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Cloudy DC, Boone EL, Kuehnert K, Smith C, Cox JO, Seashols-Williams SJ, Green TD. Statistical methods for discrimination of STR genotypes using high resolution melt curve data. Int J Legal Med 2024:10.1007/s00414-024-03289-x. [PMID: 38997516 DOI: 10.1007/s00414-024-03289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
Despite the improvements in forensic DNA quantification methods that allow for the early detection of low template/challenged DNA samples, complicating stochastic effects are not revealed until the final stage of the DNA analysis workflow. An assay that would provide genotyping information at the earlier stage of quantification would allow examiners to make critical adjustments prior to STR amplification allowing for potentially exclusionary information to be immediately reported. Specifically, qPCR instruments often have dissociation curve and/or high-resolution melt curve (HRM) capabilities; this, coupled with statistical prediction analysis, could provide additional information regarding STR genotypes present. Thus, this study aimed to evaluate Qiagen's principal component analysis (PCA)-based ScreenClust® HRM® software and a linear discriminant analysis (LDA)-based technique for their abilities to accurately predict genotypes and similar groups of genotypes from HRM data. Melt curves from single source samples were generated from STR D5S818 and D18S51 amplicons using a Rotor-Gene® Q qPCR instrument and EvaGreen® intercalating dye. When used to predict D5S818 genotypes for unknown samples, LDA analysis outperformed the PCA-based method whether predictions were for individual genotypes (58.92% accuracy) or for geno-groups (81.00% accuracy). However, when a locus with increased heterogeneity was tested (D18S51), PCA-based prediction accuracy rates improved to rates similar to those obtained using LDA (45.10% and 63.46%, respectively). This study provides foundational data documenting the performance of prediction modeling for STR genotyping based on qPCR-HRM data. In order to expand the forensic applicability of this HRM assay, the method could be tested with a more commonly utilized qPCR platform.
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Affiliation(s)
- Darianne C Cloudy
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Edward L Boone
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA, 23284, USA
| | - Kristi Kuehnert
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Chastyn Smith
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA.
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
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Ginart S, Garrigos Calivares L, Caputo M, Corach D, Sala A. Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry. Forensic Sci Int 2024; 354:111893. [PMID: 38064775 DOI: 10.1016/j.forsciint.2023.111893] [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: 06/09/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AIM To evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. MATERIAL & METHODS Biological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. RESULTS After DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016-50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. CONCLUSION We demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.
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Affiliation(s)
- S Ginart
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina.
| | - L Garrigos Calivares
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - M Caputo
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - D Corach
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - A Sala
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
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3
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Zappe K, Pirker C, Miedl H, Schreiber M, Heffeter P, Pfeiler G, Hacker S, Haslik W, Spiegl-Kreinecker S, Cichna-Markl M. Discrimination between 34 of 36 Possible Combinations of Three C>T SNP Genotypes in the MGMT Promoter by High Resolution Melting Analysis Coupled with Pyrosequencing Using A Single Primer Set. Int J Mol Sci 2021; 22:ijms222212527. [PMID: 34830407 PMCID: PMC8621402 DOI: 10.3390/ijms222212527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/12/2021] [Indexed: 11/22/2022] Open
Abstract
Due to its cost-efficiency, high resolution melting (HRM) analysis plays an important role in genotyping of candidate single nucleotide polymorphisms (SNPs). Studies indicate that HRM analysis is not only suitable for genotyping individual SNPs, but also allows genotyping of multiple SNPs in one and the same amplicon, although with limited discrimination power. By targeting the three C>T SNPs rs527559815, rs547832288, and rs16906252, located in the promoter of the O6-methylguanine-DNA methyltransferase (MGMT) gene within a distance of 45 bp, we investigated whether the discrimination power can be increased by coupling HRM analysis with pyrosequencing (PSQ). After optimizing polymerase chain reaction (PCR) conditions, PCR products subjected to HRM analysis could directly be used for PSQ. By analyzing oligodeoxynucleotide controls, representing the 36 theoretically possible variant combinations for diploid human cells (8 triple-homozygous, 12 double-homozygous, 12 double-heterozygous and 4 triple-heterozygous combinations), 34 out of the 36 variant combinations could be genotyped unambiguously by combined analysis of HRM and PSQ data, compared to 22 variant combinations by HRM analysis and 16 variant combinations by PSQ. Our approach was successfully applied to genotype stable cell lines of different origin, primary human tumor cell lines from glioma patients, and breast tissue samples.
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Affiliation(s)
- Katja Zappe
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
| | - Christine Pirker
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (C.P.); (P.H.)
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (H.M.); (M.S.)
| | - Heidi Miedl
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (H.M.); (M.S.)
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Schreiber
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (H.M.); (M.S.)
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria
| | - Petra Heffeter
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (C.P.); (P.H.)
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (H.M.); (M.S.)
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, 1090 Vienna, Austria; (G.P.); (W.H.)
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, 1090 Vienna, Austria;
- Department of Plastic, Reconstructive and Aesthetic Surgery, Landesklinikum Wiener Neustadt, 2700 Wiener Neustadt, Austria
| | - Werner Haslik
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, 1090 Vienna, Austria; (G.P.); (W.H.)
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Medical Faculty, Kepler University Hospital GmbH, Johannes Kepler University Linz, 4040 Linz, Austria;
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
- Correspondence:
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Tie J, Uchigasaki S, Isobe E. Evaluation and SNP typing of DNA from ultraviolet-irradiated human bloodstains using TaqMan assay. Sci Rep 2021; 11:8029. [PMID: 33850175 PMCID: PMC8044161 DOI: 10.1038/s41598-021-87313-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
When detecting DNA profiles from forensic materials, it is pivotal to know the extent of degradation and which DNA marker can be genotyped. Ultraviolet (UV) is one of the common external factors that causes DNA damage, through which, an attempt to reveal cardinal genetic information can be made. In this study, after irradiation with three different UV wavelengths, UV-damaged DNA in the bloodstains was analyzed with long and short TaqMan assays using real-time PCR. In addition, both short tandem repeat (STR) profiles and single nucleotide polymorphisms (SNPs) from the damaged DNA at different stages of UV exposure were also assessed. With increasing in UV irradiation cycles, there was a delay of the amplification curves accompanied with a decrease in the DNA amounts collected. Despite the amplification of STR genotype was not altered after 75 cycles of UVC irradiation, all 12 SNP loci could still be detected. Furthermore, a short-assay line was detected in the absence of an amplification of the evaluation curve. The results indicate that, although the DNA template might not be useful and suitable for analysis of STR profile, this approach is of some values in detecting SNPs.
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Affiliation(s)
- Jian Tie
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan.
| | - Seisaku Uchigasaki
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Eiji Isobe
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
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5
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Ohta J, Sakurada K. Oral gram-positive bacterial DNA-based identification of saliva from highly degraded samples. Forensic Sci Int Genet 2019; 42:103-112. [DOI: 10.1016/j.fsigen.2019.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/22/2019] [Indexed: 12/29/2022]
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Jiang E, Zhang S, Pang H. Genotyping genetic markers from LCN and degraded DNA by HRM and their application in hair shaft. Int J Legal Med 2019; 134:31-37. [PMID: 31062081 DOI: 10.1007/s00414-019-02045-w] [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: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023]
Abstract
Degraded and low copy number (LCN) DNA samples are common challenging materials in forensic casework because they increase the difficulty of sample processing and reduce the possibility of obtaining genetic information from DNA. High-resolution melting (HRM) curve analysis is promising for genotyping genetic markers and has been applied to the detection of LCN and degraded DNA in the field of forensic science. However, the exact assessment based on HRM at multiple genetic markers from both degraded and LCN DNA materials has not been optimized. To explore the ability of HRM to genotype LCN and degraded DNA samples, we selected three genetic markers to genotype in experimental LCN and degraded DNA and practical hair shaft materials, which are often encountered as degraded and LCN DNA in forensic medicine. The results show that DNA samples of as low as 100 pg and as short as 60 bp were successfully genotyped by the HRM assay at all three genetic markers, whereas in hair shaft DNA, two loci were accurately genotyped. The HRM assay established in this study can be applied to LCN and degraded DNA analysis in forensic casework and can act as a reference point before genotyping short tandem repeat markers. Developing the HRM strategy for genotyping DNA genetic markers enriches detectable targets in hair shaft samples and provides valuable data for further exploration.
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Affiliation(s)
- Enzhu Jiang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Siyi Zhang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Hao Pang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China.
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7
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Al-Koofee DAF, Ismael JM, Mubarak SMH. Point mutation detection by economic HRM protocol primer design. Biochem Biophys Rep 2019; 18:100628. [PMID: 31008377 DOI: 10.1016/j.bbrep.2019.100628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022] Open
Abstract
Globally more than 100 million SNPs in populations. These variations approximately 4-5 million SNPs in a people genome, occur almost every 1000 nucleotides on average and present either unique or in many in individuals. They can act as genetic signs, associated with illness and respond to chemicals and drugs. SNPs occurrence within or near a gene play important role in disease throughout affecting gene task. Frequently many protocols have been used to study single nucleotide polymorphism (SNP) among human variants genome. Restriction fragment length polymorphism (RFLP), Amplification refractory mutation system PCR(ARMS-PCR), sequencing and SNaPshot assays considered familial methods. The potential risk of contamination after PCR is common due to further other steps. In this direction, a high resolution melting (HRM) real-time PCR method is an alternative, reducing the post-PCR transferring steps. uVariants is clarified as appropriate website for designing primers used for SNP recognition by easy and inexpensive protocol called HRM. The researchers can focus on the interest of reference SNP ID number, or "rs" ID to avoid loss time. In this article description how to uses uVariants website for primer design used in HRM technique. Aims To describe uVariants and uDesign software, application and usefulness of HRM technique primer design in the genotyping SNPs among people and public health. Accessibility and requirements uVariants and uDesign are freely accessible at: https://www.dna.utah.edu/variants/;https://www.dna.utah.edu/udesign/app.php respectively.The network server supports the browsers: Chrome, Firefox, Torch, CoolNovo, 360 Browser, Internet Explorer, Opera, and Safari.
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Affiliation(s)
- Dhafer A F Al-Koofee
- Dept. of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Iraq
| | | | - Shaden M H Mubarak
- Dept. of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Iraq
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8
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Mehta B, Daniel R, McNevin D. HRM and SNaPshot as alternative forensic SNP genotyping methods. Forensic Sci Med Pathol 2017; 13:293-301. [PMID: 28523436 DOI: 10.1007/s12024-017-9874-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2017] [Indexed: 01/25/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia.
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, 31 Forensic Drive, Macleod, VIC, 3085, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia
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9
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Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med 2016; 131:21-37. [DOI: 10.1007/s00414-016-1490-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
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10
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Schmidt U, Hulkkonen J, Naue J. Detection of a G>C single nucleotide polymorphism within a repetitive DNA sequence by high-resolution DNA melting. Int J Legal Med 2016; 130:1181-4. [PMID: 26972692 DOI: 10.1007/s00414-016-1350-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/25/2016] [Indexed: 11/26/2022]
Abstract
In standard forensic DNA analysis, single base mutations within short tandem repeats (STR) mostly escape detection. In this study, high-resolution DNA melting (HRM) is compared to minisequencing and Sanger sequencing as to determine the most suitable method for detection of a G to C mutation within a repetitive DNA sequence, the STR system DXS10161. It shows an ATG/ATC polymorphism surrounded by a variable number of (TATC) and (ATCT) motifs. Neutral base changes like G:C to C:G result in very low differences in the melting temperature (T m) of the PCR amplicons. By enhanced resolution of fluorescence vs. temperature in HRM, the technique showed to be suitable for detecting a G to C transversion in this repetitive DNA sequence context. Compared to minisequencing, HRM is more time- and cost-effective. Results were confirmed by Sanger sequencing.
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Affiliation(s)
- Ulrike Schmidt
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany.
| | - Johannes Hulkkonen
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Department of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
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