Agilent custom 24M 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. Agilent array CGH experiment was performed according to the manufacturer's directions on DNA extracted from lymphoblastoid cell lines. HuRef genomic DNA was co-hybridized with female sample NA15510 from the Polymorphism Discovery Resource. No replicate nor dye swap was done. The Agilent 24 million features CGH array set was designed with 23.5 million 60-mer oligonucleotide probes tiled along the NCBI Build 36 assembly.