Dr. Donald Johann, professor of Biomedical Informatics, is an author on an article in the high-impact journal Genome Biology on ways to improve Next-Generation Sequencing (NGS) assays that use fixed tissue.
Precision medicine approaches are revolutionizing the practice of clinical oncology. However, formalin fixed paraffin embedded (FFPE), a routine pathology practice, brings challenges for the molecular extraction of relevant biomolecules and the quality of the molecular profiling assays that are essential to precision oncology.
To investigate the effect of FFPE on clinical specimens undergoing NGS analysis, the research team designed a comprehensive study querying crucial components.
They found commonalities among tissue sections that fail, including that sections from block surfaces were more likely to show FFPE-specific errors, similar to “edge effects” seen in histology. Meanwhile, inner samples displayed no quality degradation related to fixation time.
The team recommended avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence to assure reliable results.
The article, titled “Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples,” was published June 29.
Dr. Johann’s research interests include:
- Cancer Biology and Bioinformatics
- Next-Generation Sequencing (NGS)
- High-Resolution Identity-Based Mass Spectrometry (Proteomics)
- Laser Capture Microdissection (LCM)