Next generation sequencing (NGS) technologies encompass an ever increasing proportion of basic research
NEXT GENERATION SEQUENCING (NGS) technologies encompass an ever increasing proportion of basic research. The high potential of this technology has prioritized rapid development and validation of algorithms to extract meaningful information from these large datasets. For example, identifying single mutations important for disease diagnosis, treatment and research from billions of bases generated by a single run.
Detection of complex variation using NGS data has proven to be a difficult problem. This challenge prompted the development of UNCseqR to integrate DNA and RNA sequencing information. The result is greatly increased sensitivity of mutation detection and it shows great promise in otherwise uninformative samples of low tumor content.
Insertions and deletions (InDels) in DNA in particular have been a great challenge and can have substantial impact on function which makes their detection all the more imperative. The Lineberger Bioinformatics Core has developed a software tool called ABRA (Assembly Based Re-Aligner), which enables enhanced performance for InDel detection in both germline and somatic scenarios. ABRA is available for download.
As another example, the VirusScan algorithm developed by LBC has been used discovery and quantify viral infection in tumor specimens. VirusScan analysis enabled a deep characterization of human papillomavirus in head/neck cancer, including isotype variability, viral differential gene expression, and viral mutations. As a final example, LBC’s fusion gene pipeline detected clinically-actionable fusion genes in lung adenocarcinoma and prostate cancer, and LBC‘s efforts have set a new standard for fusion gene analysis.
B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of highly variable BCR specific gene segments accompanied by long read amplicon sequencing. This method is frequently not available for a variety of reasons including cost as well as absence from existing public datasets. To ameliorate this, the LBC has developed V'DJer which enables reconstruction of BCR repertoires from short read mRNA-seq data, enabling research and discovery that was previously not possible. V’DJer is available for download.