Genome Center for Alzheimer's Disease (GCAD)

阿尔茨海默病基因组中心 (GCAD)

基本信息

批准号：
10604370
负责人：
GERARD DAVID SCHELLENBERG
金额：
$ 397.33万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-04-15 至 2026-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10604370
关键词：
ATAC-seq Abbreviations Affect African American population Age Alleles Alzheimer&apos s Disease Alzheimer&apos s disease related dementia Alzheimer&apos s disease risk Artificial Intelligence Asian population Award Benchmarking Calibration Caregivers Caribbean Hispanic Cells ChIP-seq Clinical Cognitive Collection Communities Computer software Copy Number Polymorphism Data Data Analyses Data Collection Data Set Disease Documentation Drug Targeting Elderly Environment Epigenetic Process Equilibrium Ethnic Population European Fostering Frontotemporal Dementia Funding Genes Genetic Genetic Annotation Genetic Diseases Genome Genomics Goals Grant Hi-C Individual Infrastructure International LGR5 gene Lewy Body Dementia Machine Learning Maps Methods Methylation Molecular Conformation National Heart, Lung, and Blood Institute National Human Genome Research Institute National Institute on Aging Not Hispanic or Latino Parkinson&apos s Dementia Pathway interactions Patients Persons Phase Precision Medicine Initiative Predisposition Prevention Process Progressive Supranuclear Palsy Proteomics Public Health Quality Control Research Research Personnel Resources Risk Factors Sampling Scientist Sequence Alignment Single Nucleotide Polymorphism Source Systems Analysis Trans-Omics for Precision Medicine United States Variant Work candidate identification cognitive system collaborative environment computer code computing resources corticobasal degeneration data repository deep learning deep neural network drug candidate exome exome sequencing file format functional genomics gene network genetic variant genome analysis genome wide association study genome-wide linkage genomic data insertion/deletion mutation learning network metabolomics neural network novel therapeutic intervention phenotypic data prevent programs quality assurance reference genome therapeutic candidate therapeutic target trait transcriptome sequencing whole genome

项目摘要

Overall Project Summary Alzheimer’s disease (AD) affects 5.8 million people in the United States, and is an immense burden on patients, caregivers and on the economy. No disease-modifying treatments or preventions exist, and we need better understanding of the disease and new therapeutic strategies. Genetic discoveries are one source of candidate therapeutic targets. One source of genetic targets is the Alzheimer’s Disease Sequencing Project (ADSP), a National Institute on Aging (NIA) initiative since 2012 to sequence genomes and exomes of AD subjects and cognitively normal elderly controls. The Genome Center for Alzheimer’s Disease (GCAD) is the analysis coordinating center for the ADSP. In the previous grant cycle, GCAD processed all AD-relevant sequencing data producing harmonized genetic data for AD research. This renewal responds to the increase in the amount and complexity of ADSP sequence data, the collection of new types of data, and an expansion of the types of analysis being performed. In addition to sequence data, GCAD will harmonize functional genomics data. GCAD will provide fully quality-controlled and annotated genetic and functional genomics data that is analysis ready. In addition to AD, GCAD will also work with data for AD related disorders (ADRD). These include frontotemporal dementias (FTDs), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), Lewy body dementia (LBD), and Parkinson’s disease with dementia (PD-d). In the Y6-10 funding period, GCAD will assemble and harmonize whole-genome/whole-exome sequencing data, and provide it to ADSP investigators and the general scientific community. GCAD will work with US and non-US groups to analyze data by fostering a collaborative environment, and providing infrastructure support. GCAD will also assemble and harmonize functional genomics data which will be integral to identifying genes as candidate drug targets. The research plan will lead to a high quality, comprehensive, harmonized collection of genetic and functional data with detailed supporting resources including documentation and optimized computer codes. This resource will be invaluable for the entire AD research community.

总体项目摘要阿尔茨海默氏病（AD）在美国影响580万人，这是一个巨大的对患者，看护人和经济负担的负担。没有改良疾病的治疗或存在预防，我们需要更好地了解该疾病和新疗法策略。遗传发现是候选治疗靶点的来源。一个来源遗传目标是阿尔茨海默氏病测序项目（ADSP），美国国家研究所自2012年以来，衰老（NIA）倡议序列的AD受试者的基因组和外部认知正常的较早对照。阿尔茨海默氏病基因组中心（GCAD）是分析协调中心 adsp。在上一个赠款周期中，GCAD处理了所有与广告相关的测序数据生产用于AD研究的统一遗传数据。这种更新对数量增加的响应 ADSP序列数据的复杂性，新类型数据的收集以及扩展进行的分析类型。除序列数据外，GCAD还将和谐功能基因组学数据。 GCAD将提供完全质量控制和注释的遗传和已准备好分析的功能基因组数据。除了广告外，GCAD还将与广告相关疾病的数据（ADRD）。这些包括额颞痴呆（FTD），进行性上腹部麻痹（PSP），皮质型变性（CBD），Lewy身体痴呆症（LBD）和患有痴呆症（PD-D）的帕金森氏病。在Y6-10的资金期间，GCAD将组装和协调全基因组/全基因组对数据进行测序，并将其提供给ADSP研究人员和一般科学界。 GCAD将与我们和非US组合作，通过促进协作来分析数据环境，并提供基础设施支持。 GCAD还将组装和协调功能基因组学数据将是将基因识别为候选药物靶标的不可或缺的一部分。该研究计划将导致高质量，全面，统一的通用收集以及具有详细支持资源的功能数据，包括文档和优化计算机代码。该资源对于整个广告研究界将是无价的。

项目成果

期刊论文数量（17）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations.

DOI：
10.1016/j.xhgg.2023.100207
发表时间：
2023-07-13
期刊：
HUMAN GENETICS AND GENOMICS ADVANCES
影响因子：
0
作者：
Horimoto, Andrea R. V. R.;Boyken, Lisa A.;Blue, Elizabeth E.;Grinde, Kelsey E.;Nafikov, Rafael A.;Sohi, Harkirat K.;Nato, Alejandro Q.;Bis, Joshua C.;Brusco, Luis I.;Morelli, Laura;Ramirez, Alfredo;Dalmasso, Maria Carolina;Temple, Seth;Satizabal, Claudia;Browning, Sharon R.;Seshadri, Sudha;Wijsman, Ellen M.;Thornton, Timothy A.
通讯作者：
Thornton, Timothy A.

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.

SparkINFERNO：一个可扩展的高通量管道，用于推断非编码遗传变异的分子机制。

DOI：
10.1093/bioinformatics/btaa246
发表时间：
2020
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Kuksa,PavelP;Lee,Chien-Yueh;Amlie-Wolf,Alexandre;Gangadharan,Prabhakaran;Mlynarski,ElizabethE;Chou,Yi-Fan;Lin,Han-Jen;Issen,Heather;Greenfest-Allen,Emily;Valladares,Otto;Leung,YukYee;Wang,Li-San
通讯作者：
Wang,Li-San

Packaging Biocomputing Software to Maximize Distribution and Reuse.

打包生物计算软件以最大化分发和再利用。

DOI：
发表时间：
2020
期刊：
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
影响因子：
0
作者：
Bush,WilliamS;Wheeler,Nicholas;Beaulieu-Jones,Brett;Darabos,Christian
通讯作者：
Darabos,Christian

ODACH: a one-shot distributed algorithm for Cox model with heterogeneous multi-center data.

DOI：
10.1038/s41598-022-09069-0
发表时间：
2022-04-22
期刊：
SCIENTIFIC REPORTS
影响因子：
4.6
作者：
Luo, Chongliang;Duan, Rui;Naj, Adam C.;Kranzler, Henry R.;Bian, Jiang;Chen, Yong
通讯作者：
Chen, Yong

FILER: a framework for harmonizing and querying large-scale functional genomics knowledge.

DOI：
10.1093/nargab/lqab123
发表时间：
2022-03
期刊：
NAR genomics and bioinformatics
影响因子：
4.6
作者：
Kuksa PP;Leung YY;Gangadharan P;Katanic Z;Kleidermacher L;Amlie-Wolf A;Lee CY;Qu L;Greenfest-Allen E;Valladares O;Wang LS
通讯作者：
Wang LS