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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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2
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Connon CC. Low Volume STR Amplification Options: Coupling with Standard or Fast PCR, Traditional or Normalized DNA Extraction, and/or Traditional or Alternative Capillary Electrophoresis. Methods Mol Biol 2023; 2685:263-282. [PMID: 37439988 DOI: 10.1007/978-1-0716-3295-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
STR amplification leads directly to profile development, which is also impacted by DNA extraction and capillary electrophoresis detection. Amplification for forensic human identification purposes is inherently a costly process; reduced volume reactions have long been an effective cost-savings measure. Processing known, high-quality, single-source DNA samples (i.e., buccal samples) allows for the use of even lower reaction volumes. This chapter provides examples of 3 μL and 6 μL reactions for a variety of commercial amplification kits for use with buccal samples, including standard and fast PCR using KAPA2G™ Multiplex Mix. These reactions can be utilized with traditional DNA extracts or those obtained from a normalized extraction with the ChargeSwitch® Forensic DNA Purification Kit. They can be detected via traditional capillary electrophoresis using POP-4™ polymer and a 36 cm array, or an alternative method using POP-6™ polymer and a 22 cm array on the 3130 series Genetic Analyzer instruments. This chapter also includes protocols for the normalized extraction and alternative detection method.
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3
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Low stutter ratio by SuperFi polymerase. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Romsos EL, French JL, Smith M, Figarelli V, Harran F, Vandegrift G, Moreno LI, Callaghan TF, Brocato J, Vaidyanathan J, Pedroso JC, Amy A, Stoiloff S, Morillo VH, Czetyrko K, Johnson ED, de Tagyos J, Murray A, Vallone PM. Results of the 2018 Rapid DNA Maturity Assessment. J Forensic Sci 2020; 65:953-959. [PMID: 31985834 PMCID: PMC11034630 DOI: 10.1111/1556-4029.14267] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/25/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023]
Abstract
Three commercially available integrated rapid DNA instruments were tested as a part of a rapid DNA maturity assessment in July of 2018. The assessment was conducted with sets of blinded single-source reference samples provided to participants for testing on the individual rapid platforms within their laboratories. The data were returned to the National Institute of Standards and Technology (NIST) for review and analysis. Both FBI-defined automated review (Rapid DNA Analysis) and manual review (Modified Rapid DNA Analysis) of the datasets were conducted to assess the success of genotyping the 20 Combined DNA Index System (CODIS) core STR loci and full profiles generated by the instruments. Genotype results from the multiple platforms, participating laboratories, and STR typing chemistries were combined into a single analysis. The Rapid DNA Analysis resulted in a success rate of 80% for full profiles (85% for the 20 CODIS core loci) with automated analysis. Modified Rapid DNA Analysis resulted in a success rate of 90% for both the CODIS 20 core loci and full profiles (all attempted loci per chemistry). An analysis of the peak height ratios demonstrated that 95% of all heterozygous alleles were above 59% heterozygote balance. For base-pair sizing precision, the precision was below the standard 0.5 bp deviation for both the ANDE 6C System and the RapidHIT 200.
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Affiliation(s)
- Erica L Romsos
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
| | | | - Mark Smith
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Vincent Figarelli
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Frederick Harran
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Glenn Vandegrift
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Lilliana I Moreno
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Thomas F Callaghan
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Joanie Brocato
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Janaki Vaidyanathan
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Juan C Pedroso
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Andrea Amy
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Stephanie Stoiloff
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Victor H Morillo
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Karina Czetyrko
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Elizabeth D Johnson
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Jessica de Tagyos
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Ashley Murray
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
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Abraham A, Thirumalairaj K, Gaikwad N, Muthukkaruppan V, Reddy AG, Thangaraj K, Kim U, Vanniarajan A. Retinoblastoma discordance in families with twins. Indian J Ophthalmol 2019; 67:436-439. [PMID: 30777982 PMCID: PMC6407382 DOI: 10.4103/ijo.ijo_1245_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/28/2022] Open
Abstract
Retinoblastoma has an increased inheritance risk of germline RB1 mutations in offspring and siblings, especially twins. Three families, each having one retinoblastoma-affected twin, were selected for genetic analysis and DNA profiling. Germline RB1 mutations were found in all probands. DNA profiling carried on similar-looking twins of families I and II, proved them to be fraternal. This study demonstrates the importance of genetic analysis of RB1 gene for risk prediction in retinoblastoma families. It also emphasizes that DNA profiling is a mandate for genetic screening of families with twins, thus adding a new dimension in counseling of retinoblastoma.
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Affiliation(s)
- Aloysius Abraham
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Kannan Thirumalairaj
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Namrata Gaikwad
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | - Veerappan Muthukkaruppan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, India
| | - Alla G Reddy
- Council of Scientific and Industrial Research Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Kumarasamy Thangaraj
- Council of Scientific and Industrial Research Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
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7
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One-step DNA purification and amplification on an integrated plastic microdevice for on-site identification of foodborne pathogens. Anal Chim Acta 2018; 1040:63-73. [DOI: 10.1016/j.aca.2018.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/06/2018] [Accepted: 06/18/2018] [Indexed: 11/16/2022]
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8
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Cornelis S, Fauvart M, Gansemans Y, Vander Plaetsen AS, Colle F, Wiederkehr RS, Deforce D, Stakenborg T, Van Nieuwerburgh F. Multiplex STR amplification sensitivity in a silicon microchip. Sci Rep 2018; 8:9853. [PMID: 29959383 PMCID: PMC6026139 DOI: 10.1038/s41598-018-28229-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/18/2018] [Indexed: 11/30/2022] Open
Abstract
The demand for solutions to perform forensic DNA profiling outside of centralized laboratories is increasing. We here demonstrate highly sensitive STR amplification using a silicon micro-PCR (µPCR) chip. Exploiting industry-standard semiconductor manufacturing processes, a device was fabricated that features a small form factor thanks to an integrated heating element covering three parallel micro-reactors with a reaction volume of 0.5 µl each. Diluted reference DNA samples (1 ng–31 pg) were amplified on the µPCR chip using the forensically validated AmpFISTR Identifier Plus kit, followed by conventional capillary electrophoresis. Complete STR profiles were generated with input DNA quantities down to 62 pg. Occasional allelic dropouts were observed from 31 pg downward. On-chip STR profiles were compared with those of identical samples amplified using a conventional thermal cycler for direct comparison of amplification sensitivity in a forensic setting. The observed sensitivity was in line with kit specifications for both µPCR and conventional PCR. Finally, a rapid amplification protocol was developed. Complete STR profiles could be generated in less than 17 minutes from as little as 125 pg template DNA. Together, our results are an important step towards the development of commercial, mass-produced, relatively cheap, handheld devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.,Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | - Frederik Colle
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | - Tim Stakenborg
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
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9
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Gibson-Daw G, Crenshaw K, McCord B. Optimization of ultrahigh-speed multiplex PCR for forensic analysis. Anal Bioanal Chem 2017; 410:235-245. [DOI: 10.1007/s00216-017-0715-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 11/29/2022]
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10
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DuVall JA, Le Roux D, Thompson BL, Birch C, Nelson DA, Li J, Mills DL, Tsuei AC, Ensenberger MG, Sprecher C, Storts DR, Root BE, Landers JP. Rapid multiplex DNA amplification on an inexpensive microdevice for human identification via short tandem repeat analysis. Anal Chim Acta 2017. [PMID: 28622802 DOI: 10.1016/j.aca.2017.04.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis. Primer concentrations were adjusted specifically for microdevice amplification, resulting in well-balanced short tandem repeat (STR) profiles. Furthermore, studies were performed to push the limits of the DNA polymerase to achieve rapid, multiplexed PCR on various substrates, including transparent and black polyethylene terephthalate (Pe), and with two distinct adhesives, toner and heat sensitive adhesive (HSA). Rapid STR-based multiplexed PCR amplification is demonstrated in 15 min on a Pe microdevice using a custom-built system for fluid flow control and thermocycling for the full 10-plex, and in 10 min for a smaller multiplex consisting of six core CODIS loci plus Amelogenin with amplicons shorter than 200bp. Lastly, preliminary studies indicate the capability of this PCR microdevice platform to be integrated with both upstream DNA extraction, and downstream microchip electrophoresis. This, coupled to the use of reagents that are compatible with lyophilization (lyo-compatible) for PCR, represents the potential for a fully integrated rotationally-driven microdevice for complete forensic DNA analysis.
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Affiliation(s)
- Jacquelyn A DuVall
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Delphine Le Roux
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Brandon L Thompson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Christopher Birch
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Daniel A Nelson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Jingyi Li
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Daniel L Mills
- TeGrex Technologies, Charlottesville, VA 22904, United States
| | - An-Chi Tsuei
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | | | | | | | - Brian E Root
- Applied Research Institute, University of Virginia, Charlottesville, VA 22904, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22904, United States; Department of Pathology, University of Virginia Health Science Center, Charlottesville, VA 22904, United States; TeGrex Technologies, Charlottesville, VA 22904, United States.
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11
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Han J, Sun J, Zhao L, Zhao W, Liu Y, Li C. Validation study of a 15-plex rapid STR amplification system for human identification. Forensic Sci Int Genet 2017; 28:71-81. [DOI: 10.1016/j.fsigen.2017.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 12/19/2016] [Accepted: 01/25/2017] [Indexed: 11/16/2022]
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12
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Frégeau CJ, Dalpé C. Simulated radioactive decontamination of biological samples using a portable DNA extraction instrument for rapid DNA profiling. Forensic Sci Int 2016; 259:161-78. [DOI: 10.1016/j.forsciint.2015.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 12/09/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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13
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Iyavoo S, Wolejko A, Furmanczyk D, Graham R, Myers R, Haizel T. Reduced PCR cycling time amplification using AmpFℓSTR ® Identifiler ® kit. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Thong Z, Phua YH, Loo ES, Goh SK, Ang J, Looi WF, Syn CKC. Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell ® DNA IQ™/Identifiler ® Plus/ABI 3500xL workflow. Forensic Sci Int Genet 2015; 19:22-27. [DOI: 10.1016/j.fsigen.2015.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 11/26/2022]
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15
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Asari M, Okuda K, Hoshina C, Omura T, Tasaki Y, Shiono H, Matsubara K, Shimizu K. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers. Anal Biochem 2015; 494:16-22. [PMID: 26505528 DOI: 10.1016/j.ab.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/06/2015] [Accepted: 10/14/2015] [Indexed: 01/20/2023]
Abstract
The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Tomohiro Omura
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Yoshikazu Tasaki
- Department of Hospital Pharmacy and Pharmacology, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroshi Shiono
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kazuo Matsubara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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Romsos EL, Vallone PM. Rapid PCR of STR markers: Applications to human identification. Forensic Sci Int Genet 2015; 18:90-9. [DOI: 10.1016/j.fsigen.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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17
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Lau SKP, Sridhar S, Ho CC, Chow WN, Lee KC, Lam CW, Yuen KY, Woo PCY. Laboratory diagnosis of melioidosis: past, present and future. Exp Biol Med (Maywood) 2015; 240:742-51. [PMID: 25908634 DOI: 10.1177/1535370215583801] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Melioidosis is an emerging, potentially fatal disease caused by Burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. However, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. Isolation of B. pseudomallei from clinical specimens has been improved with the use of selective media. However, even with positive cultures, identification of B. pseudomallei can be difficult in clinical microbiology laboratories, especially in non-endemic areas where clinical suspicion is low. Commercial identification systems may fail to distinguish between B. pseudomallei and closely related species such as Burkholderia thailandensis. Genotypic identification of suspected isolates can be achieved by sequencing of gene targets such as groEL which offer higher discriminative power than 16S rRNA. Specific PCR-based identification of B. pseudomallei has also been developed using B. pseudomallei-specific gene targets such as Type III secretion system and Tat-domain protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolutionary technique for pathogen identification, has been shown to be potentially useful for rapid identification of B. pseudomallei, although existing databases require optimization by adding reference spectra for B. pseudomallei. Despite these advances in bacterial identification, diagnostic problems encountered in culture-negative cases remain largely unresolved. Although various serological tests have been developed, they are generally unstandardized "in house" assays and have low sensitivities and specificities. Although specific PCR assays have been applied to direct clinical and environmental specimens, the sensitivities for diagnosis remain to be evaluated. Metabolomics is an uprising tool for studying infectious diseases and may offer a novel approach for exploring potential diagnostic biomarkers. The metabolomics profiles of B. pseudomallei culture supernatants can be potentially distinguished from those of related bacterial species including B. thailandensis . Further studies using bacterial cultures and direct patient samples are required to evaluate the potential of metabolomics for improving diagnosis of melioidosis.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Chi-Chun Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
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18
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Rapid genotyping of 25 autosomal STRs in a Japanese population using fluorescent universal primers containing locked nucleic acids. J Forensic Leg Med 2015; 31:36-41. [PMID: 25735782 DOI: 10.1016/j.jflm.2015.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/26/2014] [Accepted: 01/09/2015] [Indexed: 12/12/2022]
Abstract
Amplification of fluorescently labeled products is one of the most popular methods for genotyping genetic variations. Two-step amplification using fluorescent universal primers simultaneously produces multiple targeted fragments labeled with fluorescent dyes, and this strategy is applicable to large-scale, cost-effective genotyping. In this study, we developed a fast PCR-based, multiple short tandem repeat (STR) genotyping method using fluorescent universal primers containing locked nucleic acids (LNAs). Four amplification reactions, each assaying six or seven markers and using 0.5-1.0 ng of genomic DNA, produced obvious Fam-labeled peaks in all 26 loci tested (25 autosomal STRs and amelogenin). The overall amplification time was 37 min. Moreover, fluorescent signals for the 25 STRs obtained from LNA-containing primers were 1.5-9.0 fold higher compared to those from non-LNA primers. Using genomic DNA from 120 Japanese individuals, 16 out of the 25 STRs had observed heterozygosity greater than 0.7. Some of these 25 STRs also had high discriminatory power, similar to that of the 13 core STRs in the Combined DNA Index System dataset. The probability of incorrectly assigning a match based on the accumulated matching probability for these 25 STRs is 1.2 × 10(-22), and their combined use can provide robust information for Japanese forensics.
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19
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Butts ELR, Vallone PM. Rapid PCR protocols for forensic DNA typing on six thermal cycling platforms. Electrophoresis 2014; 35:3053-61. [DOI: 10.1002/elps.201400179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/06/2014] [Accepted: 06/26/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Erica L. R. Butts
- National Institute of Standards and Technology; Biomolecular Measurement Division; Gaithersburg MD USA
| | - Peter M. Vallone
- National Institute of Standards and Technology; Biomolecular Measurement Division; Gaithersburg MD USA
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Bahlmann S, Hughes-Stamm S, Gangitano D. Development and evaluation of a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling. Leg Med (Tokyo) 2014; 16:227-33. [PMID: 24842299 DOI: 10.1016/j.legalmed.2014.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 11/30/2022]
Abstract
Forensic DNA profiling is a multi-step process taking approximately 10h to complete. A reduction in the amount of time required for the amplification step would allow for faster human identification and increase laboratory throughput. The goal of this work was to optimize and evaluate a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling. By pairing fast chemistries with a fast thermal cycler, we were able to reduce the amplification time by 70% (1 h). Sensitivity and heterozygous peak height ratios were comparable between the fast and standard protocols. However, there was a notable decrease (5%) in peak height ratio at the D18S51 locus with the fast cycling method. An increase in average mean stutter for combined loci of 2.6% was observed in profiles amplified using the fast protocol compared to the standard system. Our results suggest that with further optimization and validation the fast protocol can be used to replace the standard amplification conditions.
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Affiliation(s)
- Sarah Bahlmann
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX 77340-2525, United States.
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Jin HX, Seo SB, Lee HY, Cho S, Ge J, King J, Budowle B, Lee SD. Differences of PCR efficiency between two-step PCR and standard three-step PCR protocols in short tandem repeat amplification. AUST J FORENSIC SCI 2013. [DOI: 10.1080/00450618.2013.788681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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