Partial Exome Resequencing of Mouse Chaos3 Mammary Tumor
Mouse Chaos3 Seqcap Exome Sequencing
Capture Array Handling    Genomic DNA libraries of ~200bp fragment size were constructed for four Chaos3 mammary tumors and one inbred C3H  WT spleen following the standard protocol of Illumina (San Diego, CA). One microgram of tumor and control library DNA was hybridized to the 385K or 720K capture array using an X1 mixer on the NimbleGen Hybridization System (Roche-NimbleGen) at 42*C for 3 days following the manufacturer's recommended conditions. Arrays were washed; then the captured molecules were eluted from the slides using a NimbleGen Elution Station according to the manufacturer's protocol.  Eluted molecules were dried by centrifugation under vacuum and amplified by LM-PCR.   Real-time PCR of eight control amplicons was performed in the pre-capture library and post-capture library to estimate the target fold enrichment.  Enriched samples were sequenced on the Illumina Genome Analyzer.
Partial Exome Resequencing  A custom mouse 5Mb Sequence Capture array (NimbleGen) was used to enrich DNA corresponding to ~1200 breast cancer candidate gene exons, followed by Illumina GAIIx sequencing.  See supplemental material for bioinformatics methods.  Mutations were validated by Sanger sequencing.