New Recommendations for Optimal Sequencing Depth in Alternative Splicing Studies
As part of an international research team led by Olga Tsoy from the University of Hamburg,
the Division of Data Science in Biomedicine contributed to the development of new
guidelines for determining the optimal sequencing depth in RNA sequencing (RNA-Seq)
studies focusing on alternative splicing (AS). By analyzing extensive RNA-Seq datasets from
human tissues such as the heart, adipose tissue, and hypothalamus, the researchers found
that commonly used sequencing depths of 50 to 150 million reads may not be sufficient to
capture the full range of AS events, especially in lowly expressed genes.
The study recommends a sequencing depth of 150 to 200 million reads for reliably detecting
AS events in lowly expressed genes and 100 to 150 million reads for highly expressed
genes. This deeper sequencing allows for the identification of additional biologically relevant
AS events that are important for understanding disease mechanisms and tissue-specific
gene regulation.
The findings highlight the importance of careful experimental design in RNA-Seq studies and
offer valuable guidelines for researchers aiming to comprehensively assess alternative
splicing. The study also notes that large RNA-Seq projects like GTEx and TCGA may not
have sufficient sequencing depth for a complete AS analysis.
This work provides a solid foundation for future studies seeking a more thorough
understanding of complex biological processes and disease pathways.