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Qian X, Li Z, Zhou Z, Qian J, Yao Y, Shao C, Tang Q, Xie J. Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis. Genes (Basel) 2022; 13:genes13081386. [PMID: 36011297 PMCID: PMC9407227 DOI: 10.3390/genes13081386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 12/10/2022] Open
Abstract
Obtaining a full short tandem repeat (STR) profile from a low template DNA (LT-DNA) still presents a challenge for conventional methods due to significant stochastic effects and polymerase slippage. A novel amplification method with a lower cost and higher accuracy is required to improve the DNA amount. Previous studies suggested that DNA polymerases without bypass activity could not perform processive DNA synthesis beyond abasic sites in vitro and our results showed a lack of bypass activity for Phusion, Pfu and KAPA DNA polymerases in this study. Based on this feature, we developed a novel linear amplification method, termed Linear Aamplification for double-stranded DNA using primers with abasic sites near 3′ end (abLAFD), to limit the replication error. The amplification efficiency was evaluated by qPCR analysis with a result of approximately a 130-fold increase in target DNA. In a LT-DNA analysis, the abLAFD method can be employed as a pre-PCR. Similar to nested PCRs, primer sets used for the abLAFD method were designed as external primers suitable for commercial multiplex STR amplification assays. The practical performance of the abLAFD method was evaluated by coupling it to a routine PP21 STR analysis using 50 pg and 25 pg DNA. Compared to reference profiles, all abLAFD profiles showed significantly recovered alleles, increased average peak height and heterozygote balance with a comparable stutter ratio. Altogether, our results support the theory that the abLAFD method is a promising strategy coupled to STR typing for forensic LT-DNA analysis.
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Affiliation(s)
- Xiaoqin Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhimin Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jinglei Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: ; Tel.: +86-021-54237403
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Evaluating the effects of whole genome amplification strategies for amplifying trace DNA using capillary electrophoresis and massive parallel sequencing. Forensic Sci Int Genet 2021; 56:102599. [PMID: 34656831 DOI: 10.1016/j.fsigen.2021.102599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/04/2022]
Abstract
To draw robust conclusions when trace DNA samples are detected in complex cases, it is essential to successfully recover and genotype short tandem repeats (STRs) from trace DNA. However, obtaining complete STR profiles by the conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) method is generally difficult as trace DNA is often less than 100 pg. Previous studies have proven that through whole-genome amplification (WGA), the yield of DNA from trace DNA samples could be improved. In this study, we used two WGA kits, namely, REPLI-g® Single Cell kit and MALBAC® Single Cell DNA Quick-Amp Kit (hereafter referred to as REPLI and MALBAC), to amplify DNA samples with a series of dilutions (from 5.00 ng/μL to 0.391 pg/μL). Typing of STR markers in samples with and without WGA were then performed on a CE platform by the application of Goldeneye® DNA ID System 20 A kit, as well as directly calling sequences from massive parallel sequencing (MPS) for WGA samples with 1.00 ng, 125 pg and 25.0 pg as DNA inputs. Quantification results demonstrated that the yield of samples with WGA could reach the microgram level. The amplification fold was at least > 2000 and > 200 for REPLI and MALBAC, respectively. CE results showed that the number of correctly called loci was improved for trace DNA after WGA when the DNA inputs were lower than 25.0 pg for REPLI and 6.25 pg for MALBAC, respectively. WGA remarkably improved the percentage of called loci with DNA inputs lower than 50.0 pg, although poor performance in repeatability was observed. MPS results suggested that the correctly called loci calculated by MPS reads were mostly more than those calculated by CE, particularly for those of short length, implying MPS of samples after WGA is worth testing in the future. In conclusion, WGA has the potential usability for forensic trace DNA analysis at the single-cell level with good fidelity, although its repeatability requires further improvement.
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Affiliation(s)
- Qiannan Xu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Qianqian Kong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, PR China
| | - Xiaoxiao Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
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A comparative study of whole genome amplification and low-template DNA profiling. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rothe J, Nagy M. Separation of Y-chromosomal haplotypes from male DNA mixtures via multiplex haplotype-specific extraction. Forensic Sci Int Genet 2015; 19:223-231. [PMID: 26275613 DOI: 10.1016/j.fsigen.2015.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 06/05/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022]
Abstract
In forensic analysis, the interpretation of DNA mixtures is the subject of ongoing debate and requires expertise knowledge. Haplotype-specific extraction (HSE) is an alternative method that enables the separation of large chromosome fragments or haplotypes by using magnetic beads in conjunction with allele-specific probes. HSE thus allows physical separation of the components of a DNA mixture. Here, we present the first multiplex HSE separation of a Y-chromosomal haplotype consisting of six Yfiler short tandem repeat markers from a mixture of male DNA.
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Affiliation(s)
- Jessica Rothe
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité- Campus Virchow-Klinikum, Augustenburger Platz 1, Forum 4, 13353 Berlin, Germany
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Khan F, Liacini A, Arora E, Wang S, Assad M, Doulla J, Faridi RM, Berka N. Assessment of fidelity and utility of the whole-genome amplification for the clinical tests offered in a histocompatibility and immunogenetics laboratory. ACTA ACUST UNITED AC 2012; 79:372-9. [PMID: 22489946 DOI: 10.1111/j.1399-0039.2012.01857.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Increasing emphasis on the use of molecular tests in a histocompatibility and immunogenetics laboratory (HIL) poses a potential problem of lack of sufficient DNA to perform multiple genetic analyses. In this study, we report the feasibility, fidelity and utility of multiple displacement amplification (MDA) method to perform whole-genome amplification (WGA) to generate DNA specimens that can be analyzed by multiple molecular techniques and can be used for different clinical tests offered by an HIL. The MDA-generated DNA when compared with the native DNA showed 100% congruency in genotyping of 37 genes/loci using multiple downstream molecular techniques: sequence-based typing and sequence-specific primer-based typing for 5 human leukocyte antigen (HLA) class I and II genes (HLA-A, B, C, DRB1 and DQB1), luminex-based sequence-specific oligonucleotide (SSO) genotyping for a panel of 16 killer immunoglobulin-like receptor (KIR) genes and automated fragment size analysis for a panel of 15 short tandem repeat (STR) loci and amelogenin gene. For post-allogeneic hematopoietic cell transplantation (HCT) chimerism analysis, MDA-generated DNA appeared useful for enriching pre-transplant DNA but not for enriching post-transplant chimeric DNA. Overall, our results show that MDA-based WGA could generate DNA of high yield and fidelity that can be used for various clinical tests and research purposes.
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Affiliation(s)
- F Khan
- Tissue Typing Laboratory, Calgary Laboratory Services, Calgary, Alberta, Canada.
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Evaluation of circular DNA substrates for whole genome amplification prior to forensic analysis. Forensic Sci Int Genet 2012; 6:185-90. [DOI: 10.1016/j.fsigen.2011.04.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Revised: 03/03/2011] [Accepted: 04/04/2011] [Indexed: 01/05/2023]
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Jorgez CJ, Bischoff FZ. Improving enrichment of circulating fetal DNA for genetic testing: size fractionation followed by whole gene amplification. Fetal Diagn Ther 2009; 25:314-9. [PMID: 19776594 DOI: 10.1159/000235877] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 08/22/2008] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving enrichment and high-quality fetal DNA from plasma. METHODS Cell-free DNA from 31 pregnant women and 18 controls (10 males and 8 females) were size separated using agarose gel electrophoresis. DNA fragments of 100-300, 500-700 and 1,500-2,000 bp were excised and extracted, followed by whole genome amplification (WGA) of recovered fragments. Levels of beta-globin and DYS1 were measured. RESULTS Distribution of beta-globin size fragments was similar among pregnant women and controls. Among control male cases, distribution of size fragments was the same for both beta-globin and DYS1. Among maternal cases confirmed to be male, the smallest size fragment (100-300 bp) accounted for nearly 50% (39.76 +/- 17.55%) of the recovered DYS1-DNA (fetal) and only 10% (10.40 +/- 6.49%) of beta-globin (total) DNA. After WGA of plasma fragments from pregnant women, DYS1 sequence amplification was best observed when using the 100-300 bp fragments as template. CONCLUSIONS Combination of electrophoresis for size separation and WGA led to enriched fetal DNA from plasma. This novel combination of strategies is more likely to permit universal clinical applications of cell-free fetal DNA.
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Affiliation(s)
- Carolina J Jorgez
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA
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Creary LE, Girdlestone J, Zamora J, Brown J, Navarrete CV. Molecular typing of HLA genes using whole genome amplified DNA. Transfusion 2008; 49:57-63. [PMID: 18954395 DOI: 10.1111/j.1537-2995.2008.01943.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The outcome of clinical transplantation and a number of disease susceptibilities show very strong associations with genetic variants within the major histocompatibility complex, particularly in the human leukocyte antigen (HLA) genes. A problem with many association studies is the lack of sufficient DNA to perform multiple genetic analyses, particularly with transplantation outcomes where donor and recipient DNA are often in short supply. This study assesses whether a multiple-strand displacement whole genome amplification (WGA) method could generate sufficient template of high quality to perform unbiased amplification for analysis of the HLA-A, -B, -C, -DRB1, and -DQB1 genes. STUDY DESIGN AND METHODS A panel of DNA samples from various biological sources was subjected to WGA reaction using Phi29 DNA polymerase. The HLA genotypes were subsequently determined using standard polymerase chain reaction (PCR)-based methods including sequence-specific oligonucleotide probes (PCR-SSOP, Luminex, Luminex Corp.) and sequence-based typing (PCR-SBT). WGA products and original DNA samples were used to determine the sensitivity of the Luminex assay; in addition, reamplified WGA products were also genotyped. RESULTS The WGA templates, as well as serially amplified DNA for two successive rounds, yielded HLA genotypes fully concordant with those determined for the original DNA samples. WGA products and original DNA gave reproducible HLA-DQB1 genotypes with 100 to 10 ng of template. Purification of the WGA products was required for successful PCR-SBT, but not for the PCR-SSOP method. CONCLUSION Our study suggests that WGA can be a reliable method for generating unlimited DNA for medium- or high-resolution HLA typing using the techniques described above.
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Affiliation(s)
- Lisa E Creary
- Histocompatibility and Immunogenetics Research Group, Department of Histocompatibility and Immunogenetics, Colindale Centre, NHSBT, NHSBT, London, UK
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Ballantyne KN, van Oorschot RAH, Muharam I, van Daal A, John Mitchell R. Decreasing amplification bias associated with multiple displacement amplification and short tandem repeat genotyping. Anal Biochem 2007; 368:222-9. [PMID: 17583668 DOI: 10.1016/j.ab.2007.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/07/2007] [Accepted: 05/19/2007] [Indexed: 11/27/2022]
Abstract
Although multiple displacement amplification (MDA) is being used increasingly to amplify genomes, the amplification bias generated by the varphi29 polymerase can be a concern with genotyping applications. It has been noted that the bias is pronounced with small template amounts, particularly with single nucleotide polymorphism (SNP) and short tandem repeat (STR) genotyping. Bias may occur between loci, or between alleles within a locus, and may differ between sample donors at the same loci. Previous research has suggested that omitting denaturation of the template prior to amplification can reduce the observed bias significantly. Comparison of the two methods (with and without denaturation) has found that nondenaturation of template reverses the direction of bias observed between allelic pairs following MDA. By combining two MDA reactions, one denatured and one nondenatured, the bias was found to be reduced significantly, aiding copy number analysis and subsequent genotyping.
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Affiliation(s)
- Kaye N Ballantyne
- Biology Division, Victoria Police Forensic Services Department, Macleod, 3085 VIC, Australia.
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