Core 2: Genomics

核心 2：基因组学

基本信息

批准号：
10396614
负责人：
Subhajyoti De
金额：
$ 21.49万
依托单位：
RBHS -CANCER INSTITUTE OF NEW JERSEY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-05-01 至 2023-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10396614
关键词：
ATAC-seq Address Adopted Affect Aging Architecture Area BRCA deficient BRCA1 gene BRCA2 gene Benchmarking Bioinformatics Biological Models ChIP-seq Chromatin Chromosomal Rearrangement Collaborations Communities Complement Complex Computer software DNA Repair DNA Sequence Alteration DNA Sequence Rearrangement Data Data Analyses Defect Development Doctor of Philosophy Etiology Event Functional disorder Genome Genomic Instability Genomic approach Genomics Goals Grant High-Throughput DNA Sequencing Human Resources Hybrids Impairment Inherited Institutes International Maintenance Malignant Neoplasms Mammary Neoplasms Manuscripts Mediating Molecular Biology Molecular Conformation Molecular Target Mus Mutagenesis Mutation Nuclear Nucleotides Optics Pathway interactions Patients Pattern Play Point Mutation Practice Guidelines Preparation Principal Investigator Process Publications Repetitive Sequence Reporting Research Personnel Role Scientist Somatic Mutation Technology Tumor-Derived Work analysis pipeline bioinformatics pipeline bioinformatics resource brca gene cancer genome cancer genomics cancer initiation chromothripsis computer framework computerized data processing epigenomics experience gene complementation gene network genome integrity genome sequencing genomic data innovation insight mutant programs repaired targeted treatment transcriptome sequencing treatment response tumor tumor progression tumorigenesis whole genome

项目摘要

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.

抽象的基因组学核心（核心 2）将提供基因组学分析和综合生物信息学支持为所有四个项目提供分析支持，有助于实现该计划的总体目标，即了解 BRCA 网络在 DNA 损伤修复和复制保真度方面的调节机制，以及维持基因组完整性以抑制肿瘤发生。基因组学核心将由 Subhajyoti 博士领导 De 博士，国际知名基因组学科学家，在该领域拥有超过 10 年的工作经验癌症基因组学和 DNA 修复。他的实验室是一个设备齐全的最先进的基因组设施，配备了专家专门从事基因组学和生物信息学分析的人员，包括全基因组测序、RNA- Seq、ChIP-Seq、ATAC-Seq 和染色质构象测序方法。德博士广泛与该 P01 项目的主要研究人员合作，从共同的资助和出版物。 Chang Chan 博士是该核心的联合研究员，也是 Genomics 的联合负责人罗格斯大学癌症研究所与沉博士联合开展的不稳定性和癌症基因组学项目，并已与 P01 研究人员的广泛合作。另一位共同研究员王亚群博士已接近完成与 P01 调查员的合作。核心已经从小鼠肿瘤中生成了初步数据，识别基因组改变，并进行初步数据分析。基因组学核心的具体目标（核心 2）是：1）使用基因组学方法识别复杂基因组重排的架构，（ii）注释癌症基因组中复杂的染色体重排，以及（iii）进行整合 BRCA网络的生物信息学分析。基因组学核心的两个创新方面是 (i) 使用新兴的基因组技术，用于确定癌症基因组中复杂重排的模式，以及（ii）使用结构重排的序列和表观基因组背景来注释它们并预测潜在的病因。核心 2 将成为所有计划演示、报告和准备的核心试图了解 BRCA 网络在复制保真度和 DNA损伤修复。