SMURF-seq: efficient copy number profiling on long-read sequencers.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Long-read sequencing technologies offer advantages in detecting structural variations and complex genomic regions.
• Current read-counting applications are often limited by the throughput and fragment length handled by existing sequencing platforms.
• Efficiently analyzing short DNA molecules using long-read sequencers remains a challenge.

Purpose of the Study:

• To introduce SMURF-seq, a novel protocol for sequencing short DNA molecules on long-read platforms.
• To enhance the information throughput for read-counting applications by maximizing fragment utilization.
• To assess the accuracy and utility of SMURF-seq for generating copy number profiles.

Main Methods:

• SMURF-seq involves randomly ligating short DNA molecules to create longer constructs suitable for long-read sequencing.
• The protocol was applied using the Oxford Nanopore MinION platform.
• Copy number profiling was performed using SMURF-seq data and compared against Illumina sequencing data.

Main Results:

• SMURF-seq enables the sequencing of up to 30 DNA fragments per long read.
• The protocol yields an average of 6.2 million and up to 7.5 million mappable fragments per run.
• SMURF-seq generated copy number profiles with accuracy comparable to Illumina sequencing.

Conclusions:

• SMURF-seq significantly increases the information throughput of long-read sequencers for read-counting applications.
• The protocol expands the utility of long-read sequencing for quantitative genomic analyses.
• SMURF-seq provides a cost-effective and accurate alternative for generating copy number profiles.