Agilent custom 244K array CGH data for the HuRef individual

The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. We applied a multi-step sequence and microarray-based analysis to identify numerous previously unknown SVs within the first genome sequence reported from an individual. CGH experiments were performed with genomic DNA extracted from the HuRef and six HapMap lymphoblastoid cell lines, hybridized against the reference NA10851. A dye-swap experiment was performed for each experiment. The custom CGH microarray contains probes that target novel sequences that are not on the NCBI reference build 35. Instead, the probes target scaffold sequences that are unique to the Celera R27C assembly.