Version 1
: Received: 20 July 2024 / Approved: 21 July 2024 / Online: 24 July 2024 (14:45:02 CEST)
How to cite:
Mitchell, R.; Peck, M.; Gorden, E.; Just, R. MixDeR: a SNP mixture deconvolution workflow for forensic genetic genealogy. Preprints2024, 2024071705. https://doi.org/10.20944/preprints202407.1705.v1
Mitchell, R.; Peck, M.; Gorden, E.; Just, R. MixDeR: a SNP mixture deconvolution workflow for forensic genetic genealogy. Preprints 2024, 2024071705. https://doi.org/10.20944/preprints202407.1705.v1
Mitchell, R.; Peck, M.; Gorden, E.; Just, R. MixDeR: a SNP mixture deconvolution workflow for forensic genetic genealogy. Preprints2024, 2024071705. https://doi.org/10.20944/preprints202407.1705.v1
APA Style
Mitchell, R., Peck, M., Gorden, E., & Just, R. (2024). MixDeR: a SNP mixture deconvolution workflow for forensic genetic genealogy. Preprints. https://doi.org/10.20944/preprints202407.1705.v1
Chicago/Turabian Style
Mitchell, R., Erin Gorden and Rebecca Just. 2024 "MixDeR: a SNP mixture deconvolution workflow for forensic genetic genealogy" Preprints. https://doi.org/10.20944/preprints202407.1705.v1
Abstract
The generation of forensic DNA profiles consisting of single nucleotide polymorphisms (SNPs) is now being facilitated by wider adoption of next-generation sequencing (NGS) methods in casework laboratories. At the same time, and in part because of this advance, there is an intense focus on the generation of SNP profiles from evidentiary specimens for so-called forensic or investigative genetic genealogy (FGG or IGG) applications. However, FGG methods are constrained by the algorithms for genealogical database searches, which were designed for use with single-source profiles, and the fact that many forensic samples are mixtures. To enable the use of two-person mixtures for FGG, we developed a workflow, MixDeR, for the deconvolution of mixed SNP profiles. MixDeR, a flexible and easy to use R package and Shiny app, processes ForenSeq Kintelligence® (QIAGEN, Inc.) SNP genotyping results and directs deconvolution of the profiles in EuroForMix (EFM). MixDeR then filters the EFM outputs to produce inferred single-source genotypes in reports formatted for use with GEDmatch® PRO. An optional MixDeR output includes metrics that assist with testing and validation of the workflow. As the Shiny app provides a graphical user interface and the software is designed to be run offline, MixDeR should be suitable for use by any laboratory developing FGG capabilities, no matter their bioinformatic resources or expertise.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
