Homo sapiens Raw sequence reads. Homo sapiens

The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and inherent biases during library preparation, sequencing and analysis. We have developed synthetic DNA standards, termed sequins, that can mirror any genetic feature in the human genome and constitute qualitative and quantitative internal controls during genome sequencing. Reads derived from the sequins align to an in silico reference chromosome that can be indexed along with natural chromosomes during alignment. We use this approach to represent common and clinically relevant variation that ranges from single nucleotide variants to large structural rearrangements. By adjusting the relative abundance of variant to reference standards, we can emulate homozygous or heterozygous genotypes and somatic mutations across a range of allele frequencies. We assess the performance of sequins / in silico chromosome in comparison to the NA12878 reference genome and demonstrate the use of sequin standards to measure and quantify variants. Finally, we provide sequins as a standardized quantitative resource against which human genetic variation can be measured.