Validation and implementation of MPS mtDNA control region analysis for forensic casework: Determination of C-stretch lengths by the FDSTools noise correction feature

Abstract Analysis of mitochondrial DNA fragments containing a long C-stretch with Sanger sequencing is challenging. Massively parallel sequencing offers the opportunity to study C-stretch length variation within a sample in more detail, as this technology generates a sequence for each molecule rather than a consensus sequence as is done by Sanger sequencing. Insight in this variation helps for determination of MPS data analysis guidelines. We used FDSTools to catalogue the within-sample variation of C-stretch lengths in a series of reference samples with lengths of 6 to 12 Cs and investigated the effectiveness of FDSTools correction on these C-stretches. Even when noise variants were outnumbering the reads of the correct C-stretch length, FDSTools achieved a considerable reduction of C-stretch noise and correct calling of the C-stretch length.