RNA-STR/SNP: A mirror of forensic DNA-STR/SNP

Genotyping of DNA polymorphic markers, particularly short tandem repeats (STRs), remains the primary approach for individual identification and paternity testing in forensic genetics. Recently, RNA polymorphisms have attracted increasing interest, and mRNA single nucleotide polymorphism (mRNA-SNP) markers have been proposed for body fluid identification and contributor assignment. However, it is unclear whether common forensic DNA-STR/SNP markers can be genotyped at RNA level. In this study, RNA derived from peripheral blood and semen was genotyped using a massively parallel sequencing (MPS)-based panel comprising 204 STRs, 142 SNPs, and mtDNA hypervariable regions (HVRs), with genomic DNA (gDNA) analyzed in parallel for validation. The results revealed that several CODIS loci (CSF1PO, D18S51, D19S433, D22S1045, and D3S1358) were genotyped at a frequency of more than 50% in blood and/or semen RNA samples, and their genotypes were consistent with those obtained from the gDNA. Sex chromosomal STR loci, including DXS6800, DYS438, DYS453, DYS460, DYS504, DYS557, and DYS645 were genotyped in all blood RNA samples. The DYS455, DYS460, and DYS481 were genotyped in over 90% of the semen RNA samples and showed concordance with gDNA profiles. Interestingly, genotyping of certain markers demonstrated sample-type dependency; for example, D10S2325 and DYS557 loci were genotyped in all blood but not in any of the semen RNA samples. Meanwhile, some autosomal SNPs and a fragment of mtDNA (nt 16223-16365) were genotyped in both the blood and semen. In summary, our findings demonstrate that RNA can yield partial STR/SNP genotypes consistent with gDNA, with evidence of body fluid-specific expression. This study sheds new light on the transcription products of forensic DNA-STR/SNP markers, emphasizing the potential forensic value of RNA-STR/SNP markers for compromised samples and signifying the beginning of a new era in forensic RNA genotyping.