Reducing costs for DNA and RNA sequencing by sample pooling using a metagenomic approach

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• DNA and RNA sequencing are crucial for studying genomic alterations and gene expression.
• Sequencing costs have decreased, but sample preparation remains expensive, accounting for ~80% of total costs.
• Current methods involve labor-intensive DNA/RNA extraction, enrichment, and library preparation.

Purpose of the Study:

• To investigate the potential of pooling samples from different organisms before extraction to reduce preparation costs.
• To assess if intrinsic sequence diversity can enable post-sequencing read separation.
• To evaluate the cost-effectiveness and data quality of pooled sequencing.

Main Methods:

• Developed a method for pooling samples from different organisms prior to DNA/RNA isolation and library preparation.
• Applied the method to pooled samples of three related bacterial organisms.
• Analyzed sequencing data to ensure read separation and data quality.

Main Results:

• Demonstrated successful pooled sequencing of three related bacterial organisms without compromising data quality.
• Achieved an approximate 50% cost reduction in DNA- and RNA-sequencing preparation steps.
• Confirmed the approach's high efficiency, applicable down to the genus level.

Conclusions:

• Pooling organism samples before nucleic acid extraction is a viable strategy for cost reduction in sequencing.
• The method is broadly applicable to diverse sample pools in sequencing facilities and companies.
• This approach significantly lowers the barrier to entry for genomic and transcriptomic analyses.