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Gaston SM, Grizzle WE, Rais-Bahrami S, Kearney GP. Nitrocellulose tissue prints: an innovative approach to preparing high quality DNA and RNA from prostate biopsies without compromising the cores for pathology diagnosis. Transl Androl Urol 2018; 7:S514-S518. [PMID: 30363516 PMCID: PMC6178309 DOI: 10.21037/tau.2018.09.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much of the research that has been done on prostate cancer tissue biomarkers has relied on radical prostatectomies for biospecimens. However, it is well recognized that important groups of patients are under-represented or missing entirely from biorepository collections of radical prostatectomy specimens. Using prostate biopsy tissues for molecular biomarker research significantly expands the range of available patients to include men whose biopsies show no cancer as well as men who are treated non-surgically or who choose active surveillance. However, one of the challenges of biopsy-based biomarker research is the limited amount of tissue that can be obtained from each core. To address this challenge, we have developed and fully implemented innovative biopsy tissue print technologies that allow us to obtain high quality RNA and DNA from each biopsy core without compromising the specimen for a pathologic diagnosis. Prostate biopsy tissue print samples have been successfully utilized for gene expression profiling, genotyping, DNA methylation and sequencing analyses. Emerging biopsy tissue print applications include studies using viable cells to study tumor metabolism and drug response.
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Affiliation(s)
- Sandra M Gaston
- Tufts Medical Center, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
| | - William E Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Soroush Rais-Bahrami
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gary P Kearney
- Harvard Medical School, Boston, MA, USA.,Longwood Urology, Boston, MA, USA
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2
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Cho Y, Kim HS, Kim M, Park M, Kwon H, Lee YH, Lee DS. Validation of Reduced Reagent Volumes in the Implementation of the Quantifiler
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Trio Quantification Kit. J Forensic Sci 2017. [DOI: 10.1111/1556-4029.13578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoonjung Cho
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Hyo Sook Kim
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Min‐Hee Kim
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Moonhee Park
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Hansol Kwon
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Yang Han Lee
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
| | - Dong Sub Lee
- Forensic DNA Division National Forensic Service 10 Ipchun‐ro Wonju 26460 Gangwon‐doKorea
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3
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Chen L, Tai Y, Qiu P, Du W, Liu C. A silent allele in the locus D5S818 contained within the PowerPlex®21 PCR Amplification Kit. Leg Med (Tokyo) 2015; 17:509-11. [PMID: 26593999 DOI: 10.1016/j.legalmed.2015.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/06/2015] [Accepted: 10/30/2015] [Indexed: 02/06/2023]
Abstract
Three paternity tests cases were found with a single locus mismatch at the locus D5S818 with PowerPlex®21 PCR Amplification Kit (Promega). Forward and reverse primers were redesigned to type the samples again and to evaluate if there were alleles dropped out. The results showed the existence of a silent allele 12 in all the three families, due to a point mutation that changed cytosine to adenine at 90 nucleotides upstream from the 5' end of the AGAT repeat sequences in all the six individuals. A single locus mismatch due to a silent allele may occur in any locus using any kit. Therefore, we recommend using multiple kits to confirm the results in paternity testing cases with mismatches, especially when there is a single locus mismatch with homozygote involved.
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Affiliation(s)
- Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Yunchun Tai
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Pingming Qiu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Weian Du
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China; Guangzhou Forensic Science Institute, Guangzhou, Guangdong Province 510030, PR China.
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4
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Lee SB, McCord B, Buel E. Advances in forensic DNA quantification: a review. Electrophoresis 2014; 35:3044-52. [PMID: 25088961 DOI: 10.1002/elps.201400187] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/27/2014] [Accepted: 07/27/2014] [Indexed: 01/11/2023]
Abstract
This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification.
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Affiliation(s)
- Steven B Lee
- Department of Justice Studies, San Jose State University, San Jose, CA, USA
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5
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Nathalie Z, Hadi S, Goodwin W. Development of PCR internal controls for DNA profiling with the AmpFℓSTR® SGM Plus® amplification kit. Electrophoresis 2012; 33:2833-9. [PMID: 23019100 DOI: 10.1002/elps.201200252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Forensic DNA profiling uses a series of commercial kits that co-amplify several loci in one reaction; the products of the PCR are fluorescently labelled and analysed using CE. Before CE, an aliquot of the PCR is mixed with formamide and an internal lane size standard. Using the SGM Plus amplification kit, we have developed two internal non-amplified controls of 80 bp and 380 bp that are labelled with ROX fluorescent dye and added to the PCR. Combined with two internal amplification controls of 90 bp and 410 bp, they provide additional controls for the PCR, electrokinetic injection, and CE and also function as an internal size standard.
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Affiliation(s)
- Zahra Nathalie
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK
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6
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Pflugradt R, Sänger T, Schlauderer N, Hauschke D, Lutz-Bonengel S, Schmidt U. DNA-Quantifizierung in der forensischen Spurenkunde. Rechtsmedizin (Berl) 2012. [DOI: 10.1007/s00194-012-0834-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Cell free DNA as a component of forensic evidence recovered from touched surfaces. Forensic Sci Int Genet 2012; 6:26-30. [DOI: 10.1016/j.fsigen.2011.01.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/04/2011] [Accepted: 01/07/2011] [Indexed: 11/20/2022]
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8
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Boesenberg-Smith KA, Pessarakli MM, Wolk DM. Assessment of DNA Yield and Purity: an Overlooked Detail of PCR Troubleshooting. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.clinmicnews.2011.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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9
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Higgins D, Kaidonis J, Austin J, Townsend G, James H, Hughes T. Dentine and cementum as sources of nuclear DNA for use in human identification. AUST J FORENSIC SCI 2011. [DOI: 10.1080/00450618.2011.583278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Lee HY, Kim NY, Park MJ, Sim JE, Yang WI, Shin KJ. DNA typing for the identification of old skeletal remains from Korean War victims. J Forensic Sci 2011; 55:1422-9. [PMID: 20456584 DOI: 10.1111/j.1556-4029.2010.01411.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains.
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-Gu, Seoul 120-752, Korea
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11
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Alaeddini R, Ahmadi M, Walsh SJ, Abbas A. Semi-quantitative PCR Analysis of DNA Degradation. AUST J FORENSIC SCI 2011. [DOI: 10.1080/00450618.2010.498026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Lee HY, Park MJ, Kim NY, Sim JE, Yang WI, Shin KJ. Simple and highly effective DNA extraction methods from old skeletal remains using silica columns. Forensic Sci Int Genet 2010; 4:275-80. [DOI: 10.1016/j.fsigen.2009.10.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/09/2009] [Accepted: 10/10/2009] [Indexed: 11/30/2022]
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13
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Grgicak CM, Urban ZM, Cotton RW. Investigation of Reproducibility and Error Associated with qPCR Methods using Quantifiler® Duo DNA Quantification Kit*. J Forensic Sci 2010; 55:1331-9. [DOI: 10.1111/j.1556-4029.2010.01460.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Abstract
DNA amplification is a fundamental yet costly process used in DNA analysis. This study evaluated half-reaction amplification (12.5, 12, and 13 microL) using the Promega Powerplex 16 Kit with the hope of reducing sample analysis costs by half. A sensitivity study was completed, along with the testing of various blood stain samples including those with low (<0.40 ng) and high DNA concentrations (>3.0 ng), peak height imbalances, and allelic drop-out. Also, 467 samples submitted to the MUFSC laboratory for testing were analyzed. Results indicate that half-reaction amplification produced higher quality profiles than full-reactions. Average peak heights increased by 85%, peak height imbalances improved, and drop-out was eliminated in 75.8% of samples. Only eight of 467 case samples required re-amplification, a success rate of 94% was observed, and the repeat rate decreased significantly. Finally, a DNA input of 0.25-1.0 ng is ideal for half-reaction amplification.
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Affiliation(s)
- Nicole H Hoffman
- Marshall University Forensic Science Center, DNA Laboratory, 1401 Forensic Science Drive, Huntington, WV, USA.
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15
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199
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