ENHANCED PERF AND THROUGHPUT OF AUTOMATED DNA SEQUENCE

增强自动化 DNA 序列的性能和吞吐量

• 批准号: 6413367
• 负责人: Clark Tibbetts
• 金额: $ 3.64万
• 依托单位: VIRGINIA POLYTECHNIC INST AND ST UNIV
• 依托单位国家: 美国
• 财政年份: 1992
• 资助国家: 美国
• 起止时间: 1992-02-01 至 2001-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6413367
• 关键词: automated data processing; bioengineering /biomedical engineering; biomedical equipment; computer assisted sequence analysis; computer program /software; computer system design /evaluation; human genetic material tag; nucleic acid sequence

The research objectives of this proposal are enhanced performance and increased throughput for gel-based automated DNA sequencing instruments in genome sequencing laboratories. We propose to integrate our established basecalling system with upstream data acquisition hardware and software, and with downstream processing and analysis of DNA sequences. We recently determined that the CCD-camera detector of the new ABI 377 DNA sequencer can be externally driven, to bypass its default limits on lateral scanning resolution and spectral bandwidth. We propose to increase scanning from 194 to 600 pixels per 1.5 second traverse of the gel, and to increase sampling from 4 to 64 wavelength intervals (filters) per pixel. Throughput would increase from the default 36 to 96 or more distinguishable sample lanes per gel. Increased detector bandwidth will improve the deconvolution performance for multiple dye sets. This invites applications with more than the standard four dye labels, including alternative fluorescent dye markers. We will investigate deconvolution and pattern recognition multiplex strategies, to determine favorable conditions for sequence analysis with multiple DNA samples per lane. We will evaluate and further develop lane tracking software, to analyze gel images with significantly increased numbers of sample lines. We will use our contextual pattern recognition approach to auto-editing of primary DNA sequence as an engine to generate Bayesian basecall confidence metrics. This will support automated reconciliation of basecalling discrepancies in downstream multiple sequence alignments, and thus facilitate consensus editing as a sequence finishing task. These ABI 377-based studies will be useful models for applications with new sequencing platforms under development. Capillary and microchannel hardware will challenge contemporary basecalling systems, with increased flow of raw imaging data that is required to monitor their accelerated separations and dense arrays of sequencing ladders. This research contributes to cost-effective and accurate large scale DNA sequencing, a significant technical objective of the Human Genome Initiative. This technology is essential in the long term for investigation and critical understanding of the structure, function, and sequence diversity of medically important genes.

本提案的研究目标是提高性能 并提高了基于凝胶的自动DNA测序的通量 基因组测序实验室的仪器。 我们建议把现有的基本判定系统， 上游数据采集硬件和软件， DNA序列的下游处理和分析。 我们 最近确定，新ABI的CCD摄像头探测器 377 DNA测序仪可外接驱动，绕过其默认 横向扫描分辨率和光谱带宽的限制。 我们 建议将扫描速度从每1.5秒194像素提高到600像素 横向的凝胶，并增加采样从4至64 每个像素的波长间隔（滤波器）。 投资将增加 从默认的36个到96个或更多可区分的样品通道， 凝胶 增加检测器带宽将改善反卷积 多种染料组合的性能。 这将邀请具有 超过标准的四种染料标签，包括替代 荧光染料标记。 我们将研究反卷积， 模式识别多重策略，确定有利的 多个DNA样品的序列分析条件， 巷 我们将评估并进一步开发车道跟踪软件， 为了分析凝胶图像， 线 我们将使用我们的上下文模式识别方法， 自动编辑主要的DNA序列作为一个引擎， Bayesian basecall confidence metrics. 这将支持自动化 下游多重碱基判定差异的核对 序列比对，从而促进作为一种 序列完成任务。 这些基于ABI 377的研究将是有用的 新测序平台的应用模型 发展 毛细管和微通道硬件将挑战 现代碱基识别系统，原材料流量增加， 监测其加速分离所需的成像数据 和密集排列的测序梯。 该研究有助于成本效益和准确的大规模 DNA测序，人类基因组学的一个重要技术目标 基因组计划。 从长远来看，这项技术是必不可少的， 研究和批判性理解的结构，功能， 和重要医学基因的序列多样性。

项目成果

Refinement of the spinal muscular atrophy locus to the interval between D5S435 and MAP1B.

将脊髓性肌萎缩症基因座细化至 D5S435 和 MAP1B 之间的间隔。

• DOI: 10.1006/geno.1993.1069
• 发表时间: 1993
• 期刊: Genomics
• 影响因子: 4.4
• 作者: Soares,VM;Brzustowicz,LM;Kleyn,PW;Knowles,JA;Palmer,DA;Asokan,S;Penchaszadeh,GK;Munsat,TL;Gilliam,TC
• 通讯作者: Gilliam,TC

Autosomal dominant distal spinal muscular atrophy in four generations.

常染色体显性遗传性远端脊髓性肌萎缩症已传四代。

• DOI: 10.1212/wnl.45.4.699
• 发表时间: 1995
• 期刊: Neurology
• 影响因子: 9.9
• 作者: Boylan,KB;Cornblath,DR;Glass,JD;Alderson,K;Kuncl,RW;Kleyn,PW;Gilliam,TC
• 通讯作者: Gilliam,TC

Fine-mapping of the spinal muscular atrophy locus to a region flanked by MAP1B and D5S6.

脊髓性肌萎缩症位点精细定位到 MAP1B 和 D5S6 两侧的区域。

• DOI: 10.1016/0888-7543(92)90012-h
• 发表时间: 1992
• 期刊: Genomics
• 影响因子: 4.4
• 作者: Brzustowicz,LM;Kleyn,PW;Boyce,FM;Lien,LL;Monaco,AP;Penchaszadeh,GK;Das,K;Wang,CH;Munsat,TL;Ott,J
• 通讯作者: Ott,J

Pattern recognition for automated DNA sequencing: I. On-line signal conditioning and feature extraction for basecalling.

自动 DNA 测序的模式识别：I. 用于碱基识别的在线信号调节和特征提取。

• 发表时间: 1993
• 期刊: Proceedings. International Conference on Intelligent Systems for Molecular Biology
• 作者: Golden3rd,JB;Torgersen,D;Tibbetts,C
• 通讯作者: Tibbetts,C