title: Representing genetic variation with synthetic DNA standards.
abstract: The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and by 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. Sequencing reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, which allows them 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 we 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.
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.|School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, New South Wales, Australia.
authors: Ira W
authors: IW
authors: Deveson
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.|St. Vincents Clinical School, Faculty of Medicine, The University of New South Wales, New South Wales, Australia.
authors: Wendy Y
authors: WY
authors: Chen
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.
authors: Ted
authors: T
authors: Wong
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.|St. Vincents Clinical School, Faculty of Medicine, The University of New South Wales, New South Wales, Australia.
authors: Simon A
authors: SA
authors: Hardwick
authors: Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Queensland, Australia.
authors: Stacey B
authors: SB
authors: Andersen
authors: Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Queensland, Australia.
authors: Lars K
authors: 0000-0001-8191-3511
authors: LK
authors: Nielsen
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.|St. Vincents Clinical School, Faculty of Medicine, The University of New South Wales, New South Wales, Australia.
authors: John S
authors: 0000-0002-7680-7527
authors: JS
authors: Mattick
authors: Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.|St. Vincents Clinical School, Faculty of Medicine, The University of New South Wales, New South Wales, Australia.
authors: Tim R
authors: TR
authors: Mercer
mesh_terms: D022201:Chromosomes, Artificial / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics*; D056915:DNA Copy Number Variations; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards
chemical_list: D004247:DNA