Genomic DNA was extracted from peripheral blood lymphocytes using standard protocols, and ten micrograms of DNA from each of four individuals with Miller syndrome in kindred’s 1, 2, and 3 was used for construction of a shotgun sequencing library as described previously2 using adaptors for single-end sequencing on an Illumina Genome Analyzer II (GAII). Each shotgun library was hybridized to two Agilent 244K microarrays for target enrichment, followed by washing, elution and additional amplification2. The first array targeted CCDS (2007), while the second was designed against targets poorly captured by the first array plus updates to CCDS in 2008. Enriched libraries were then sequenced on a GAII.
