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Vajpayee K, Dash HR, Parekh PB, Shukla RK. PCR inhibitors and facilitators - Their role in forensic DNA analysis. Forensic Sci Int 2023; 349:111773. [PMID: 37399774 DOI: 10.1016/j.forsciint.2023.111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.
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Affiliation(s)
- Kamayani Vajpayee
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Hirak Ranjan Dash
- National Forensic Science University, New Delhi Campus, New Delhi, India
| | - Prakshal B Parekh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Ritesh K Shukla
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India.
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Lee SJ, Park SY, Lee KH, Lee MW, Yu CY, Maeng J, Kim HD, Kim SW. Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase. Int J Mol Sci 2023; 24:11405. [PMID: 37511160 PMCID: PMC10379934 DOI: 10.3390/ijms241411405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Taq DNA polymerases have played an important role in molecular biology for several years and are frequently used for polymerase chain reaction (PCR); hence, there is an increasing interest in developing a convenient method for preparing Taq DNA polymerase for routine use in laboratories. We developed a method using Escherichia coli (E. coli) that expresses thermostable Taq DNA polymerase directly in the PCR without purification. The Taq gene was transformed into E. coli and expressed. After overnight incubation and washing, E. coli-expressing Taq DNA polymerase (EcoliTaq) was used as the DNA polymerase without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. With a high-pH buffer containing 2% Tween 20 and 0.4 M trehalose, EcoliTaq facilitated direct PCR amplification from anticoagulated whole blood samples. EcoliTaq exhibited good performance in allele-specific PCR using both purified DNA and whole blood samples. Furthermore, it proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification. We developed a simple and cost-effective direct and hot-start PCR method in which EcoliTaq was used directly as a PCR enzyme, thus eliminating the laborious and time-consuming steps of polymerase purification.
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Affiliation(s)
- Sun Ju Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Sang-Yong Park
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Kwang-Ho Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, ASAN Medical Center, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Min-Woo Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Chae-Yeon Yu
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Jaeyoung Maeng
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Hyeong-Dong Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Suhng Wook Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
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Foley MM. Rapid DNA Profile Development with Applied Biosystems RapidHIT™ ID System. Methods Mol Biol 2023; 2685:367-396. [PMID: 37439994 DOI: 10.1007/978-1-0716-3295-6_23] [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
The RapidHIT™ ID System by Applied Biosystems allows the generation of a CODIS compatible STR profile in 90 min. The preloaded cartridges, fully automated workflow, and user-friendly computer interface allow for quick and simple single sample processing both in the laboratory and outside by non-laboratory personnel, like law enforcement officers. DNA processing utilizes a direct amplification workflow to generate an STR profile targeting the CODIS or ESS core loci. In conjunction with the RapidLINK™ Software, the system performs an initial analysis, flagging any profiles that do not meet single-source full profile parameters. Additionally, the RapidLINK™ allows for users to manage a multi-instrument/multi-location Rapid DNA system and view results in real-time. This gives users off-site the ability to track and even analyze results. The system allows for rapid reference sample analysis in locations like booking stations and national or border security agencies to obtain quick feedback of database hits for investigative leads while the subject is still in custody. RapidHIT™ ID DNA systems can also be set up at sites to aid in victim identification during mass disasters. The following chapter describes the process of generating a forensic DNA profile using the RapidHIT™ ID instrumentation from start to finish. Additionally, basic use and analysis using the RapidLINK™ and GeneMarker™ HID software is included.
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Affiliation(s)
- Megan M Foley
- Department of Forensic Sciences, The George Washington University, Washington, DC, USA.
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Alyethodi RR, Singh U, Kumar S, Alex R, Sengar GS, Raja TV, Deb R, Prakash B. Designing, optimization, and validation of whole blood direct T-ARMS PCR for precise and rapid genotyping of complex vertebral malformation in cattle. BMC Biotechnol 2021; 21:36. [PMID: 34022869 PMCID: PMC8141239 DOI: 10.1186/s12896-021-00696-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/11/2021] [Indexed: 12/04/2022] Open
Abstract
Background DNA testing in the cattle industry undergoes multiple hurdles. Successful genotyping involves the transportation of samples from the field to the laboratory in a chilled environment followed by DNA extraction, and finally, a specific genotyping protocol is followed. Various researches are focused on overcoming these issues. Microcards offer blood transportation at ambient temperature. Direct PCR methods can save the time of DNA extraction but available only for simplex PCR. Tetra Primer-Amplification Refractory Mutation System based Polymerase Chain Reaction (T-ARMS PCR) can make DNA testing faster in a low-cost setting. The present study was aimed to design, optimize, and validate a T-ARMS PCR for faster DNA testing of SNP responsible for Complex Vertebral Malformation (CVM)-an important genetic disease of the cattle industry. Further, a direct T-ARMS PCR from whole blood was developed to avoid the DNA extraction steps. Lastly, using the optimized protocol, genotyping of blood spotted on Microcard eliminates the need for cold chain maintenance in the transportation of samples. Results The present study demonstrated a novel T-ARMS PCR-based genotyping of the SNP rs438228855, which is responsible for CVM. Here, wild genotypes were recognized by 389 bp and 199 bp bands in agarose gel, while the carrier genotype showed an additional 241 bp band. The developed protocol was validated using PCR-Primer Introduced Restriction Analysis (PCR-PIRA) and sequencing. The present study further established a direct T-ARMS PCR for this SNP from whole blood. Different conditions such as heparin and EDTA treated blood, the need for pre-treatment, and two different DNA Polymerases for the direct PCR were optimized. Finally, our optimized protocol successfully genotyped the whole blood samples dried on Insta™DNA cards. Conclusions The present study reported the usefulness of primer modified T-ARMS PCR for detecting CVM for the first time. To the best of our knowledge, direct PCR in T-ARMS PCR has never been reported. Lastly, the use of microcards in the developed protocol can make the assay useful in the DNA testing of field samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00696-5.
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Affiliation(s)
- R R Alyethodi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Garacharma, Andaman and Nicobar Islands, 744101, India.
| | - U Singh
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Kumar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Alex
- Animal genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - G S Sengar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - T V Raja
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Deb
- ICAR-National Research centre on Pig, Guwahati, Assam, India
| | - B Prakash
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
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Nakano S, Tomaru Y, Kubota T, Takase H, Mochizuki M, Shimizu N, Sugita S. Multiplex Solid-Phase Real-Time Polymerase Chain Reaction without DNA Extraction: A Rapid Intraoperative Diagnosis Using Microvolumes. Ophthalmology 2020; 128:729-739. [PMID: 32987046 DOI: 10.1016/j.ophtha.2020.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Current polymerase chain reaction (PCR) methods for the diagnosis of infections are time consuming and require large sample volume and skilled technicians. We developed a novel, easy-to-use, and rapid (processing time, 1 minute; total time, 33 minutes) multiplex real-time PCR test (Direct Strip PCR) that did not require DNA extraction to detect 9 pathogens that could cause uveitis in 20-μl samples. DESIGN Multicenter prospective evaluation of a diagnostic PCR test. PARTICIPANTS A total of 511 participants (patients with infectious uveitis and controls) were examined at 18 institutes worldwide. METHODS After validation, intraocular fluid samples were subjected to etiologic or exclusive diagnosis, including intraoperative rapid diagnosis. MAIN OUTCOME MEASURES The concordance and correlations between Direct Strip PCR and quantitative PCR (qPCR) results. RESULTS Direct Strip PCR exhibited rapid detection, good repeatability and specificity, long storage stability, and detection ability equal to that of qPCR. It also showed low interinstitutional variability compared with qPCR, even when PCR beginners used various real-time PCR machines. The Direct Strip PCR for 9 pathogens exhibited high concordance against the qPCR (positive concordance rate, 98.8%-100%; negative concordance rate, 99.8%-100%; κ coefficient, 0.969-1.000; P < 0.001-0.031). Additionally, results obtained using Direct Strip PCR and qPCR were highly correlated (ρ = 0.748; P < 0.001). This assay was used for rapid intraoperative diagnosis. CONCLUSIONS The Direct Strip PCR test may improve the prognosis of various infectious diseases because it facilitates rapid etiologic evaluation at the first hospital visit and can be used for intraoperative diagnosis.
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Affiliation(s)
- Satoko Nakano
- Department of Ophthalmology, Oita University, Yufu, Japan
| | - Yasuhiro Tomaru
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Hiroshi Takase
- Department of Ophthalmology & Visual Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Manabu Mochizuki
- Department of Ophthalmology & Visual Science, Tokyo Medical and Dental University, Tokyo, Japan; Miyata Eye Hospital, Miyakonojo, Japan
| | - Norio Shimizu
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sunao Sugita
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
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Liu X, Zhang C, Hua K, Liang J, Li H, Ma T, Zhu J, Cui Y. Direct genotyping from whole blood using alkaline polyethylene glycol. Anal Biochem 2019; 582:113351. [DOI: 10.1016/j.ab.2019.113351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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Park JH, Han JH, Park G. Rapid and Reliable One-Step ABO Genotyping Using Direct Real-Time Allele-Specific PCR and Melting Curve Analysis Without DNA Preparation. Indian J Hematol Blood Transfus 2019; 35:531-537. [PMID: 31388269 DOI: 10.1007/s12288-018-1053-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/24/2018] [Indexed: 11/26/2022] Open
Abstract
ABO genotyping is a molecular diagnostic technique important for transfusion and transplantation in medicine, and human identification in forensic science. Because ABO genotyping are labor intensive and time consuming, the genotyping cannot be firstly used to resolve the serological ABO discrepancy in blood bank. For rapid one-step ABO genotyping, we developed direct, real-time, allele-specific polymerase chain reaction (PCR), and melting curve analysis (DRAM assay) without DNA preparation. In DRAM assay, we used a special PCR buffer for direct PCR, a rapid RBC lysis buffer, white blood cells as template without DNA preparation, allele-specific primers for discriminating three ABO alleles (261G/del, 796C/A, and 803G/C), and melting curve analysis as a detection method. There was 100% concordance among the results of ABO genotyping by the DRAM assay, serologic typing, PCR-RFLP and PCR-direct sequencing of 96 venous blood samples. We were able to reduce the number of manual steps to three and the hands-on time to 12 min, compared to seven steps and approximately 40 min for conventional ABO genotyping using allele-specific PCR with purified DNA and agarose gel electrophoresis. We have established and validated the DRAM assay for rapid and reliable one-step ABO genotyping in a closed system. The DRAM assay with an appropriate number of allele-specific primers could help in resolving ABO discrepancies and should be valuable in clinical laboratory and blood bank.
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Affiliation(s)
- Jun-Hee Park
- 1Department of Otolaryngology-Head and Neck Surgery, Chosun University College of Medicine, 365 Pilmun-daero, Dong-gu, Gwangju, 61453 South Korea
| | - Ji-Hye Han
- 1Department of Otolaryngology-Head and Neck Surgery, Chosun University College of Medicine, 365 Pilmun-daero, Dong-gu, Gwangju, 61453 South Korea
| | - Geon Park
- 2Department of Laboratory Medicine, Chosun University College of Medicine, 365 Pilmun-daero, Dong-gu, Gwangju, 61453 South Korea
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Li L, He JA, Wang W, Xia Y, Song L, Chen ZH, Zuo HZ, Tan XP, Ho AHP, Kong SK, Loo JFC, Li HW, Gu D. Development of a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for clinical Zika diagnosis. Int J Infect Dis 2019; 85:167-174. [PMID: 31202908 DOI: 10.1016/j.ijid.2019.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/28/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE The nucleic acid-based polymerase chain reaction (PCR) assay is commonly applied to detect infection with Zika virus (ZIKV). However, the time- and labor-intensive sample pretreatment required to remove inhibitors that cause false-negative results in clinical samples is impractical for use in resource-limited areas. The aim was to develop a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for ZIKV diagnosis directly from clinical samples. METHODS The combination of inhibitor-tolerant polymerases, polymerase enhancers, and dirRT-qPCR conditions was optimized for various clinical samples including blood and serum. Sensitivity was evaluated with standard DNA spiked in simulated samples. Specificity was evaluated using clinical specimens of other infections such as dengue virus and chikungunya virus. RESULTS High specificity and sensitivity were achieved, and the limit of detection (LOD) of the assay was 9.5×101 ZIKV RNA copies/reaction. The on-site clinical diagnosis of ZIKV required a 5μl sample and the diagnosis could be completed within 2h. CONCLUSIONS This robust dirRT-qPCR assay shows a high potential for point-of-care diagnosis, and the primer-probe combinations can also be extended for other viral detection. It realizes the goal of large-scale on-site screening for viral infections and could be used for early diagnosis and the prevention and control of viral outbreaks.
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Affiliation(s)
- Lang Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Jian-An He
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Wei Wang
- Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China
| | - Yun Xia
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Li Song
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Ze-Han Chen
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Hang-Zhi Zuo
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Xuan-Ping Tan
- Shenzhen gene-one Biotechnology Co., Ltd., 518000, PR China
| | - Aaron Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Jacky Fong-Chuen Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China.
| | - Hua-Wen Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China.
| | - Dayong Gu
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China; Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China.
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Guan F, Jin Y, Zhao J, Ai J, Luo Y. A Novel Direct PCR Lysis Buffer Can Improve PCR from Meat Matrices. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-018-1342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lee JW, Jung JY, Lim SK. Simple and rapid identification of saliva by detection of oral streptococci using direct polymerase chain reaction combined with an immunochromatographic strip. Forensic Sci Int Genet 2018; 33:155-160. [DOI: 10.1016/j.fsigen.2017.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/14/2017] [Accepted: 12/19/2017] [Indexed: 01/25/2023]
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Direct DNA and RNA detection from large volumes of whole human blood. Sci Rep 2018; 8:3410. [PMID: 29467420 PMCID: PMC5821888 DOI: 10.1038/s41598-018-21224-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/21/2018] [Indexed: 11/25/2022] Open
Abstract
PCR inhibitors in clinical specimens negatively affect the sensitivity of diagnostic PCR and RT-PCR or may even cause false-negative results. To overcome PCR inhibition, increase the sensitivity of the assays and simplify the detection protocols, simple methods based on quantitative nested real-time PCR and RT-PCR were developed to detect exogenous DNA and RNA directly from large volumes of whole human blood (WHB). Thermus thermophilus (Tth) polymerase is resistant to several common PCR inhibitors and exhibits reverse transcriptase activity in the presence of manganese ions. In combination with optimized concentrations of magnesium ions and manganese ions, Tth polymerase enabled efficient detection of DNA and RNA from large volumes of WHB treated with various anticoagulants. The applicability of these methods was further demonstrated by examining WHB specimens collected from different healthy individuals and those stored under a variety of conditions. The detection limit of these methods was determined by detecting exogenous DNA, RNA, and bacteria spiked in WHB. To the best of our knowledge, direct RNA detection from large volumes of WHB has not been reported. The results of the developed methods can be obtained within 4 hours, making them possible for rapid and accurate detection of disease-causing agents from WHB.
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Gorakshakar A, Gogri H, Ghosh K. Evolution of technology for molecular genotyping in blood group systems. Indian J Med Res 2018; 146:305-315. [PMID: 29355136 PMCID: PMC5793464 DOI: 10.4103/ijmr.ijmr_914_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The molecular basis of the blood group antigens was identified first in the 1980s and 1990s. Since then the importance of molecular biology in transfusion medicine has been described extensively by several investigators. Molecular genotyping of blood group antigens is one of the important aspects and is successfully making its way into transfusion medicine. Low-, medium- and high-throughput techniques have been developed for this purpose. Depending on the requirement of the centre like screening for high- or low-prevalence antigens where antisera are not available, correct typing of multiple transfused patients, screening for antigen-negative donor units to reduce the rate of alloimmunization, etc. a suitable technique can be selected. The present review discusses the evolution of different techniques to detect molecular genotypes of blood group systems and how these approaches can be used in transfusion medicine where haemagglutination is of limited value. Currently, this technology is being used in only a few blood banks in India. Hence, there is a need for understanding this technology with all its variations.
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Affiliation(s)
- Ajit Gorakshakar
- Department of Transfusion Medicine, ICMR- National Institute of Immunohaematology, Mumbai, India
| | - Harita Gogri
- Department of Transfusion Medicine, ICMR- National Institute of Immunohaematology, Mumbai, India
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Ambers A, Wiley R, Novroski N, Budowle B. Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ ® swabs. Forensic Sci Int Genet 2018; 32:80-87. [DOI: 10.1016/j.fsigen.2017.10.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 11/26/2022]
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Farid AH, Rupasinghe PP. A fast and accurate method of detecting Aleutian mink disease virus in blood and tissues of chronically infected mink. Can J Microbiol 2017; 63:341-349. [PMID: 28177788 DOI: 10.1139/cjm-2016-0567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The objective of this study was to assess the sensitivity of the Omni Klentaq-LA DNA polymerase for detecting Aleutian mink disease virus (AMDV) in mink blood and tissues by PCR without DNA extraction. The presence of AMDV DNA was directly tested by Klentaq in the plasma, serum, whole blood, and spleen homogenates of 188 mink 4 and 16 months after inoculation with the virus. Samples from bone marrow, small intestine, liver, lungs, kidneys, and lymph nodes of 20 of the same mink were also tested by Klentaq. DNA was extracted from paired samples of plasma and the aforesaid tissues by a commercial nucleic acid extraction kit (Dynabeads Silane) and tested by PCR. Compared with the extracted DNA, Klentaq detected a significantly greater number of samples in the whole blood, serum, plasma, spleen, and small intestine. It was concluded that Klentaq is a preferred system for directly detecting AMDV DNA in mink blood and tissues. The lower success rate of extracted DNA compared with Klentaq could be the result of DNA losses during the extraction process. This is an important factor in chronically infected mink, which have a low AMDV copy number in the bloodstream. Direct AMDV detection also reduces the cost of PCR amplification and lowers the risk of sample contamination.
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Affiliation(s)
- A H Farid
- Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada.,Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada
| | - P P Rupasinghe
- Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada.,Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada
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16
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Silvy M, Brès JC, Grimaldi A, Movia C, Muriel V, Roubinet F, Chiaroni J, Bailly P. A simple genotyping procedure without DNA extraction to identify rare blood donors. Vox Sang 2015; 109:173-80. [PMID: 25854538 DOI: 10.1111/vox.12261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/14/2015] [Accepted: 01/19/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Transfusion-induced alloimmunization has severe clinical consequences including haemolytic transfusion reactions, impaired transfused RBCs longevity and greater difficulty in finding compatible blood. Molecular analysis of genomic DNA now permits prediction of blood group phenotypes based on identification of single nucleotide polymorphisms. Implementation of molecular technologies in donor centres would be helpful in finding RBC units for special patient populations, but DNA extraction remains an obstacle to donor genotyping. MATERIALS AND METHODS We propose a simple method compatible with high throughput that allows blood group genotyping using a multiplex commercial kit without the need for DNA extraction. The principle relies on pre-PCR treatment of whole blood using heating/cooling procedure in association with a recombinant hotstart polymerase. RESULTS In a prospective analysis, we yielded 5628 alleles identification and designated 63 donors with rare blood, that is either negative for a high-frequency antigen or with a rare combination of common antigens. CONCLUSION The procedure was optimized for simplicity of use in genotyping platform and would allow not only to supply antigen-matched products to recipients but also to find rare phenotypes. This methodology could also be useful for establishing a donor repository for human platelet antigens (HPA)-matched platelets since the same issues are involved for patients with neonatal alloimmune thrombocytopenia or post-transfusion purpura.
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Affiliation(s)
- M Silvy
- Établissement Français du Sang, Blood Cell Grand Sud, Montpellier-Marseille, France.,UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
| | - J-C Brès
- Établissement Français du Sang, Blood Cell Grand Sud, Montpellier-Marseille, France
| | - A Grimaldi
- UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
| | - C Movia
- UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
| | - V Muriel
- UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
| | - F Roubinet
- Établissement Français du Sang, Blood Cell Grand Sud, Montpellier-Marseille, France
| | - J Chiaroni
- Établissement Français du Sang, Blood Cell Grand Sud, Montpellier-Marseille, France.,UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
| | - P Bailly
- Établissement Français du Sang, Blood Cell Grand Sud, Montpellier-Marseille, France.,UMR 7268 ADÉS Aix-Marseille Université-EFS-CNRS, Marseille, France
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17
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Killelea T, Ralec C, Bossé A, Henneke G. PCR performance of a thermostable heterodimeric archaeal DNA polymerase. Front Microbiol 2014; 5:195. [PMID: 24847315 PMCID: PMC4019886 DOI: 10.3389/fmicb.2014.00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/12/2014] [Indexed: 11/17/2022] Open
Abstract
DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.
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Affiliation(s)
- Tom Killelea
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Céline Ralec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Audrey Bossé
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Ghislaine Henneke
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
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18
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Aboud M, Oh HH, McCord B. Rapid direct PCR for forensic genotyping in under 25 min. Electrophoresis 2013; 34:1539-47. [DOI: 10.1002/elps.201200570] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/17/2013] [Accepted: 02/18/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Maurice Aboud
- Department of Chemistry and Biochemistry and International Forensic Research Institute; Florida International University; Miami; FL; USA
| | - Hye Hyun Oh
- DNA Forensic Division; Supreme Prosecutors’ Office; Seoul; Korea
| | - Bruce McCord
- Department of Chemistry and Biochemistry and International Forensic Research Institute; Florida International University; Miami; FL; USA
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19
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Sim JE, Park SJ, Lee HC, Kim SY, Kim JY, Lee SH. High-Throughput STR Analysis for DNA Database Using Direct PCR,. J Forensic Sci 2013; 58:989-92. [DOI: 10.1111/1556-4029.12166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/22/2012] [Accepted: 06/30/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Jeong Eun Sim
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Su Jeong Park
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Han Chul Lee
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Se-Yong Kim
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | | | - Seung Hwan Lee
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
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20
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Abstract
PCR is an important and powerful tool in several fields, including clinical diagnostics, food analysis, and forensic analysis. In theory, PCR enables the detection of one single cell or DNA molecule. However, the presence of PCR inhibitors in the sample affects the amplification efficiency of PCR, thus lowering the detection limit, as well as the precision of sequence-specific nucleic acid quantification in real-time PCR. In order to overcome the problems caused by PCR inhibitors, all the steps leading up to DNA amplification must be optimized for the sample type in question. Sampling and sample treatment are key steps, but most of the methods currently in use were developed for conventional diagnostic methods and not for PCR. Therefore, there is a need for fast, simple, and robust sample preparation methods that take advantage of the accuracy of PCR. In addition, the thermostable DNA polymerases and buffer systems used in PCR are affected differently by inhibitors. During recent years, real-time PCR has developed considerably and is now widely used as a diagnostic tool. This technique has greatly improved the degree of automation and reduced the analysis time, but has also introduced a new set of PCR inhibitors, namely those affecting the fluorescence signal. The purpose of this chapter is to view the complexity of PCR inhibition from different angles, presenting both molecular explanations and practical ways of dealing with the problem. Although diagnostic PCR brings together scientists from different diagnostic fields, end-users have not fully exploited the potential of learning from each other. Here, we have collected knowledge from archeological analysis, clinical diagnostics, environmental analysis, food analysis, and forensic analysis. The concept of integrating sampling, sample treatment, and the chemistry of PCR, i.e., pre-PCR processing, will be addressed as a general approach to overcoming real-time PCR inhibition and producing samples optimal for PCR analysis.
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Affiliation(s)
- Johannes Hedman
- Swedish National Laboratory of Forensic Science, Linköping, Sweden.
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21
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Laurin N, DeMoors A, Frégeau C. Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards. Forensic Sci Int Genet 2012; 6:621-9. [PMID: 22405517 DOI: 10.1016/j.fsigen.2012.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/16/2012] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing.
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Affiliation(s)
- Nancy Laurin
- Royal Canadian Mounted Police, Forensic Science and Identification Services, National Services and Research, 1200 Vanier Parkway, Ottawa, ON, Canada.
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22
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Park G, Kim HR, Na CH, Choi KC, Shin BS. Genetic study in a case of birt-hogg-dubé syndrome. Ann Dermatol 2011; 23:S188-92. [PMID: 22148047 PMCID: PMC3229062 DOI: 10.5021/ad.2011.23.s2.s188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 02/18/2011] [Accepted: 03/15/2011] [Indexed: 11/29/2022] Open
Abstract
Birt-Hogg-Dubé syndrome (BHDS) is an autosomal dominantly inherited disorder characterized by multiple trichodiscomas, fibrofolliculomas, and acrocordons. There is also an increased risk of developing renal neoplasms and lung cysts/spontaneous pneumothorax. We present a 43-year-old man with multiple, 2~4 mm sized, dome-shaped, and skin-colored papules on his cheek and neck. On the basis of clinical finding and histopathologic examination on the cheek lesion, it was diagnosed as multiple trichodiscomas. Subsequently, molecular analysis revealed a mutation in the folliculin gene. We report a rare case of BHDS with a proved gene mutation.
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Affiliation(s)
- Geon Park
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Korea
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23
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Hayashida M, Iwao-Koizumi K, Murata S, Yokoyama A, Kinoshita K. Genotyping of polymorphisms in alcohol and aldehyde dehydrogenase genes by direct application of PCR-RFLP on dried blood without DNA extraction. ANAL SCI 2010; 26:503-5. [PMID: 20410576 DOI: 10.2116/analsci.26.503] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have developed a simple, labor-saving, inexpensive, and rapid single nucleotide polymorphism (SNP) genotyping method that works directly on whole human blood. This single-tube genotyping method was used to successfully and reliably genotype ADH1B and ALDH2 polymorphisms without DNA isolation using a 1.2-mm disc of dried blood and the KOD FX PCR enzyme kit. SNP genotyping was performed by a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. In addition to the labor and expense advantages, the possibility of sample contamination was considerably decreased, since the DNA extraction step was eliminated. In the post-genome era, a simple and inexpensive method for diagnostic analysis is in high demand, and this method will be very useful for genetic diagnoses in biological and medical laboratories.
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Affiliation(s)
- Mariko Hayashida
- School of Pharmaceutical Sciences, Mukogawa Women's University, Koshien, Nishinomiya 663-8179, Japan
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24
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Kim SW, Heo JH, Kim CH, Yoo DC, Won DH, Lee SG, Cho KJ, Song JH, Park SJ, Yang YG, Choi DW. Rapid and direct detection of apolipoprotein E genotypes using whole blood from humans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2010; 73:1502-1510. [PMID: 20954076 DOI: 10.1080/15287394.2010.511573] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Polymerase chain reaction (PCR) is a powerful molecular biological tool in the field of toxicity testing and diagnostics. The use of PCR for large-scale genetic testing requires an effective method of sample processing. Unfortunately, isolation of PCR-quality DNA is time-consuming. PCR performed directly on whole blood is preferred because of time efficiency, cost of the procedure, and possible automation for large-scale toxicity evaluation and diagnosis. The apolipoprotein E (APOE) gene contains two single-nucleotide polymorphisms (SNP) located at codons 112 and 158, producing three APOE protein isoforms known to be associated with the risks of developing cardiovascular disease and susceptibility to Alzheimer's disease. In the present study, an attempt was made to use the AnyDirect solution for APOE genotyping by PCR using whole blood directly without DNA purification. Results for two PCR methods, (1) conventional PCR using purified DNA and conventional buffer and (2) direct PCR using whole blood and AnyDirect solution, were compared in four different PCR-based APOE genotyping methods including PCR restriction-fragment-length polymorphism (PCR-RFLP), allele-specific PCR, SNaPshot mini-sequencing, and multiplex tetra-primer amplification refractory mutation system (T-ARMS) PCR. There was complete concordance in the APOE genotypes between conventional PCR and direct PCR, in all four different PCR-based APOE genotyping methods. Data demonstrated that the four different PCR-based APOE genotyping methods are able to determine the APOE genotypes successfully using whole blood directly with the use of AnyDirect solution. The direct multiplex T-ARMS PCR using whole blood may be the most rapid, simple, and inexpensive method for detecting APOE genotypes among four different APOE genotyping methods.
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25
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Park J, Chung JL, Lee SH, Hong YJ. Cytomegalovirus as a Cause of Recurrent Anterior Uveitis in Immunocompetent Patients. JOURNAL OF THE KOREAN OPHTHALMOLOGICAL SOCIETY 2010. [DOI: 10.3341/jkos.2010.51.9.1245] [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]
Affiliation(s)
- Jihyun Park
- Department of Ophthalmology, Kim's Eye Hospital, Konyang University College of Medicine, Seoul, Korea
| | - Jae Lim Chung
- Department of Ophthalmology, Kim's Eye Hospital, Konyang University College of Medicine, Seoul, Korea
- Nune Eye Hospital, Seoul, Korea
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26
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Lee SH, Park G, Yang YG, Lee SG, Kim SW. Rapid ABO Genotyping Using Whole Blood without DNA Purification. Ann Lab Med 2009; 29:231-7. [DOI: 10.3343/kjlm.2009.29.3.231] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sung Ho Lee
- R&D Center, Lumieye Genetics Co., Ltd., Seoul, Korea
| | - Geon Park
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
| | | | - Seung Gwan Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Korea University, Seoul, Korea
| | - Suhng Wook Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Korea University, Seoul, Korea
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27
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HAYASHIDA M, IWAO-KOIZUMI K, MURATA S, KINOSHITA K. Single-Tube Genotyping from a Human Hair Root by Direct PCR. ANAL SCI 2009; 25:1487-9. [DOI: 10.2116/analsci.25.1487] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | | | - Kenji KINOSHITA
- School of Pharmaceutical Sciences, Mukogawa Women's University
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28
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Park SJ, Kim JY, Yang YG, Lee SH. Direct STR amplification from whole blood and blood- or saliva-spotted FTA without DNA purification. J Forensic Sci 2008; 53:335-41. [PMID: 18366565 DOI: 10.1111/j.1556-4029.2008.00666.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA purification step has been thought to be essential for typing of STR DNA. However, this process is time-consuming, and there is a risk of unexpected cross-contamination during purification. We report a new method for direct short tandem repeat (STR) amplification using a newly developed direct PCR buffer, AnyDirect, which can amplify STR loci from whole blood and blood- or saliva-spotted FTA cards without DNA purification. The autosomal and Y chromosomal STR loci were analyzed for whole blood and blood or saliva spots of random individuals, followed by comparison of the results with those of corresponding purified DNA. The results from whole blood and blood spots showed perfect concordance with those from purified DNA without allele or locus drop-out. However, in the case of saliva spots, no amplification or locus drop-out was observed in some of the samples, which offers a topic for further study. Additionally, some commercial hot-start DNA polymerases other than AmpliTaq Gold DNA polymerase were also found to be compatible with this buffer system. Therefore, this direct PCR buffer was demonstrated to be useful for fast forensic DNA analysis or criminal DNA databases for which there is no need to store DNA samples.
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Affiliation(s)
- Su Jeong Park
- DNA Analysis Lab, Forensic Science Division, Supreme Prosecutors' Office, Seocho-Gu, Seoul, Korea
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