Analytical methods for disease association studies with immunogenetic data.

Disease association studies involving highly polymorphic immunogenetic data may involve analyses at one or many units of analysis, including amino acid, allele, genotype and haplotype levels, as well as consideration of gene-gene or gene-environment interactions. The selection of the appropriate statistical tests is critical and will be dependent on the nature of the dataset (e.g., case-control vs. family data) as well as the specific research hypotheses being tested. This paper describes the various study and analysis categories used for such analyses, including the advantages and limitations of such techniques.

[1]  C. Falk,et al.  Haplotype relative risks: an easy reliable way to construct a proper control sample for risk calculations , 1987, Annals of human genetics.

[2]  Steven J Mack,et al.  Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. , 2008, Human immunology.

[3]  C. Hurley,et al.  Diversity is demonstrated in class I HLA-A and HLA-B alleles in Cameroon, Africa: description of HLA-A*03012, *2612, *3006 and HLA-B*1403, *4016, *4703. , 2000, Tissue antigens.

[4]  D J Schaid,et al.  Comparison of statistics for candidate-gene association studies using cases and parents. , 1994, American journal of human genetics.

[5]  H. Erlich,et al.  Genetic origin of the Swedish Sami inferred from HLA class I and class II allele frequencies , 2008, European Journal of Human Genetics.

[6]  H. Volk,et al.  KIR/HLA Ligand Incompatibility in Kidney Transplantation , 2007, Transplantation.

[7]  E. S. Pearson,et al.  THE USE OF CONFIDENCE OR FIDUCIAL LIMITS ILLUSTRATED IN THE CASE OF THE BINOMIAL , 1934 .

[8]  G. Thomson,et al.  HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population. , 2007, Tissue antigens.

[9]  G. Thomson.  AGFAP Method: Applicability under different ascertainment schemes and a parental contributions test , 1993, Genetic epidemiology.

[10]  S. Hiby,et al.  How Does the maternal immune system contribute to the development of pre-eclampsia? , 2007, Placenta.

[11]  C. Hurley,et al.  HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. , 2009, Tissue antigens.

[12]  W. Klitz,et al.  HLA diversity, differentiation, and haplotype evolution in Mesoamerican Natives. , 2001, Human immunology.

[13]  H. Erlich,et al.  HLA class II polymorphism in the Ticuna of Brazil: evolutionary implications of the DRB1*0807 allele. , 1998, Tissue antigens.

[14]  L. Field.  Non-HLA region genes in insulin dependent diabetes mellitus. , 1991, Bailliere's clinical endocrinology and metabolism.

[15]  T. Bergström,et al.  Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism. , 1999, American journal of human genetics.

[16]  T. Beaty,et al.  Applications of the case-control method in genetic epidemiology. , 1994, Epidemiologic reviews.

[17]  C. Moore,et al.  Killer immunoglobulin-like receptors and HLA act both independently and synergistically to modify HIV disease progression , 2005, Genes and Immunity.

[18]  M. Gedil,et al.  KIR3DL2: diversity in a hematopoietic stem cell transplant population. , 2007, Tissue antigens.

[19]  M. Crawford,et al.  Genetic variation among the Golla pastoral caste subdivisions of Andhra Pradesh, India, according to the HLA system. , 2001, Human immunology.

[20]  S. Forman,et al.  Killer Ig-like receptor (KIR) compatibility plays a role in the prevalence of acute GVHD in unrelated hematopoietic cell transplants for AML , 2005, Bone Marrow Transplantation.

[21]  H. Erlich,et al.  HLA antigens, alleles and haplotypes among the Yup'ik Alaska natives: report of the ASHI Minority Workshops, Part II. , 2002, Human immunology.

[22]  Richard H. Scheuermann,et al.  Departments of Pathology and , 2022 .

[23]  Richard M. Single,et al.  Signatures of Demographic History and Natural Selection in the Human Major Histocompatibility Complex Loci , 2006, Genetics.

[24]  S. Khakoo,et al.  Hanging in the balance: KIR and their role in disease , 2005 .

[25]  C. Nechemias,et al.  HLA antigens and islet cell antibodies in gestational diabetes. , 1981, Human immunology.

[26]  L. Lanier.  Natural killer cells fertile with receptors for HLA-G? , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[27]  M. Greaves,et al.  JC and BK virus sequences are not detectable in leukaemic samples from children with common acute lymphoblastic leukaemia , 1999, British Journal of Cancer.

[28]  Mary Carrington,et al.  KIR and disease: a model system or system of models? , 2006, Immunological reviews.

[29]  G. Thomson.  Mapping disease genes: family-based association studies. , 1995, American journal of human genetics.

[30]  A. Valdés,et al.  Conditional genotype analysis: detecting secondary disease loci in linkage disequilibrium with a primary disease locus. , 2007 .

[31]  Salim I. Khakoo,et al.  HLA and NK Cell Inhibitory Receptor Genes in Resolving Hepatitis C Virus Infection , 2004, Science.

[32]  M. Stoneking,et al.  Evolution of Pacific/Asian populations inferred from HLA class II allele frequency distributions. , 2000, Tissue antigens.

[33]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[34]  K. Cao,et al.  Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. , 2001, Human immunology.

[35]  Carl D Langefeld,et al.  Juvenile idiopathic arthritis and HLA class I and class II interactions and age-at-onset effects. , 2010, Arthritis and rheumatism.

[36]  W. Klitz,et al.  HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. , 2007, Tissue antigens.

[37]  P. Bingley,et al.  Relative predispositional effects of HLA class II DRB1-DQB1 haplotypes and genotypes on type 1 diabetes: a meta-analysis. , 2007, Tissue antigens.

[38]  Anna Genell,et al.  Bias in odds ratios by logistic regression modelling and sample size , 2009, BMC medical research methodology.

[39]  T. Bergström,et al.  HLA class II alleles in Amerindian populations: implications for the evolution of HLA polymorphism and the colonization of the Americas. , 2004, Hereditas.

[40]  K. Taylor,et al.  Susceptibility to Crohn’s disease is mediated by KIR2DL2/KIR2DL3 heterozygosity and the HLA-C ligand , 2009, Immunogenetics.

[41]  M. Stoneking,et al.  Genetic variability and linkage disequilibrium within the HLA-DP region: analysis of 15 different populations. , 2001, Tissue antigens.

[42]  J. Knight,et al.  The human Major Histocompatibility Complex as a paradigm in genomics research. , 2009, Briefings in functional genomics & proteomics.

[43]  C. Hurley,et al.  HLA haplotypes in Singapore: a study of mothers and their cord blood units. , 2007, Human immunology.

[44]  G. Thomson.  Analysis of complex human genetic traits: an ordered-notation method and new tests for mode of inheritance. , 1995, American journal of human genetics.

[45]  W. Klitz,et al.  Association of HLA class I and II alleles and extended haplotypes with nasopharyngeal carcinoma in Taiwan. , 2002, Journal of the National Cancer Institute.

[46]  J. Orange,et al.  Natural killer cells inhibit hepatitis C virus expression , 2004, Journal of leukocyte biology.