Human cancers are caused by the accumulation of mutations in specific genes. Technological developments have recently made it possible to analyze genetic alterations in human cancer at unprecedented scale. However, many of the key tumor suppressor genes and oncogenes responsible for cancer initiation and progression remain to be identified. During the previous project period, our group was the first to determine the sequence of the protein coding genes in any human cancer and we have completed this analysis in several tumor types. Through this work, we were able to identify candidate genes which had not been previously linked to tumorigenesis, define the basic genetic landscape of common human tumors, and point to pathways that underlie the complex genetic alterations in individual tumor types. These have included IDH genes in gliomas, PI3K pathway genes in colorectal and breast cancers, ARID1A in ovarian clear cell carcinoma, chromatin remodeling genes in medulloblastoma, and NOTCH1 in head and neck cancers. We have also used whole-genome sequencing approaches to analyze chromosomal rearrangements, copy number changes, and sequence alterations in the pediatric tumor neuroblastoma and identified rearrangements and sequence changes in the chromatin remodeling genes ARID1A and ARID1B in this tumor type. The purpose of this competitive renewal application is to use whole-genome cancer sequencing approaches to perform large-scale analyses of structural and sequence alterations in a variety of human cancers. These will include colorectal, breast, pancreatic, ovarian, brain, and head and neck tumors. Twenty four tumors of each type will be analyzed for rearrangements including those resulting from translocations, inversions, deletions, duplications and amplifications. In parallel, we will perform high resolution analyses of copy number alterations using a modification of an approach we have previously termed Digital Karyotyping. These analyses will be integrated with the sequence alterations of the protein coding genes we have already obtained in these tumor samples, thereby leveraging valuable information from the previous project period. These data will be analyzed to identify the compendium of genes and pathways enriched for genetic alterations in these tumors. Finally, we will use our recently developed personalized analysis of rearranged ends (PARE) approach to evaluate the use of tumor-specific rearrangements as personalized biomarkers for detection and monitoring of human cancers. We envision that whole-genome analyses of structural alterations in human tumors will allow us to identify genes not known to be involved in human cancer, provide insights into pathways involved in tumor initiation and progression, and allow direct translation of patient-specific genomic alterations for diagnostic analyses. The studies described in this application should lead to a greater understanding of cancer etiology, improved tools for cancer detection and diagnosis, new targets for therapeutic and preventative intervention, and opportunities for individualized detection, monitoring and treatment.