Optimization of Nanopore Genomic DNA Sequencing
Optimization of Nanopore Genomic DNA Sequencing
批准号:
8901265
负责人:
MARK A AKESON
金额:
$72.9万
依托单位国家:
美国
项目类别:
财政年份:
2014
资助国家:
美国
项目状态:
已结题
起止时间:
2014-08-01 至 2017-06-30
关键词:
Animal ModelArabidopsisBasic ScienceBiologicalCell NucleusCellsCommunitiesComputing MethodologiesCpG dinucleotideCytosineDNADNA DamageDNA ResequencingDNA SequenceDevelopmentDevicesEnzymesEpigenetic ProcessEscherichia coliGenomic DNAGoalsHealthHealthcareHeterogeneityHumanIndividualLengthLibrariesMalignant NeoplasmsMeasurableMedical ResearchMethodsMethylationModificationMotorMusNoiseNucleotidesOrganismProteinsReadingReference StandardsRegenerative MedicineReportingResearchSystemTechniquesTechnologyTestingTimeTouch sensationbasebiophysical propertiesdesignhelicaseimprovedmotor controlmutantnanoporenanoscalenucleobasesensorsingle molecule
中文摘要
描述(由申请人提供):该提案涉及基因组DNA片段单分子测序的酶,孔和计算方法的优化。它是基于我们在UCSC的团队实现的一个成熟的纳米孔设备。该装置由一个传感器组成,当一个进程酶马达推进DNA链时,该传感器触摸并检查捕获的DNA链中的每个核苷酸。虽然纳米孔测序的总体目标是在非常长的链上重新读取,但在这里,我们也将重点关注在基础研究(小鼠,大肠杆菌和拟南芥)和医疗保健(人类)中重要生物体的DNA重测序。我们关注从头测序和重测序有两个原因:1)生物DNA的纳米孔测序尚未公开记录。因此,需要对参考标准进行纳米孔重测序,以获得社区认可,并且重要的是,揭示影响从头测序准确性的技术弱点;2)纳米孔重测序在这个应用中意味着直接读取基因组DNA,因此将包括表观遗传修饰。这将是对研究界的一个直接的、重要的贡献。
英文摘要
DESCRIPTION (provided by applicant): This proposal concerns optimization of enzymes, pores, and computational methods for single molecule sequencing of genomic DNA fragments. It is based on a proven nanopore device implemented by our group at UCSC. This device is comprised of a sensor that touches and examines each nucleotide within a captured DNA strand as a processive enzyme motor advances the strand. Although the overall goal of nanopore sequencing is de novo reads on very long strands, here we will also focus on resequencing of DNA from organisms important in basic research (mouse, E. coli & Arabidopsis) and in healthcare (human). We are focusing on both de novo and resequencing for two reasons: 1) nanopore sequencing of biological DNA has not been documented publicly. Therefore, nanopore resequencing of reference standards is required for community acceptance, and, importantly, to reveal weaknesses in the technology that impact de novo sequencing accuracy; 2) nanopore resequencing in this application means reading genomic DNA directly and therefore will include epigenetic modifications. This would be an immediate, important contribution to the research community.
期刊论文(0)
专著(0)
科研奖励(0)
会议论文
A Unified Nanopore Platform for Direct Sequencing of Individual Full Length RNA Strands Bearing Modified Nucleotides
-
批准号:10163247
-
项目类别:
-
资助金额:$95.48万
-
财政年份:2018
-
负责人:MARK A AKESON
-
依托单位:
Optimization of Nanopore Genomic DNA Sequencing
-
批准号:9109648
-
项目类别:
-
资助金额:$72.7万
-
财政年份:2014
-
负责人:MARK A AKESON
-
依托单位:
Optimization of Nanopore Genomic DNA Sequencing
-
批准号:8749195
-
项目类别:
-
资助金额:$76.06万
-
财政年份:2014
-
负责人:MARK A AKESON
-
依托单位:
Optimization of Processive Enzymes for DNA Sequencing using Nanopores
-
批准号:8183739
-
项目类别:
-
资助金额:$129.17万
-
财政年份:2011
-
负责人:MARK A AKESON
-
依托单位:
Optimization of Processive Enzymes for DNA Sequencing using Nanopores
-
批准号:8319314
-
项目类别:
-
资助金额:$118.47万
-
财政年份:2011
-
负责人:MARK A AKESON
-
依托单位:
Optimization of Processive Enzymes for DNA Sequencing using Nanopores
-
批准号:8512765
-
项目类别:
-
资助金额:$113.7万
-
财政年份:2011
-
负责人:MARK A AKESON
-
依托单位:
Analysis of Single DNA Polymerase Complexes at 5 Angstrom Precision in Real Time
-
批准号:8510662
-
项目类别:
-
资助金额:$25.99万
-
财政年份:2010
-
负责人:MARK A AKESON
-
依托单位:
Analysis of Single DNA Polymerase Complexes at 5 Angstrom Precision in Real Time
-
批准号:8102719
-
项目类别:
-
资助金额:$26.79万
-
财政年份:2010
-
负责人:MARK A AKESON
-
依托单位:
Analysis of Single DNA Polymerase Complexes at 5 Angstrom Precision in Real Time
-
批准号:8288098
-
项目类别:
-
资助金额:$26.9万
-
财政年份:2010
-
负责人:MARK A AKESON
-
依托单位:
Analysis of Single DNA Polymerase Complexes at 5 Angstrom Precision in Real Time
-
批准号:7980777
-
项目类别:
-
资助金额:$27.9万
-
财政年份:2010
-
负责人:MARK A AKESON
-
依托单位:
Controlling Large DNA Fragments During Nanopore Sequencing
-
批准号:7936362
-
项目类别:
-
资助金额:$53.35万
-
财政年份:2009
-
负责人:MARK A AKESON
-
依托单位:
Controlling Large DNA Fragments During Nanopore Sequencing
-
批准号:7853410
-
项目类别:
-
资助金额:$56.22万
-
财政年份:2009
-
负责人:MARK A AKESON
-
依托单位:
A Comprehensive Structural and Dynamic Map of DNA Duplex Ends
-
批准号:7024252
-
项目类别:
-
资助金额:$17.28万
-
财政年份:2006
-
负责人:MARK A AKESON
-
依托单位:
A Comprehensive Structural and Dynamic Map of DNA Duplex Ends
-
批准号:7229898
-
项目类别:
-
资助金额:$14.36万
-
财政年份:2006
-
负责人:MARK A AKESON
-
依托单位:
A Comprehensive Structural and Dynamic Map of DNA Duplex Ends
-
批准号:7447802
-
项目类别:
-
资助金额:$10.03万
-
财政年份:2006
-
负责人:MARK A AKESON
-
依托单位:
RAPID ELECTROCHEMICAL CHARACTERIZATION OF RNA AND DNA
-
批准号:2209683
-
项目类别:
-
资助金额:$13.25万
-
财政年份:1995
-
负责人:MARK A AKESON
-
依托单位:
海外基金