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Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments
Karen H Miga1, Christopher Eisenhart2, W James Kent2
1Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA khmiga@soe.ucsc.edu.
Nucleic Acids Research
|July 12, 2015
Summary
This study introduces new mapping targets to improve the human reference genome by including repeat-rich regions. This significantly reduces artifacts in genomic data analysis, enhancing large-scale studies.
Area of Science:
- Genomics
- Bioinformatics
Background:
- The human reference assembly is incomplete, particularly in repeat-rich centromeric and acrocentric regions.
- Underrepresented sequences cause alignment issues and artifactual peaks in genomic data analysis.
Purpose of the Study:
- To develop mapping targets for previously omitted, repeat-rich human genome regions.
- To improve the accuracy of genomic analyses by addressing assembly limitations.
Main Methods:
- Construction of novel mapping targets representing ~8% of the human genome.
- Integration of these targets into standard mapping and peak-calling pipelines.
Main Results:
- Demonstrated a 10-fold reduction in artifactual signals in previously problematic regions.
- Identified a comprehensive set of regions exhibiting improved mapping sensitivity with the new targets.
Conclusions:
- The developed mapping targets significantly enhance the human reference assembly.
- This approach mitigates artifacts, improving reliability for hypothesis testing and large-scale genomic studies.
