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ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA
Marian Thieme1, Claudio Lottaz, Harald Niederstätter
1Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str, 9, D-93053 Regensburg, Germany. marian.thieme@klinik.uni-regensburg.de
BMC Bioinformatics
|December 24, 2009
Summary
ReseqChip software automates human mitochondrial genome resequencing using Affymetrix MitoChip v2.0. This tool enhances sequence accuracy and base call rates by analyzing local context probes.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- The Affymetrix MitoChip v2.0 is designed for human mitochondrial genome resequencing.
- It utilizes oligonucleotide tiling arrays with probes for heavy and light strands.
- Alternative local context probes for known mtDNA variants exist but are underutilized due to lack of software.
Purpose of the Study:
- To develop and present ReseqChip, a software solution for automated analysis of MitoChip v2.0 data.
- To leverage alternative local context probes for improved mitochondrial DNA (mtDNA) variant detection.
Main Methods:
- Development of ReseqChip software for automated resequencing analysis.
- Utilizing multiple local context probes on the MitoChip v2.0 array.
- Automated consolidation of base calls from alternative probes.
Main Results:
- ReseqChip significantly improves base call rate.
- ReseqChip enhances sequence accuracy for mtDNA resequencing.
- The software automates the analysis of alternative local context probes.
Conclusions:
- ReseqChip enables automated analysis of alternative local context probes on the MitoChip v2.0.
- The software improves the accuracy of human mitochondrial genome resequencing.
- ReseqChip reduces the number of non-called bases in mtDNA sequencing data.
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