Integrated Bioinformatics Analysis Suite for deep, targeted amplicon sequencing

用于深度、靶向扩增子测序的集成生物信息学分析套件

• 批准号: 8315541
• 负责人: Brian Clifton Haynes
• 金额: $ 24.29万
• 依托单位: ASURAGEN, INC.
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-25 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8315541
• 关键词: Address; Algorithms; Amendment; Bioinformatics; Biological Markers; Cell Line; Clinical; Clinical Research; Computer software; Controlled Study; Copy Number Polymorphism; Data; Data Analyses; Detection; Development; Diagnostic; Dideoxy Chain Termination DNA Sequencing; Escherichia coli; Evaluation; Fine needle aspiration biopsy; Gene Mutation; Generations; Genetic Variation; Genetic screening method; Genome; Genomics; Goals; Ions; Laboratories; Life; Light; Malignant Neoplasms; Methods; Modeling; Mutation; Nucleotides; Oligonucleotides; Outcome; Pharmacogenomics; Pharmacologic Substance; Phase; Positioning Attribute; Preparation; Process; Reading; Sampling; Screening procedure; Semiconductors; Services; Single Nucleotide Polymorphism; Software Tools; Source; Specificity; Specimen; System; Technology; Testing; Thyroid Gland; Time; Titrations; Validation; Variant; Work; base; cancer type; computerized data processing; cost; design; drug discovery; improved; insertion/deletion mutation; instrument; instrumentation; next generation; research clinical testing; tool

DESCRIPTION (provided by applicant): The aim of this proposal is to develop a bioinformatics pipeline, or Integrated Bioinformatics Analysis Suite (IBAS), specific for ultra-deep, targeted amplicon sequencing on the new Ion Torrent Personal Genome Machine (PGM). This will improve the accuracy of variation detection and enable analysis of genetic variations in different types of cancer. The technology used in the PGM is based on non-optical detection with semiconductor technology and so is sufficiently unique to enable its use as an orthogonal platform for confirmatory testing when other technologies are used for initial sequencing. The PGM offers a significant advantage over other methods of next generation sequencing by enabling the process of sample preparation to data generation to be completed in one day. However, it suffers from the inherent limitations of the technology, mainly errors at the 32 end. Additionally, currently available SNP callers are not particularly suited to high-throughput, ultra deep amplicon sequencing and there are few algorithms available for detecting other types of genomic variations. The proposed pipeline aims to address these issues and fill the urgent need for bioinformatics optimized for the panel-designed amplicon sequencing technology employed in the PGM. To achieve the proposed aims, 1) an IBAS that incorporates different approaches to read preprocessing, alignment to reference sequences, and error modeling to enable detection of single nucleotide polymorphisms (SNPS), insertion/deletions (indels), copy number variation (CNV) and other structural variation will be constructed; and 2) a comprehensive evaluation of the sources of variation will be performed, and the IBAS optimized for amplicon sequencing. The optimized pipeline will then be validated by processing data from the PGM for orthogonal validation of mutations detected in clinical thyroid fine needle aspiration biopsies. Successful outcome will enable Asuragen to provide a high-throughput ultra-deep sequencing service for clinical research and diagnostics. PUBLIC HEALTH RELEVANCE: We aim to develop a bioinformatics application specific for the technology employed in the recently launched Ion Torrent Personal Genome Machine (PGM) that will improve the accuracy of detecting genetic variations in different types of cancer. The PGM is a compact, bench-top next generation sequencing instrument that enables rapid sequencing of an entire genome and at a much lower cost than established systems. The application will be used by Asuragen to offer a high-throughput sequencing service for clinical research and diagnostics.

描述（由申请人提供）：本提案的目的是开发一个生物信息学管道或集成生物信息学分析套件（IBAS），专门用于在新的 Ion Torrent 个人基因组机（PGM）上进行超深度、靶向扩增子测序。这将提高变异检测的准确性，并能够分析不同类型癌症的遗传变异。 PGM 中使用的技术基于半导体技术的非光学检测，因此非常独特，可以在使用其他技术进行初始测序时用作验证性测试的正交平台。与其他下一代测序方法相比，PGM 具有显着优势，可以在一天内完成样品制备到数据生成的过程。但它受到技术固有的限制，主要是32端的错误。此外，目前可用的 SNP 识别器并不特别适合高通量、超 深度扩增子测序，并且很少有算法可用于检测其他类型的基因组变异。拟议的管道旨在解决这些问题，并满足针对 PGM 中采用的面板设计扩增子测序技术进行优化的生物信息学的迫切需求。为了实现所提出的目标，1) IBAS 结合了不同的读取预处理、参考序列比对和错误建模方法，以实现单核苷酸多态性 (SNPS)、插入/删除 (indels)、拷贝数变异 (CNV) 的检测将建造其他结构变化； 2) 对变异来源进行全面评估，并对 IBAS 进行扩增子测序优化。然后，将通过处理来自 PGM 的数据来验证优化的流程，以对临床甲状腺细针抽吸活检中检测到的突变进行正交验证。成功的成果将使 Asuragen 能够为临床研究和诊断提供高通量超深度测序服务。 公共健康相关性：我们的目标是开发一种专门针对最近推出的 Ion Torrent 个人基因组机 (PGM) 所采用的技术的生物信息学应用程序，该技术将提高检测不同类型癌症的遗传变异的准确性。 PGM 是一款紧凑的台式下一代测序仪器，能够对整个基因组进行快速测序，并且成本比现有系统低得多。 Asuragen 将使用该应用程序为临床研究和诊断提供高通量测序服务。

项目成果

Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel.

• DOI: 10.1186/s12920-014-0062-0
• 发表时间: 2014-11-14
• 期刊: BMC medical genomics
• 影响因子: 2.7
• 作者: Choudhary A;Mambo E;Sanford T;Boedigheimer M;Twomey B;Califano J;Hadd A;Oliner KS;Beaudenon S;Latham GJ;Adai AT
• 通讯作者: Adai AT