A pilot GWAS in children from the BEECH study using the H3Africa chip

Purpose: Stunting is known to be heavily influenced by environmental factors, so the genetic contribution has received little attention. Here we report an exploration of genetic influences in stunted Zambian children with environmental enteropathy.
Method: Children with stunting (LAZ < -2) were enrolled and given nutritional therapy. Those that were non-responsive to therapy were designated as cases, and children with good growth (LAZ > -1) from the same community as controls. Blood and stool samples were taken to measure biomarkers of intestinal inflammation, epithelial damage, and microbial translocation. Single nucleotide polymorphism array genotyping was carried out on saliva samples using the H3Africa consortium array.
Results: Genome wide associations were analysed in 117 cases and 41 controls. While no significant associations with stunting were observed at P<5x10-8, likely due to the small sample size, interesting associations were observed at lower thresholds. SNPs ass..., , , # A pilot GWAS in children from the BEECH study using the H3Africa chip

This is a dataset from children in the BEECH study made from genotyping data using the H3Africa Consortium Array (Illumina). Full description of laboratory procedures used to derive this data are found there: 10.1371/journal.pone.0291311

## Description of the data and file structure

There are 2 file:

1. BEECH_H3Africa_Zambia.zip: This contains 3 files of the genotyped data for this study in PLINK format i.e. .bim, .bed and .fam files. These three files are used together to look at summary statistics and carry out association analysis with additional metadata.
Detailed description of these files can be found here:
In summary;

1. BEECH_H3Africa.bed: Primary representation of genotype calls at biallelic variants.
2. BEECH_H3Africa.bim: Extended variant information file accompanying a .bed binary genotype table
3. BEECH_H3Africa.fam: Sample information file accompanying a .bed binary genoty...