Optimization of primer-specific filter metrics for the assessment of mitochondrial DNA sequence data

Abstract

Filter metrics are used as a quick assessment of sequence trace files in order to sort data into different categories (i.e. high quality, review, and low quality) without human intervention. The filter metrics consist of two numerical parameters for sequence quality assessment: trace score (TS) and contiguous read length (CRL). Primer-specific settings for the TS and CRL were established using a calibration dataset of 2817 traces and validated using a concordance dataset of 5617 traces. Prior to optimization, 57% of the traces required manual review before import into a sequence analysis program, whereas after optimization only 28% of the traces required manual review. After optimization of primer-specific filter metrics for mitochondrial DNA sequence data, an overall reduction of review of trace files translates into increased throughput of data analysis and decreased time required for manual review.

Keywords::

• Filter metrics
• expert systems
• trace score
• contiguous read length
• quality assessment

Acknowledgements

The research conducted in this paper was in partial fulfillment of Pamela Musslewhite's (Curtis) master's thesis entitled, ‘Optimization of Filter Metrics for mtDNA Sequence Analysis’, August 2009. Support for this project was partially funded by NIJ Cooperative Agreement 2008-DN-BX-K192, Forensic DNA Unit Efficiency Improvement, FY 2008.

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.