Stutter analysis of complex STR MPS data

•We analysed the stuttering rate of complex STRs in MPS.•We found that different alleles created different degrees of stutter.•We analysed all uninterrupted stretches of the alleles to identify the missing motifs, when comparing stutter and parent sequences.•We defined a new predictor of stutter ratio: The block length of the missing motif (BLMM).•We saw improved performance for complex STRs, when using the BLMM as a predictor of stutter ratio, instead of the longest uninterrupted stretch (LUS). Stutters are common and well documented artefacts of amplification of short tandem repeat (STR) regions when using polymerase chain reaction (PCR) occurring as strands one or more motifs shorter or longer than the parental allele. Understanding the mechanism and rate by which stutters are created is especially important when the samples contain small amounts of DNA or DNA from multiple contributors. It has been shown that there is a linear relationship between the longest uninterrupted stretch (LUS) and the stutter ratio. This holds if there is only a single type of stutter variant. However, with massively parallel sequencing (MPS), we see that alleles may create different stutters corresponding to stuttering of different parts of the parental allele. This calls for a refinement of the LUS concept. We analysed all uninterrupted stretches, here called blocks, and identified the block from which the stutter originated. We defined the block length of the missing motif (BLMM) as the length of the identified block. We found that the relationship between the stutter ratio and BLMM was linear using a simple system of recurrence relations. We found that the mean square error decreased by a factor up to 17.5 for compound and complex autosomal markers when using BLMM instead of LUS.