A.H. and M.T. contributed equally to this work.
Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes†
Article first published online: 11 JUL 2008
© 2008 Wiley-Liss, Inc.
Volume 30, Issue 1, pages 115–122, January 2009
How to Cite
Hartmann, A., Thieme, M., Nanduri, L. K., Stempfl, T., Moehle, C., Kivisild, T. and Oefner, P. J. (2009), Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum. Mutat., 30: 115–122. doi: 10.1002/humu.20816
Communicated by Paolo M. Fortina
- Issue published online: 13 JAN 2009
- Article first published online: 11 JUL 2008
- Manuscript Accepted: 9 APR 2008
- Manuscript Received: 8 FEB 2008
- Bavarian Genome Research Network (BayGene)
- mitochondrial DNA;
- mutation detection;
The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip® Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of ≥99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of ≥4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing. Hum Mutat 0,1–8, 2008. © 2008 Wiley-Liss, Inc.