Phantom mutation hotspots in human mitochondrial DNA

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30000 published hypervariable segment 1 sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

Beam energy dependence of the pi(-)/pi(+) ratio

Using the isopin- and momentum-dependant hadronic transport model IBUU04, the effect of symmetry energy on the pi(-)/pi(+) ratio are studied. Our investigations are based on the calculations of the Sn-132+Sn-124 semi-central collisions at beam energies of 400/ A MwV, 600/ A MeV and 800MeV. It is found that both the transverse momentum and kinetic energy distributions of the pi(-)/pi(+) ratio are rather sensitive to the symmetry energy, especially around the Colomb peaks. The position of the coulomb peak is shown to be nearly indrpendant of beam energy. The sesitivity of the pi(-)/pi(+) ratio to the symmetry ebergy decreases as the beam energy increases from 600/ A MeV to 800/ A MeV.