1A diabetes locus telomeric of the major histocompatibility complex. Diabetes 57 (2008) 770-776
17. O'Connell J.R., and Weeks D.E. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am. J. Hum. Genet. 63 (1998) 259-266
18. Abecasis G.R., Cherny S.S., Cookson W.O., and Cardon L.R. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30 (2002) 97-101
19. Rubinstein P., Walker M., Carpenter C., Carrier C., Krassner J., Falk C., and Ginsberg F. Genetics of HLA-disease associations: the use of the haplotype relative risk (HRR) and the "haplo-delta" (Dh) estimates in juvenile diabetes from three racial groups. Hum. Immunol. 3 (1981) 384
20. Raum D., Awdeh Z., Yunis E.J., Alper C.A., and Gabbay K.H. Extended major histocompatibility complex haplotypes in type I diabetes mellitus. J. Clin. Invest. 74 (1984) 449-454
21. Thomson G. Mapping disease genes: family-based association studies. Am. J. Hum. Genet. 57 (1995) 487-498
22. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
23. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
24. Valdes A.M., Erlich H.A., and Noble J.A. Human leukocyte antigen class I B and C loci contribute to Type 1 Diabetes (T1D) susceptibility and age at T1D onset. Hum. Immunol. 66 (2005) 301-313
25. Nejentsev S., Howson J.M., Walker N.M., Szeszko J., Field S.F., Stevens H.E., Reynolds P., Hardy M., King E., Masters J., Hulme J., Maier L.M., Smyth D., Bailey R., Cooper J.D., Ribas G., Campbell R.D., Clayton D.G., and Todd J.A. Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A. Nature 450 (2007) 887-892
26. Smith W.P., Vu Q., Li S.S., Hansen J.A., Zhao L.P., and Geraghty D.E. Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 87 (2006) 561-571
27. Awdeh Z.L., Alper C.A., Eynon E., Alosco S.M., Stein R., and Yunis E.J. Unrelated individuals matched for MHC extended haplotypes and HLA-identical siblings show comparable responses in mixed lymphocyte culture. Lancet 2 (1985) 853-856
28. Fennessy M., Metcalfe K., Hitman G.A., Niven M., Biro P.A., Tuomilehto J., and Tuomilehto-Wolf E. A gene in the HLA class I region contributes to susceptibility to IDDM in the Finnish population. Childhood Diabetes in Finland (DiMe) Study Group. Diabetologia 37 (1994) 937-944
29. Noble J.A., Valdes A.M., Bugawan T.L., Apple R.J., Thomson G., and Erlich H.A. The HLA class I A locus affects susceptibility to type 1 diabetes. Hum. Immunol. 63 (2002) 657-664
30. Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., McDonald G.J., Ackerman H.C., Campbell S.J., Altshuler D., Cooper R., Kwiatkowski D., Ward R., and Lander E.S. Detecting recent positive selection in the human genome from haplotype structure. Nature 419 (2002) 832-837
31. Walsh E.C., Sabeti P., Hutcheson H.B., Fry B., Schaffner S.F., de Bakker P.I.W., Varilly P., Palma A.A., Roy J., Cooper R., Winkler C., Zeng Y., de The G., Lander E.S., O'Brien S., and Altshuler D. Searching for signals of evolutionary selection in 168 genes related to immune function. Hum. Genet. 119 (2006) 92-102
32. Jeffreys A.J., Kauppi L., and Neumann R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29 (2001) 217-222
33. Cullen M., Perfetto S.P., Klitz W., Nelson G., and Carrington M. High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am. J. Hum. Genet. 71 (2002) 759-776
34. McQuillan R., Leutenegger A.L., Abdel-Rahman R., Franklin C.S., Pericic M., Barac-Lauc L., Smolej-Narancic N., Janicijevic B., Polasek O., Tenesa A., Macleod A.K., Farrington S.M., Rudan P., Hayward C., Vitart V., Rudan I., Wild S.H., Dunlop M.G., Wright A.F., Campbell H., and Wilson J.F. Runs of homozygosity in European populations. Am. J. Hum. Genet. 83 (2008) 359-372