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Integrated biochemical and bioinformatic technologies for accurate transcriptome-wide full-length RNA assembly.

集成生物化学和生物信息技术，用于准确的转录组全长 RNA 组装。

基本信息

批准号：
9119934
负责人：
Colin Noel Dewey
金额：
$ 0.5万
依托单位：
LUCIGEN CORPORATION
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-04-20 至 2017-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9119934
关键词：
Affect Alleles Alternative Splicing Animals Behavioral Benchmarking Biochemical Bioinformatics Biology Brain Cataloging Catalogs Cells Cellular biology Chimera organism Cloning Code Complementary DNA Complex Computer software DNA DNA Resequencing Data Data Analyses Development Dideoxy Chain Termination DNA Sequencing Disease Enzymes Epigenetic Process Event Exons Face Gene Expression Profile Gene Expression Regulation Generations Genes Genetic Genome Genomics Goals Grant Haplotypes Health Human Individual Length Libraries Malignant Neoplasms Maps Messenger RNA Methods Modification Natural regeneration Neurologic Nucleotides Pattern Phase Physiological Plants Process Protein Isoforms Proteins Protocols documentation RNA RNA Editing RNA Sequences RNA Splice Sites RNA Splicing Reading Regulation Research Resort Reverse Transcription Sampling Scientist Sequence Analysis Site Small Business Innovation Research Grant Staging Stress Technology Time Transcript Universities Variant Walking Wisconsin base cDNA Library cell type computerized data processing computerized tools cost differential expression genome sequencing human reference genome innovation neurological pathology new technology next generation sequencing novel open source programs single molecule success tool tool development transcriptome sequencing transcriptomics

项目摘要

DESCRIPTION (provided by applicant): The human transcriptome is significantly more complex than its cognate genome, due to the hundreds of thousands of possible isoforms, allele-specific expression issues, variable RNA editing changes, and differential expression patterns spanning cell types, developmental stages, and physiological stresses. Next- generation sequencing (NGS) platforms are fundamentally altering genetic and genomic research by providing massive amounts of data in a low-cost, high-throughput format. The main drawback of existing technologies is the short sequence read lengths they produce (Illumina) or the high error rate (PacBio). Identifying single nucleotide variations is problematic with the long read technology and de novo assembly of most transcripts is compromised with short read NGS technologies alone. Even with a high quality reference human genome (which is a mosaic of the parental alleles), transcriptome sequencing and assembly is a significant challenge. Haplotyping across an entire mRNA is critical for understanding the full extent of RNA editing and is not readily achieved without resorting to cloned DNA. New tools that bridge the gap between massively parallel short read sequencing technologies and the need to assemble complete mRNA molecules are clearly needed. The SBIR Phase I of this grant proposes to develop the short read NGS technology to accurately sequence mRNAs along their entire length, regardless of size. This technology will enable the accurate assembly of complex transcriptomes, without cDNA cloning and primer walking using Sanger sequencing based strategies. The development of these tools could enable the de novo sequencing of daunting transcriptomes, reduce computational costs of transcriptome assembly significantly, produce more complete and accurate catalogs of RNA edited transcripts, and make personal transcriptome resequencing tractable.