Resequencing the mitochondrial tumor genome

While most human cells contain two copies of nuclear DNA, they may possess up to 100,000 copies of mitochondrial DNA. The majority of these copies are identical immediately after birth. Somatic mutations will give rise to variant mtDNA copies or heteroplasmy over a lifetime contributing to the initiation and progression of cancer.Array based resequencing of mitochondrial DNA has to cope with the high variability of these genomes, which can compromise hybridization to a reference sequence background. The Affymetrix MitoChip v2.0 probes both the reference sequence and known genetic variants using multiple alternative context probes. These probes have been neglected in most studies due to the lack of software for their automated analysis.

Together with the Oefner lab (Regensburg), we have developed ReseqChip, a free software that automates the process of resequencing using multiple local context probes. ReseqChip significantly improves base call rate and sequence accuracy. It is available >> here <<