Representing genetic variation with synthetic DNA standards

The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and biases that arise during library preparation, sequencing and analysis. We have developed a set of synthetic DNA standards, termed ‘sequins’, that emulate human genetic features and constitute qualitative and quantitative spike-in controls for genome sequencing. Reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, allowing them to be partitioned for parallel analysis. Here we use this approach to represent common and clinically relevant genetic variation, ranging from single nucleotide variants to large structural rearrangements and copy number variation. We validate the design and performance of sequin standards by comparison to examples in the NA12878 reference genome and demonstrate their utility during the detection and quantification of variants. We provide sequins as a standardized, quantitative resource against which human genetic variation can be measured and diagnostic performance assessed.