Massively parallel sequencing of 231 autosomal SNPs with a custom panel:a SNP typing assay developed for human identification with Ion Torrent PGM

作     者：Suhua Zhang Yingnan Bian Anqi Chen Hancheng Zheng Yuzhen Gao Yiping Hou Chengtao Li Suhua Zhang;Yingnan Bian;Anqi Chen;Hancheng Zheng;Yuzhen Gao;Yiping Hou;Chengtao Li

作者机构：Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformInstitute of Forensic SciencesMinistry of JusticePRCShanghaiChina State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina Department of Forensic MedicineMedical College of Soochow UniversitySuzhouChina Department of Forensic GeneticsWest China School of Preclinical and Forensic MedicineSichuan UniversityChengduChina 

出 版 物：《Forensic Sciences Research》 (法庭科学研究（英文）)

年 卷 期：2017年第2卷第1期

页      面：26-33页

学科分类：0202[经济学-应用经济学] 02[经济学] 020205[经济学-产业经济学] 

基　　金：supported by grants from the National Natu-ral Science Foundation of China[grant number 81330073],[grant number 81302620] the Ministry of Science and Technology of China[grant number 2016YFC0800703] the Science and Technology Commission of Shanghai Municipality[grant number 14DZ2270800] 

主　　题：Forensic science forensic genetics single nucleotide polymorphism(SNP) massively parallel sequencing(MPS) Ion Torrent personal genome machine(Ion Torrent PGM) 

摘      要：The custom-designed single nucleotide polymorphism(SNP)panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing(MPS)technology and Ion Torrent personal genome machine(PGM).SNPs were chosen from SNPforID,IISNP,HapMap,dbSNP,and related published *** concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 *** SNPs(rs4606077,rs334355,rs430046,rs2920816,rs4530059,rs1478829,rs1498553,rs7141285,rs12714757 and rs2189011)with low coverage or heterozygote imbalance should be optimized or excluded from the *** data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS-SNP panel.A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input *** testing with this panel is possible through analysis of the F MAR(frequency of major allele reads)values at most loci with enough high coverage depth and low level of sequencing *** results indicate the potential advantage of the custom MPS-SNP assays and Ion Torrent PGM platform for forensic study.