A new approach combining forensic thresholds and a multiple-tubes approach to unravel false microsatellite profiles from
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METHODS AND RESOURCES ARTICLE
A new approach combining forensic thresholds and a multiple‑tubes approach to unravel false microsatellite profiles from cross‑contaminated sample material Kathrin Mäck1 · Andreas Scharbert2 · Ralf Schulz1 · René Sahm1,3 Received: 14 January 2020 / Accepted: 1 October 2020 © The Author(s) 2020
Abstract Contamination and degradation are known challenges for reliable genotyping, since they can cause, among other problems, false microsatellite profiles. In this study we described a method to decrease the proportion of false microsatellite profiles from fish scale samples of endangered allis shads (Alosa alosa) from a reintroduction program, where cross-contamination with DNA from other individuals and potentially degradation of samples occurred. To maximize the portion of reliably measurable results, we modified and combined two known approaches—thresholds used in forensic DNA analyses and a multiple-tubes approach. This combined approach increased reliable microsatellite profiles compared with single approaches. The forensic thresholds and the multiple-tubes approach increased the measurable results from 55 to 67% and 75%, respectively, whereas the combined approach accomplished an increase to 90%. This illustrates the potential of the combined approach for other studies with comparable problems or sample material. Keywords Allis shad · Alosa alosa · Endangered species · Reintroduction
Introduction Contamination of samples with DNA from other individuals of the same species (intraspecific) or from other species (interspecific), but also degradation, are typical problems one faces working with historical or non-invasively obtained wildlife samples, like hair or swabs, and forensic sample material. Microsatellite analyses are plagued with crosscontamination during sampling, microbial contamination problems resulting from inappropriate storage, as well as degradation processes, which cause additional false alleles or missing peaks, through allelic dropout and null alleles Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01175-3) contains supplementary material, which is available to authorized users. * Kathrin Mäck maeck‑k@uni‑landau.de 1
iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
2
Rhenish Fisheries Federation of 1880 e.V., Siegburg, Germany
3
German Environment Agency, Berlin, Germany
(Bradley and Vigilant 2002; Taberlet et al. 1996). Hence several approaches have been developed to minimize problems during microsatellite analyses (Frantz et al. 2003; Taberlet et al. 1996). In forensic DNA analyses, interpretation of crime scene traces is controlled by a guideline and includes three important thresholds in order to ensure the reliability of the data and to unravel the number and genotypes of contributors in a sample (Scientific Working Group on DNA Analysis Methods 2010). The first is an analytical threshold, which has to be determined for each automatic seq
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