For the exome sequence, slightly fewer reads were aligned independently of their mate-pair than for whole-exome sequencing, perhaps suggesting that rearrangements within the coding region occurred less frequently in Capan-1 than in non-genic regions . Sequence depth across the LDK378 genome was compared to data generated by array comparative genomic hybridization . Generally the median depth for each chromosome identified by Masitinib citations sequencing matched the copy number profile generated by aCGH . For example, chromosomes such as 4 and 6, that by aCGH appeared to be present in two copies, predominantly showed even depth across their whole length. In addition, the single copy X chromosome returned approximately half the number of reads of chromosomes 4 and 6. The previously reported homozygous deletion of 9p21 involving CDKN2A, and loss of the majority of chromosome Y, were also confirmed by sequencing . To identify candidate structural rearrangements, we analysed the whole genome sequence of Capan-1 using BreakDancer . We used a stringent filtering method that only identified rearrangements supported by at least ten reads . This approach identified 354 large structural variations in Capan-1, which were sub-classified as intrachromosomal deletions, insertions, inversions, or interchromosomal direct or inverted translocations . No insertions were detected in this analysis, as they all fell within the boundaries of normal fragment size distribution . Given that Capan-1 is a BRCA2 deficient model, we investigated the possibility that medium depth, whole genome sequencing could be used to distinguish BRCA1 and BRCA2 deficient tumours from non-familial forms. To date, two BRCA2 deficient tumours, two BRCA1 deficient tumours, and two BRCA1 deficient cell lines have also been subjected to mediumdepth whole genome sequencing, as part of a wider study of primary breast tumours and cell lines . We obtained the raw data from this study , and processed it through our own pipeline, which included analysis with BreakDancer. In this way, we were able to directly compare the frequency and type of structural rearrangements identified in Capan-1 with both BRCA deficient and proficient primary breast tumours and cell lines . Of all the genomes studied, Capan-1 exhibited the most structural rearrangements, both inter- and intrachromosomal .