Hybridization of single-cell WGA products to DNA microarrays or SNP arrays allows uncovering copy number changes in the cell. SNP arrays provide

a distinct advantage as copy number calls can be integrated with B allele fractions of SNPs and with genotype calls [31], thus also allowing the discovery of copy neutral LOH changes in a cell [32 and 33], or even to haplotype its entire genome [34 and 35]. Despite the use of ultra-high resolution array platforms and the development of state-of-the-art computational and statistical Androgen Receptor Antagonist order methods, the majority of array-based methods can only reliably detect copy number changes encompassing millions of bases in a solitary cell [36, 37, 38• and 39]. The main difficulty is to distinguish a genuine copy number change from a local allelic WGA artefact due to %GC-bias, ADO or VX-809 in vitro PA events [28]. In addition, the cell-cycle stage of the isolated cell can complicate the analysis as cells in S phase can have 2, 3 or 4 copies for a diploid locus, leading to false

structural DNA-imbalance discoveries [40]. Remarkably, a recent study reported the detection of copy number alterations as small as 56 kb in single-cell PCR WGA products hybridized to 180 K oligo-arrays [41]. Array profiling of single cells has been applied to study the biology of CTCs [42••] and DTCs [38• and 39]. Heitzer et al. used the technology to profile genetic relationships between primary colorectal

carcinomas, metastases and CTCs derived from the same patients [ 42••]. Although CTCs shared a number of gains and losses with the primary tumour and/or the metastasis, interestingly, they also observed private copy number changes in CTCs as well as heterogeneity between CTCs. Such results are paving the way for using CTCs as a liquid biopsy to guide clinical decision-making. Decitabine Sequencing of single-cell WGA-products recently improved the resolution of a cell’s DNA-copy number profile by algorithmic focal sequence-read depth analyses [16, 17••, 27•• and 43] (Figure 3b). Ni et al. [ 44••] demonstrated that copy number aberration patterns of CTCs in different patients with the same lung cancer subtype can be extraordinarily similar, but dissimilar when compared to copy number landscapes of CTCs in patients with different lung cancer subtypes, and thus be of diagnostic significance. Furthermore, driven to understand intra-tumour cell population structure and genome evolution in breast cancer, Navin and colleagues [ 16 and 17••] developed single-nucleus sequencing for copy number profiling of single cancer cells able to detect alterations with a resolution of 54 kb on average. By phylogenetic analyses, they could infer common ancestors, clonal expansions and divergence of subpopulations. Genome-wide profiling of structural variation in a single cell is still in its infancy.