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Wan TY, Hwa HL, Lee TT, Lu YW. High efficiency sperm enrichment from forensic mock samples in bubble-based acoustic filtration devices for short tandem repeat (STR) analysis. LAB ON A CHIP 2024; 24:434-445. [PMID: 38086663 DOI: 10.1039/d3lc00632h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
A bubble-based acoustofluidic filtration (BAF) microfluidic device, which employs cross-flow filtration (CFF) and acoustic streaming, separates cells with high efficiency for forensic analysis. Forensic samples are typically complex and contain a substantial number of squamous epithelial cells from the female vagina, which tend to have fouling problems during filtration due to their morphological and cell adhesion differences. To overcome this issue, the BAF device utilizes bubble oscillation by bulk acoustic wave (BAW) to generate acoustic streaming, which offers additional hydrodynamic forces for side flushing cleaning and achieves effective removal within a mere 0.5 seconds. Our device is tested with imbalanced cell mixtures of sperm and epithelial cells with large disparity ratios. By concurrently employing CFF and acoustic streaming, the samples with our sperm-enrichment can achieve 91.72-97.78% for the recovery rate and 74.58-89.26% for the purity in the sperm enrichment. They are further subjected to short tandem repeat (STR) profiling, enabling the identification of perpetrators. Notably, even samples with minimal sperm cells demonstrated a significant increase in the male donor DNA ratio, while the peak heights of female alleles became virtually undetectable. The exceptional cell separation capability demonstrated by our BAF device highlights its potential applications in forensic sciences and other areas of cell biology.
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Affiliation(s)
- Ting-Yu Wan
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan.
| | - Hsiao-Lin Hwa
- Graduate Institute of Forensic Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsui-Ting Lee
- Graduate Institute of Forensic Medicine, National Taiwan University, Taipei, Taiwan
| | - Yen-Wen Lu
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan.
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Tie J, Uchigasaki S, Isobe E. Evaluation and SNP typing of DNA from ultraviolet-irradiated human bloodstains using TaqMan assay. Sci Rep 2021; 11:8029. [PMID: 33850175 PMCID: PMC8044161 DOI: 10.1038/s41598-021-87313-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
When detecting DNA profiles from forensic materials, it is pivotal to know the extent of degradation and which DNA marker can be genotyped. Ultraviolet (UV) is one of the common external factors that causes DNA damage, through which, an attempt to reveal cardinal genetic information can be made. In this study, after irradiation with three different UV wavelengths, UV-damaged DNA in the bloodstains was analyzed with long and short TaqMan assays using real-time PCR. In addition, both short tandem repeat (STR) profiles and single nucleotide polymorphisms (SNPs) from the damaged DNA at different stages of UV exposure were also assessed. With increasing in UV irradiation cycles, there was a delay of the amplification curves accompanied with a decrease in the DNA amounts collected. Despite the amplification of STR genotype was not altered after 75 cycles of UVC irradiation, all 12 SNP loci could still be detected. Furthermore, a short-assay line was detected in the absence of an amplification of the evaluation curve. The results indicate that, although the DNA template might not be useful and suitable for analysis of STR profile, this approach is of some values in detecting SNPs.
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Affiliation(s)
- Jian Tie
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan.
| | - Seisaku Uchigasaki
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Eiji Isobe
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
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Yang TW, Li YH, Chou CF, Lai FP, Chien YH, Yin HI, Lee TT, Hwa HL. DNA mixture interpretation using linear regression and neural networks on massively parallel sequencing data of single nucleotide polymorphisms. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2020.1807050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ta-Wei Yang
- Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan
| | - Yi-Hao Li
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Fu Chou
- Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Fei-Pei Lai
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Lin Hwa
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
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Hwa HL, Wu MY, Lin CP, Hsieh WH, Yin HI, Lee TT, Lee JCI. A single nucleotide polymorphism panel for individual identification and ancestry assignment in Caucasians and four East and Southeast Asian populations using a machine learning classifier. Forensic Sci Med Pathol 2019; 15:67-74. [PMID: 30649693 DOI: 10.1007/s12024-018-0071-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 11/26/2022]
Abstract
Single nucleotide polymorphism (SNP) profiling is an effective means of individual identification and ancestry inferences in forensic genetics. This study established a SNP panel for the simultaneous individual identification and ancestry assignment of Caucasian and four East and Southeast Asian populations. We analyzed 220 SNPs (125 autosomal, 17 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs) of the DNA samples from 563 unrelated individuals of five populations (89 Caucasian, 234 Taiwanese Han, 90 Filipino, 79 Indonesian and 71 Vietnamese) and 18 degraded DNA samples. Informativeness for assignment (In) was used to select ancestry informative SNPs (AISNPs). A machine learning classifier, support vector machine (SVM), was used for ancestry assignment. Of the 220 SNPs, 62 were individual identification SNPs (IISNPs) (51 autosomal and 11 X-chromosomal SNPs) and 191 were AISNPs (100 autosomal, 13 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs). The 51 autosomal IISNPs offered cumulative random match probabilities (cRMPs) ranging from 1.56 × 10-21 to 3.16 × 10-22 among these five populations. Using AISNPs with the SVM, the overall accuracy rate of ancestry inference achieved in the testing dataset between Caucasian, Taiwanese Han, and Filipino populations was 88.9%, whereas it was 70.0% between Caucasians and each of the four East and Southeast Asian populations. For the 18 degraded DNA samples with incomplete profiling, the accuracy rate of ancestry assignment was 94.4%. We have developed a 220-SNP panel for simultaneous individual identification and ethnic origin differentiation between Caucasian and the four East and Southeast Asian populations. This SNP panel may assist with DNA analysis of forensic casework.
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Affiliation(s)
- Hsiao-Lin Hwa
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Ming-Yih Wu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Wei Hsin Hsieh
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - James Chun-I Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan.
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Hwa HL, Wu MY, Chung WC, Ko TM, Lin CP, Yin HI, Lee TT, Lee JCI. Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software. Int J Legal Med 2018; 133:25-37. [DOI: 10.1007/s00414-018-1961-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
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Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, 't Hoen PAC. A SNP panel for identification of DNA and RNA specimens. BMC Genomics 2018; 19:90. [PMID: 29370748 PMCID: PMC5785835 DOI: 10.1186/s12864-018-4482-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping. RESULTS To determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy-Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 × 10- 20 when assuming no family relations and 1.2 × 10- 10 when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood. CONCLUSIONS This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.
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Affiliation(s)
- Soheil Yousefi
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Tooba Abbassi-Daloii
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter van 't Hof
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Leen M 't Hart
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands.,Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.,Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Amber van der Heijden
- Department of Epidemiology and Biostatistics, VU Medical Center, Amsterdam, The Netherlands.,Department of General Practice and Elderly Care Medicine, VU Medical Center, Amsterdam, The Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands. .,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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A 1204-single nucleotide polymorphism and insertion–deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures. Forensic Sci Int Genet 2018; 32:94-101. [DOI: 10.1016/j.fsigen.2017.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022]
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8
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Du Y, Martin JS, McGee J, Yang Y, Liu EY, Sun Y, Geihs M, Kong X, Zhou EL, Li Y, Huang J. A SNP panel and online tool for checking genotype concordance through comparing QR codes. PLoS One 2017; 12:e0182438. [PMID: 28926565 PMCID: PMC5604942 DOI: 10.1371/journal.pone.0182438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 01/02/2023] Open
Abstract
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (forQR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.
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Affiliation(s)
- Yonghong Du
- School of Statistics, Beijing Normal University, Beijing, China
| | - Joshua S. Martin
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John McGee
- NC Translational and Clinical Sciences Institute, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yuchen Yang
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Eric Yi Liu
- Department of Computer Science, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yingrui Sun
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts, United States of America
| | - Matthias Geihs
- Department of Computer Science, Technische Universität Darmstadt, Darmstadt, Germany
| | - Xuejun Kong
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Eric Lingfeng Zhou
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (YL); (JH)
| | - Jie Huang
- Boston VA Research Institute, Boston, Massachusetts, United States of America
- Brigham Women’s Hospital Division of Aging, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (YL); (JH)
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A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians. Forensic Sci Med Pathol 2017; 13:177-187. [DOI: 10.1007/s12024-017-9863-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
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10
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Caputo M, Bobillo M, Sala A, Corach D. Optimizing direct amplification of forensic commercial kits for STR determination. J Forensic Leg Med 2017; 47:17-23. [DOI: 10.1016/j.jflm.2017.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/02/2017] [Accepted: 01/16/2017] [Indexed: 01/23/2023]
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Zhang S, Bian Y, Chen A, Zheng H, Gao Y, Hou Y, Li C. Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM. Forensic Sci Int Genet 2017; 27:50-57. [DOI: 10.1016/j.fsigen.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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Zhang S, Bian Y, Chen A, Zheng H, Gao Y, Hou Y, Li C. Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM. Forensic Sci Res 2017; 2:26-33. [PMID: 30483616 PMCID: PMC6197105 DOI: 10.1080/20961790.2017.1281011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 11/26/2022] Open
Abstract
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 literatures. Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls. Ten 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 panel. Sequence 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 DNA. Mixture testing with this panel is possible through analysis of the FMAR (frequency of major allele reads) values at most loci with enough high coverage depth and low level of sequencing noise. These results indicate the potential advantage of the custom MPS–SNP assays and Ion Torrent PGM platform for forensic study.
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Affiliation(s)
- Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Anqi Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hancheng Zheng
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
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