title: DNaseq of C-HAC: huam artifical chromosome
design: DNA for sequencing was isolated using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA) and sheared with the Biorupter Next Gen UCD-300 sonicator (Diagenode, Lie_ge, Belgium). TruSeq DNA sequencing libraries (Illumina, San Diego, CA, USA) were generated according to manufacturer instructions. To detect structural variants, we performed split-read and discordant read-pair analysis. In brief, paired-end sequences were mapped with BWA-MEM (http://arxiv.org/abs/1303.3997), enabling the detection of split reads. Since C-HAC segregates in a hamster cell line, the reads were mapped to a synthetic reference genome that consists of the human reference genome (GRCh37; hg19), the hamster reference genome (criGri1) and in-house nucleotide sequences of alphaSAT20 and of the constructs Neo-loxP-3HPRT1, TEL08-cBAp-BLAS- loxP and TEL08-SV40-DNA-5HPRT-loxP. As the L-HAC passaged through both hamster and mouse genetic backgrounds, its reads were mapped to the same synthetic reference genome expanded with the mouse reference genome (mm10). Following mapping, PCR duplicates were removed using Picard, and split reads were identified.