Core 2: Genomics

ABSTRACT The Genomics Core (Core 2) will provide support with genomics profiling and integrative bioinformatics analysis support for all the four projects, contributing towards the Program's overall goal to understand the regulatory mechanisms of the BRCA network in DNA damage repair and replication fidelity, and the maintenance of genomic integrity to suppress tumorigenesis. The Genomics Core will be led by Dr. Subhajyoti De, PhD, who is an internationally known genomics scientist with >10 years experience working in the area of cancer genomics and DNA repair. His lab is a state-of-the-art fully equipped genomic facility staffed with expert personnel specializing in genomics and bioinformatics analysis including whole genome sequencing, RNA- Seq, ChIP-Seq, ATAC-Seq, and chromatin conformation sequencing approaches. Dr. De has extensively collaborated with the principal investigators on this P01 project, as evident from shared grantsmanship and publications. Dr. Chang Chan, PhD, co-investigator on this core is also the co-leader of the Genomics Instability and Cancer Genomics program at the Rutgers Cancer Institute jointly with Dr. Shen, and has extensive collaborations with the P01 investigators. Dr. Yaqun Wang, PhD, the other co-investigator has close collaborations with the P01 investigators. The Core has generated preliminary data from the mouse tumors, identified genomic alterations, and performed initial data analysis. The specific aims of the Genomics Core (Core 2) are: 1) identify architecture of complex genomic rearrangements using genomics approaches, (ii) annotate complex chromosomal rearrangements in cancer genomes, and (iii) perform integrative bioinformatics analysis of BRCA network. Two innovative aspects of the Genomics Core are (i) usage of emerging genomic technologies to determine patterns of complex rearrangements in cancer genomes, and (ii) use both sequence and epigenomic contexts of the structural rearrangements to annotate them and predict underlying etiologies. Core 2 will be central to the preparation of all Program presentations, reports, and manuscripts that seek to understand the regulatory mechanisms of the BRCA network in replication fidelity and DNA damage repair.