title: Parallel Analysis of 124 Universal SNPs for Human Identification by Targeted Semiconductor Sequencing.
abstract: SNPs, abundant in human genome with lower mutation rate, are attractive to genetic application like forensic, anthropological and evolutionary studies. Universal SNPs showing little allelic frequency variation among populations while remaining highly informative for human identification were obtained from previous studies. However, genotyping tools target only dozens of markers simultaneously, limiting their applications. Here, 124 SNPs were simultaneous tested using Ampliseq technology with Ion Torrent PGM platform. Concordance study was performed with 2 reference samples of 9947A and 9948 between NGS and Sanger sequencing. Full concordance were obtained except genotype of rs576261 with 9947A. Parameter of FMAR (%) was introduced for NGS data analysis for the first time, evaluating allelic performance, sensitivity testing and mixture testing. FMAR values for accurate heterozygotes should be range from 50% to 60%, for homozygotes or Y-SNP should be above 90%. SNPs of rs7520386, rs4530059, rs214955, rs1523537, rs2342747, rs576261 and rs12997453 were recognized as poorly performing loci, either with allelic imbalance or with lower coverage. Sensitivity testing demonstrated that with DNA range from 10 ng-0.5 ng, all correct genotypes were obtained. For mixture testing, a clear linear correlation (R(2) = 0.9429) between the excepted FMAR and observed FMAR values of mixtures was observed.
authors.affiliation: Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China.|State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China.
authors.forename: Suhua
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China.
authors.forename: Yingnan
authors.initials: Y
authors.lastname: Bian
authors.affiliation: Invitrogen Trading (Shanghai) Co., LTD, Shanghai 200050, P.R.China.
authors.forename: Zheren
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Invitrogen Trading (Shanghai) Co., LTD, Shanghai 200050, P.R.China.
authors.forename: Hancheng
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, P.R. China.
authors.forename: Lagabaiyila
authors.initials: L
authors.lastname: Zha
authors.affiliation: Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, P.R. China.
authors.forename: Jifeng
authors.initials: J
authors.lastname: Cai
authors.affiliation: Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, P.R. China.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China.
authors.forename: Chaoneng
authors.initials: C
authors.lastname: Ji
authors.affiliation: Department of Forensic Genetics, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, P.R.China.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Hou
authors.affiliation: Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai 200063, P.R. China.
authors.forename: Chengtao
authors.initials: C
authors.lastname: Li
mesh_terms: D044466:Asian People / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D005006:Ethnicity / Q000235:genetics; D018732:Forensic Anthropology / Q000379:methods*; D005787:Gene Frequency / Q000235:genetics; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA