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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

UMARS: Un-MAppable Reads Solution.

Sung-Chou Li¹, Wen-Ching Chan, Chun-Hung Lai

¹Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.

BMC Bioinformatics

|February 24, 2011

Summary

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Un-MAppable Reads Solution (UMARS) identifies biological relevance in un-mappable next-generation sequencing (NGS) reads. This pipeline detects viral fragments and novel splicing events, preventing data loss.

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Next-generation sequencing (NGS) generates high-throughput data, but a fraction of reads often fail to map to reference genomes.
These un-mappable reads are typically discarded as sequencing errors.
This represents a potential loss of valuable biological information.

Purpose of the Study:

To investigate the biological relevance and sources of un-mappable reads.
To develop a computational tool for analyzing these discarded reads.
To identify viral genomic fragments and novel alternative splicing events.

Main Methods:

Developed the Un-MAppable Reads Solution (UMARS) pipeline.
Collected viral genomes and exon-exon junction sequences for reference.

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Created an automated alignment interface within the UMARS service.

Tested UMARS with simulated and real datasets.

Main Results:

UMARS successfully detected expected Epstein-Barr virus (EBV) genomic fragments.
Identified exon-exon junctions indicative of novel alternative splicing isoforms.
Experimental validation confirmed the pipeline's accuracy.
The UMARS web service is publicly available.

Conclusions:

Un-mappable reads can originate from biological sources like viral infections or transcript splicing, not just sequencing errors.
The UMARS pipeline offers a method to analyze and repurpose discarded NGS data.
This approach enhances the utility of sequencing data by recovering potentially significant biological insights.