The dichotomy between disease phenotype databases and the implications for understanding complex diseases involving the major histocompatibility complex

International Journal of Immunogenetics

Volumn 42, Issue 6, 2015, Pages 413-422

  Clark, P M ^a   Kunkel, M ^a   Monos, D S ^a,b  

^a CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APC PROTEIN; BETA CATENIN; FIBRILLIN 1; GLYCOGEN SYNTHASE KINASE 3; MAJOR HISTOCOMPATIBILITY ANTIGEN; WNT PROTEIN;

ENZYME PHOSPHORYLATION; EXOME; GENE MUTATION; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; IMMUNOGENETICS; IMMUNOPATHOLOGY; MAJOR HISTOCOMPATIBILITY COMPLEX; MONOGENIC DISORDER; NEXT GENERATION SEQUENCING; PHENOTYPE; PRIORITY JOURNAL; RARE DISEASE; REVIEW; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOMAL MAPPING; DISEASE PREDISPOSITION; GENETIC ASSOCIATION STUDY; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; IMMUNOLOGY; MUTATION;

CHROMOSOME MAPPING; DATABASES, GENETIC; DISEASE SUSCEPTIBILITY; GENETIC ASSOCIATION STUDIES; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; MUTATION; PHENOTYPE;

EID: 84946405803     PISSN: 17443121     EISSN: 1744313X     Source Type: Journal    
DOI: 10.1111/iji.12236     Document Type: Review

References (39)

1. de Bakker, P.I. & Raychaudhuri, S. (2012) Interrogating the major histocompatibility complex with high-throughput genomics. Human Molecular Genetics, 21, R29.
2. Becker, K.G., Barnes, K.C., Bright, T.J. & Wang, S.A. (2004) The genetic association database. Nature Genetics, 36, 431.
3. Browning, S.R. & Browning, B.L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. American Journal of Human Genetics, 81, 1084.
4. Chang, A.L., Raber, I., Xu, J., Li, R., Spitale, R., Chen, J. et al. (2015) Assessment of the genetic basis of rosacea by genome-wide association study. The Journal of Investigative Dermatology, 135, 1548.
5. Dilthey, A.T., Moutsianas, L., Leslie, S. & McVean, G. (2011) HLA*IMP-an integrated framework for imputing classical HLA alleles from SNP genotypes. Bioinformatics, 27, 968.
6. Dilthey, A., Leslie, S., Moutsianas, L., Shen, J., Cox, C., Nelson, M.R. & McVean, G. (2013) Multi-population classical HLA type imputation. PLoS Computational Biology, 9, e1002877.
7. Handunnetthi, L., Ramagopalan, S.V., Ebers, G.C. & Knight, J.C. (2010) Regulation of major histocompatibility complex class II gene expression, genetic variation and disease. Genes and Immunity, 11, 99.
8. Hanson, C.A. & Miller, J.R. (2005) Non-traditional roles for the Adenomatous Polyposis Coli (APC) tumor suppressor protein. Gene, 361, 1.
9. Horton, R., Wilming, L., Rand, V., Lovering, R.C., Bruford, E.A., Khodiyar, V.K. et al. (2004) Gene map of the extended human MHC. Nature Reviews Genetics, 5, 889.
10. Inoki, K., Ouyang, H., Zhu, T., Lindvall, C., Wang, Y., Zhang, X. et al. (2006) TSC2 integrates Wnt and energy signals via a coordinated phosphorylation by AMPK and GSK3 to regulate cell growth. Cell, 126, 955.
11. Ioannidis, J.P., Thomas, G. & Daly, M.J. (2009) Validating, augmenting and refining genome-wide association signals. Nature Reviews Genetics, 10, 318.
12. Kiezun, A., Garimella, K., Do, R., Stitziel, N.O., Neale, B.M., McLaren, P.J. et al. (2012) Exome sequencing and the genetic basis of complex traits. Nature Genetics, 44, 623.
13. Klitz, W., Hedrick, P. & Louis, E.J. (2012) New reservoirs of HLA alleles: pools of rare variants enhance immune defense. Trends in Genetics, 28, 480.
14. Kulkarni, S., Savan, R., Qi, Y., Gao, X., Yuki, Y., Bass, S.E. et al. (2011) Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature, 472, 495.
15. Kumanovics, A., Takada, T. & Lindahl, K.F. (2003) Genomic organization of the mammalian MHC. Annual Review of Immunology, 21, 629.
16. Landrum, M.J., Lee, J.M., Riley, G.R., Jang, W., Rubinstein, W.S., Church, D.M. & Maglott, D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42, D980.
17. Lessard, C.J., Li, H., Adrianto, I., Ice, J.A., Rasmussen, A., Grundahl, K.M. et al. (2013) Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjogren's syndrome. Nature Genetics, 45, 1284.
18. Levin, A.M., Adrianto, I., Datta, I., Iannuzzi, M.C., Trudeau, S., McKeigue, P., Montgomery, C.G. & Rybicki, B.A. (2014) Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and -DPB1. BMC Genetics, 15, 72.
19. Martin, M.P., Qi, Y., Gao, X., Yamada, E., Martin, J.N., Pereyra, F. et al. (2007) Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1. Nature Genetics, 39, 733.
20. Miretti, M.M., Walsh, E.C., Ke, X., Delgado, M., Griffiths, M., Hunt, S. et al. (2005) A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. American Journal of Human Genetics, 76, 634.
21. Mitsunaga, S., Suzuki, Y., Kuwana, M., Sato, S., Kaneko, Y., Homma, Y. et al. (2012) Associations between six classical HLA loci and rheumatoid arthritis: a comprehensive analysis. Tissue Antigens, 80, 16.
22. Ollila, H.M., Ravel, J.M., Han, F., Faraco, J., Lin, L., Zheng, X. et al. (2015) HLA-DPB1 and HLA class I confer risk of and protection from narcolepsy. American Journal of Human Genetics, 96, 136.
23. Ozcan, U., Ozcan, L., Yilmaz, E., Duvel, K., Sahin, M., Manning, B.D. & Hotamisligil, G.S. (2008) Loss of the tuberous sclerosis complex tumor suppressors triggers the unfolded protein response to regulate insulin signaling and apoptosis. Molecular Cell, 29, 541.
24. Parkes, M., Cortes, A., van Heel, D.A. & Brown, M.A. (2013) Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nature Reviews Genetics, 14, 661.
25. Peiffer, D.A. & Gunderson, K.L. (2009) Design of tag SNP whole genome genotyping arrays. Methods in Molecular Biology, 529, 51.
26. Petersdorf, E.W., Malkki, M., Gooley, T.A., Martin, P.J. & Guo, Z. (2007) MHC haplotype matching for unrelated hematopoietic cell transplantation. PLoS Medicine, 4, e8.
27. Petersdorf, E.W., Malkki, M., Horowitz, M.M., Spellman, S.R., Haagenson, M.D. & Wang, T. (2013) Mapping MHC haplotype effects in unrelated donor hematopoietic cell transplantation. Blood, 121, 1896.
28. Reith, W. & Mach, B. (2001) The bare lymphocyte syndrome and the regulation of MHC expression. Annual Review of Immunology, 19, 331.
29. Rosenfeld, J.A., Mason, C.E. & Smith, T.M. (2012) Limitations of the human reference genome for personalized genomics. PLoS ONE, 7, e40294.
30. Sanchez-Mazas, A. & Meyer, D. (2014) The relevance of HLA sequencing in population genetics studies. Journal of Immunology Research, 2014, 971818.
31. Sansom, O.J., Meniel, V.S., Muncan, V., Phesse, T.J., Wilkins, J.A., Reed, K.R., Vass, J.K., Athineos, D., Clevers, H. & Clarke, A.R. (2007) Myc deletion rescues Apc deficiency in the small intestine. Nature, 446, 676.
32. Shiina, T., Hosomichi, K., Inoko, H. & Kulski, J.K. (2009) The HLA genomic loci map: expression, interaction, diversity and disease. Journal of Human Genetics, 54, 15.
33. Stenson, P.D., Ball, E.V., Mort, M., Phillips, A.D., Shaw, K. & Cooper, D.N. (2012) The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Curr Protoc Bioinformatics, Chapter 1: Unit1.13.
34. Stenzel, A., Lu, T., Koch, W.A., Hampe, J., Guenther, S.M., De La Vega, F.M., Krawczak, M. & Schreiber, S. (2004)Patterns of linkage disequilibrium in the MHC region on human chromosome 6p. Human Genetics, 114, 377.
35. Stewart, C.A., Horton, R., Allcock, R.J., Ashurst, J.L., Atrazhev, A.M., Coggill, P. et al. (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Research, 14, 1176.
36. The MHC Sequencing Consortium (1999) Complete sequence and gene map of a human major histocompatibility complex. Nature, 401, 921.
37. Vandiedonck, C., Taylor, M.S., Lockstone, H.E., Plant, K., Taylor, J.M., Durrant, C., Broxholme, J., Fairfax, B.P. & Knight, J.C. (2011) Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex. Genome Research, 21, 1042.
38. Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Research, 42, D1001.
39. Zheng, X., Shen, J., Cox, C., Wakefield, J.C., Ehm, M.G., Nelson, M.R. & Weir, B.S. (2014) HIBAG-HLA genotype imputation with attribute bagging. The Pharmacogenomics Journal, 14, 192.