Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes

Abstract

Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted “bidirectional analysis,” which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples.

Molecular analysis for sex determination in forensic dentistry: a systematic review

“…More than 50 copies of this gene reside in the Y chromosome, and each copy carries the DYS14 marker. The genomic DNA DYS14 marker appears widely in tissues and can be obtained from blood specimens, saliva, or intraoral epithelial cells (Blagodatskikh et al 2010;Masuyama et al 2017).…”

Przewidywanie cech wyglądu człowieka na podstawie markerów DNA do celów medyczno-sądowych i kryminalistycznych

“…Określenie płci może dostarczyć istotnych informacji w badaniach kryminalistycznych, w szczególności w sprawach dotyczących napaści na tle seksualnym oraz w poszukiwaniach osób zaginionych lub w identyfikacji nieznanych szczątków [24]. Płeć można określić na podstawie morfologii kości osobników dorosłych (elementy diagnostyczne dla płci można znaleźć na czaszce, miednicy i różnych fragmentach szkieletu; rozwijają się one w okresie pokwitania, dlatego też największym ograniczeniem metod morfologicznych jest niemożność określania płci dzieci) lub jeśli stan zachowania szkieletu uniemożliwia badanie makroskopowe a zabezpieczone zostały ślady biologiczne to na podstawie markerów DNA.…”

Study of Sexual Dimorphism in Metatarsal Bones: Geometric and Inertial Analysis of the Three-Dimensional Reconstructed Models

“…Although bone and teeth can provide some protection against DNA degradation, the environment for preservation is highly demanding, such as temperature, moisture levels, oxygen levels, soil composition, and pH value (22). Y chromosome deletions or mutations in the priming or binding sites can lead to incorrect estimation of sex and reduce the accuracy of DNA analysis (23)(24)(25). Studies show that the accuracy of DNA analysis in determining the sex of ancient human remains ranges from 52% to 95% (23)(24)(25).…”

“…Y chromosome deletions or mutations in the priming or binding sites can lead to incorrect estimation of sex and reduce the accuracy of DNA analysis (23)(24)(25). Studies show that the accuracy of DNA analysis in determining the sex of ancient human remains ranges from 52% to 95% (23)(24)(25). For bone fossils, the older the fossil, the lower the amount of extractable DNA.…”