title: Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples.
abstract: In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these "nucleosome protected STRs" (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types.
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, No. 361 Zhongshan East Road, Shijiazhuang 050017, PR China.
authors.forename: Chun-Nan
authors.initials: CN
authors.lastname: Dong
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1-104 Beichen West Road, ChaoYang, Beijing 100101, PR China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ya-Dong
authors.initials: YD
authors.lastname: Yang
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, No. 361 Zhongshan East Road, Shijiazhuang 050017, PR China.
authors.forename: Shu-Jin
authors.initials: SJ
authors.lastname: Li
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1-104 Beichen West Road, ChaoYang, Beijing 100101, PR China.
authors.forename: Ya-Ran
authors.initials: YR
authors.lastname: Yang
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, No. 361 Zhongshan East Road, Shijiazhuang 050017, PR China.
authors.forename: Xiao-Jing
authors.initials: XJ
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1-104 Beichen West Road, ChaoYang, Beijing 100101, PR China.
authors.forename: Xiang-Dong
authors.initials: XD
authors.lastname: Fang
authors.affiliation: Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1-104 Beichen West Road, ChaoYang, Beijing 100101, PR China.
authors.forename: Jiang-Wei
authors.initials: JW
authors.lastname: Yan
authors.affiliation: Department of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, No. 361 Zhongshan East Road, Shijiazhuang 050017, PR China.
authors.forename: Bin
authors.initials: B
authors.lastname: Cong
mesh_terms: D015415:Biomarkers / Q000032:analysis*; D004247:DNA / Q000235:genetics*; D005554:Forensic Medicine / Q000379:methods*; D015894:Genome, Human; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D009707:Nucleosomes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D015415:Biomarkers; D009707:Nucleosomes; D004247:DNA