Quantitative trait loci as indicators of potential susceptibility to allele-specific dropout for forensic RNA markers

In recent years, the potential to associate donor (from DNA results) with specific cell types (based on RNA analysis) using single nucleotide polymorphisms (SNPs) has been explored and recognized as a major advancement in forensic RNA typing. This method relies on SNPs in transcribed regions of body fluid-specific mRNA to link a cell type to a specific donor, whose presence is inferred from conventional forensic DNA typing. While the approach is promising, discrepancies frequently arise between the DNA and RNA-SNP data, primarily due to allelic dropout of RNA alleles. Understanding the mechanism underlying allele-specific expression is essential for advancing this method towards casework implementation. To address this, the role of quantitative trait loci (QTLs) as a potential cause of allele-specific expression (ASE) was investigated. Findings show how QTLs help explain the previously unresolved discrepancies and how QTL analysis can serve as a predictor of a gene's susceptibility to ASE. Additionally, guidelines are provided for handling genes with increased risks of ASE, aiding the implementation of DNA and RNA-SNP-based donor-to-cell-type association in forensic casework.