Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing

Abstract Background Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs), which have predominately focused on individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The more recent African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans, showed that North Africa individuals are expected to show genetic differences from previously studied African populations. Results We present single nucleotide variant (SNV) results from whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G. We provide a summary of the SNVs by genomic position, gene context and effect on protein coding. Comparison of genome-wide information of the Moroccan individuals to individuals from 1000G by principal component analysis revealed a substantial genomic distinction between the Moroccan population and sub-Saharan African populations. Conclusions We conclude that Moroccan samples lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of new SNVs and aid in functional characterisation of the genome.