Core 2: Genomics

核心 2：基因组学

• 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
• 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

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.

摘要 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， BRCA网络在DNA损伤修复和复制保真度中的调节机制，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博士是一位国际知名的基因组学科学家，在基因组学领域拥有超过10年的工作经验。 癌症基因组学和DNA修复。他的实验室是最先进的设备齐全的基因组设施， 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。德博士广泛地 在这个P01项目上与主要研究者合作，从共享的花岗岩和 出版物。Chang Chan博士是该核心的共同研究者，也是基因组学的共同领导者。 不稳定和癌症基因组学项目在罗格斯大学癌症研究所与沈博士联合， 与P01研究人员进行了广泛的合作。另一位合作研究者王亚群博士 与P01研究人员合作。核心已经从小鼠肿瘤中产生了初步数据， 鉴定基因组改变，并进行初始数据分析。基因组学核心的具体目标 (Core 2）是：1）使用基因组学方法鉴定复杂基因组重排的结构，（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 确定癌症基因组中复杂重排模式的新兴基因组技术，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 潜在病因。核心2将是所有计划演示文稿、报告和 试图了解BRCA网络在复制保真度方面的调控机制的手稿， DNA损伤修复