NimbleGen 42M 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. The HuRef genomic DNA (from lymphoblastoid cell line) was co-hybridized with the female sample NA15510 (from lymphoblastoid cell line) from the Polymorphism Discovery Resources. The NimbleGen platform consists of 20 NimbleGen HD2 chips, each containing 2.1M probes, and each chip is further subdivided into 3 equal-sized subarrays containing about 726K probes. The probes target the NCBI Build 36 genome, with the exception that no homology filter was applied, allowing coverage of segmentally duplicated regions.