Computational protocol: Lymphocyte Antigen 75 Polymorphisms Are Associated with Disease Susceptibility and Phenotype in Japanese Patients with Inflammatory Bowel Disease

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Protocol publication

[…] The R software Haploview version 4.2 [] was used to evaluate the haplotype structure of the 5 SNPs on LY75. Pairwise linkage disequilibrium (LD) patterns and haplotype frequency analysis for all SNPs in patients and controls were analyzed by the block definition established by Gabriel et al. []. We assessed the significance of allele distribution between patients and controls using the χ 2 test by means of 2 × 2 comparisons (df = 1). A P value of less than 0.05 was considered to be statistically significant. We adjusted P values using Bonferroni's correction (P c) by multiplication of each locus by 5. Association strength was estimated by calculating the odds ratio (OR) and 95% confidence interval (CI). Statistical analysis of findings was performed using IBM SPSS Statistics version 21.0 (IBM, New York, NY, USA) and StatFlex version 6.0 (Artech Co., Ltd. Osaka, Japan) software. […]

Pipeline specifications

Software tools Haploview, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens
Diseases Colitis, Ulcerative, Crohn Disease, Thrombasthenia, Inflammatory Bowel Diseases