BACKGROUND:Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users.RESULTS:Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling).CONCLUSIONS:All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.

Background: The hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) is the most frequent hereditary colorectal cancer syndrome. It has been associated with different types of cancers besides the early onset of the disease. To define HNPCC the Amsterdam or Bethesda criteria have to be met. Causative for the Lynch syndrome is a germline mutation of one of the four mismatch repair genes MLH1, MSH2, MSH6 and PMS2. The detection of pathogenic alterations is of vital importance for the patient as well as for their relatives. The analyses for the PMS2 gene have been severely complicated by the presence of multiple pseudogenes with high homologies to the gene especially in its 5 ́-region. The PMS2CL pseudogene has a high homology to the 3 ́-region of PMS2, in particular the exons 9 and 11- 15, which result in recombination events between the paralogues. Objectives: In this study, we established the newly developed technique of long-range-PCR for mutation detection within the PMS2 gene. Using this method we could clearly discriminate gene from pseudogene which makes it a significant advancement in the detection of pathogenic mutations in PMS2 compared to previously used methods. Until recently mutation detections had been performed with a method, which is now obsolete. It has been the aim of this study to implement the new method of long-range-PCR in the daily diagnostic routine. However, within the study we examined only exons 11-15 of PMS2 equal to the long-range-PCR product 3, because this region contains the highly homologous region to the PMS2CL pseudogene and is known to undergo recombination. Furthermore, it was the aim of this study to make a statement about occuring recombination events and their nature, frequency and consequences. The sequence of the pseudogene has been amplified as well. Methods: Patients were selected based on an isolated loss for PMS2 in the immunohisto- chemistry of their tumor. The long-range-PCR was performed on DNA from blood leukocytes. The amplicons of both the gene and pseudogene were confirmed on gel electrophoresis and used as template for ensuing exon-specific nested-PCR prior to sequencing. Multiplex ligation-depend amplification (MLPA) was performed to screen for deleterious alterations. Results: The study comprised 23 patients. We identified pathogenic mutations in 14 patients (61 %). Four of these mutations are located in the 5 ́-region (upstream exon 8), ten mutations were found in the 3 ́-region (downstream exon 9). Those mutations were nearly evenly distrib- uted over the exons 11-14, whereas two mutations in exon 14 were large deletions. There was no mutation found in exon 15. Moreover we identified one putative pathogenic mutation in exon 12. The second part of this study aimed at the analysis of recombination events between PMS2 and PMS2CL. We identified 27 paralogous sequence variants, which were classified by un- derlying recombination patterns. We found patients without any recombination as well as re- combination events encompassing the exons 13-15. In 14 of 23 patients (61 %) a recombination event could be confirmed occurring primarily in the exons 13-15. The overall number of recombination events are benign and consequences for cancer development are not clear, except one patient who presented with a malignant tumor and carried a sequence recombina- tion in exon 11, which had not been found in former studies. Conclusion: From now on the long-range-PCR should be gold standard for detection of path- ogene alterations in the PMS2 gene. The mechanism and the verification of recombination events encompassing the whole gene PMS2 should be point of interest in further studies.