title: Evaluation of the protective capabilities of nucleosome STRs obtained by large-scale sequencing.
abstract: Partial DNA profiles are often obtained from degraded forensic samples and are hard to analyze and interpret. With in-depth studies on degraded DNA, an increasing number of forensic scientists have focused on the intrinsic structural properties of DNA. In theory, nucleosomes offer protection to the bound DNA by limiting access to enzymes. In our study, we performed large-scale DNA sequencing on nucleosome core DNA of human leucocytes. Five nucleosome short tandem repeats (STRs) were selected (including three forensic common STRs (i.e. TPOX, TH01, and D10S1248) and two unpublished STRs (i.e. AC012568.7 and AC007160.3)). We performed a population genetic investigation and forensic genetic statistical analysis of these two unpublished loci on 108 healthy unrelated individuals of the HeBei Han population in China. We estimated the protective capabilities of five selected nucleosome loci and MiniFiler™ loci with artificial degraded DNA and case samples. We also analyzed differences between sequencing results and software predicted results. Our findings showed that nucleosome STRs were more likely to be detected than MiniFiler™ loci. They were well protected from degradation by nucleosomes and could be candidates for further nucleosome multiplex construction, which would increase the chances of obtaining a better balanced profile with fewer allelic drop-outs.
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, P. R. China.
authors.forename: Chunnan
authors.initials: C
authors.lastname: Dong
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang, Beijing, P. R. China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang, Beijing, P. R. China.
authors.forename: Jiangwei
authors.initials: J
authors.lastname: Yan
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, P. R. China.
authors.forename: Lihong
authors.initials: L
authors.lastname: Fu
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, P. R. China.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, P. R. China.
authors.forename: Bin
authors.initials: B
authors.lastname: Cong
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, P. R. China.
authors.forename: Shujin
authors.initials: S
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D002681:China; D004247:DNA / Q000235:genetics; D005260:Female; D053803:Forensic Genetics / Q000379:methods*; D005828:Genetics, Population; D006801:Humans; D007962:Leukocytes / Q000378:metabolism; D008297:Male; D018895:Microsatellite Repeats; D009707:Nucleosomes / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D009707:Nucleosomes; D004247:DNA
keywords: Degraded DNA; Forensic genetics; Nucleosome; Short tandem repeat