Computational protocol: Genetic diversity of lactase persistence in East African populations

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Protocol publication

[…] To investigate the genetic diversity of lactase persistence alleles among East African populations, a total of 488 saliva samples of unrelated individuals from 12 different East-African ethnic groups from the Sudan, South Sudan and Ethiopia were collected from different geographical area in the Sudan prior to separation.The samples used in the present study were collected and studied with ethical approval and informed consent (ref. SUM/2010/7). All protocols were approved by the IRB of the Sudan Medical and Scientific Research Institute (SUMASRI) at the University of Medical Sciences and Technology in Khartoum, and were carried out in accordance with the approved guidelines.Appropriate informed consent and questionnaires were obtained from all participants before sample collection; and samples were grouped according to their self-declared ethnic background of parents and grandparents, and languages. Sample sizes, geographic origin, and linguistic affiliation for each population are reported in Table . Saliva samples were collected using OrageneTM collection kits (DNA Genotek, Ontario, Canada). The DNA isolation, purification, and genotyping were performed at Radboud University Medical Center, Nijmegen, The Netherlands, following the manufacturer’s standard protocols.All samples were genotyped for three SNPs in the MCM6 gene, which have previously been shown to regulate transcriptional activity of the LCT promoter and therefore confer tolerance to lactose (C/G-13907 (rs41525747), C/T-13910 (rs4988235) and T/G-13915 (rs41380347)) []. SNPs were genotyped using Sanger sequencing, and for C/T-13910 we additionally performed TaqMan genotyping to confirm the Sanger sequencing results. In order to compare the African samples with samples from European origin, we genotyped the MCM6 SNPs in DNA isolated from blood samples collected from 46 healthy Dutch volunteers. Isolation was performed using the Gentra Pure Gene Blood kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s protocol. Data analysis was performed using Arlequin v.3 and Genetic Data Analysis v.1.0 programs [, ]. The data set supporting the results of this article summarized in the Additional file of this article. […]

Pipeline specifications

Software tools Arlequin, GDA
Applications Population genetic analysis, GWAS
Organisms Homo sapiens
Chemicals Lactose