Computational protocol: A Worldwide Analysis of Beta-Defensin Copy Number Variation Suggests Recent Selection of a High-Expressing DEFB103 Gene Copy in East Asia

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Protocol publication

[…] Summary statistic calculations and analysis of variance were performed using Microsoft Excel. Principal component analysis and biplot generation was performed using R, on 54 populations where the number of samples was greater than 12. Mapping was performed using Surfer 8.0 (Golden Software, Golden, CO), FST permutation tests performed using Arlequin [Excoffier et al., ], and randomization Monte Carlo simulation tests performed using macros written using Visual Basic for Excel. Sliding window nucleotide divergence analysis was performed using DnaSP 4.0 [Rozas et al., ], with bootstrap tests for heterogeneity performed using Excel. Tree and network generation was performed using Splitstree 4.0 [Huson and Bryant, ].The genome-wide scan for single nucleotide polymorphisms SNPs associating with beta-defensin copy number and previously published RHD copy number [McCarroll et al., ] was performed on the founder CEU individuals (n = 60, 2.3 million SNPs), founder YRI individuals (n = 60, 2.6 million SNPs), and unrelated JPT/CHB samples (n = 90, 4 million SNPs) in PLINK 1.07 by linear regression under an additive model [Purcell et al., ]. P-Values were calculated in PLINK 1.07 by the Wald test and adjusted for multiple testing by a Bonferroni correction. Whole-genome SNP genotypes were downloaded from HapMap (release 23) and regional SNP association plots were generated. Pairwise LD (r2) between the selected “lead” SNP (red diamond) and neighboring HapMap SNPs were calculated using ssSNPer with the method described (http://gump.qimr.edu.au/general/daleN/ssSNPer/). CNV positions were taken from published data [Conrad et al., ], and all genome coordinates were based on hg18 (NCBI Build 36). […]

Pipeline specifications

Software tools Arlequin, DnaSP, SplitsTree, PLINK
Applications Phylogenetics, Population genetic analysis, GWAS
Organisms Pan troglodytes, Homo sapiens, Cucumber necrosis virus
Diseases Communicable Diseases
Chemicals Defensins, beta-Defensins