Sukawutthiya, P. | Search bioRxiv

bioRxiv2023

The concordance of length- and sequence-based STRs used in forensic markers with guidance for practice

Next-generation sequencing (NGS) technology has shed light on every aspect of genetic discoveries, including forensic genetics. The Miseq(R) FGx Forensic Genetic System (Verogen) is one of the pioneering forensic NGS that provided a complete system from library preparation to data analysis. The system has been validated by several studies and led to a more practical aspect. Short tandem repeat (STR) is a well-established marker that was designed specifically for human individualization. Since NGS provides different data from fragment analysis, a new STR nomenclature is established to make NGS backward compatible with the previous data. In this study, Thai population were used to evaluate the Miseq(R) FGx Forensic genetic system (Verogen) in practical aspect, including concordance study and forensic population parameters. In summary, we purposed a practical guideline for sequence-based STRs.

genetics↗

bioRxiv2023

STRategy: A support system for collecting and analyzing short tandem repeats for forensic science

Short tandem repeats (STRs) are short repeated sequences commonly found in the human genome. They provide many advantages to forensic sciences, such as identifying individuals, estimating the likelihood of kinship, and analyzing mixtures. Next-generation sequencing (NGS) technologies, e.g., ForenSeq Signature Prep, have been proposed for sequencing STRs, obtaining the sequence of each locus and SNPs, and inferring length-based alleles. However, even though the sequenced STRs from ForenSeq offer more insights into the STRs, which lead to the genetic analysis of population and sub-population structures, no open-source software platform enables the collection and management of STR data from NGS and incorporates related analysis tools in one place. Here, we introduce STRategy, a standalone web-based application supporting essential STR data management and analysis capabilities. The analyzed data will be visualized in various forms, for example, charts, maps, and pattern alignments. The system implemented a role-based access control that allows users to search or access specific data depending on their responsibilities. It enables public users to search for data. In addition, they can view statistical data, for example, detailed alleles and genetic variation. Lab users can add, update, and see the information of individuals and explore pattern alignments for a specific locus within the population. Administrators can customize the system, for example, configure maps according to the samples geographic data, and manage reference STR repeat motifs. We designed and developed the STRategy using software engineering principles for flexible extension and easy deployment utilizing the Docker container. The source code is publicly available at https://github.com/cucpbioinfo/STRategy. Also, we deployed a showcase system on a cloud computing service where its URL is included on the GitHub repository. The current version only supports the ForenSeq sample detail report files.

genetics↗