I have a problem with DNA extracted from FFPE samples (human heart). Our method for mtDNA amplification and sequencing (twelve fragments) that has been working perfectly works now with few samples only. I have optimized PCR and the samples have been purified with commercial kit (Illumina). The purification resulted in weak improvement in the amplification. I will test WGA kits to get more mtDNA next.
I know that I could amplify smaller fragments but the sequencing gets too expensive with small fragments. Furthermore, I do not have the heart tissue, only DNA.
So, have you been struggling with FFPE samples? Have you solved the problem with mtDNA fragmentation?
WBR
Laura