Human whole genome sequencing in South Africa

Abstract

The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council's Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.

Figure 1

FastQC mean quality scores. FastQC quality scores for all seven samples were obtained. The higher the phred score, the better the base call. For all seven samples, bases for all samples were considered high quality (green). In addition, the quality scores remained consistent across the entire read length.

Figure 2

FastQC per sequence quality scores for all seven samples sequenced. All samples had universally high-quality scores.

Figure 3

FastQC per sequence GC content. The GC content for all seven samples is normally distributed.

Figure 4

Error rates of each of the samples sequenced. The error rate is calculated using mismatches per base mapped.

Figure 5

Average number of single nucleotide variants (SNVs) in all of the samples.

Figure 6

FastQC mean quality scores for Sample A. FastQC quality scores for Sample A were obtained. The quality scores are representative of those obtained from both the MGISEQ-2000 in South Africa and the BGISEQ-500 in China.