1
|
Liu P, Seo TS, Beyor N, Shin KJ, Scherer JR, Mathies RA. Integrated Portable Polymerase Chain Reaction-Capillary Electrophoresis Microsystem for Rapid Forensic Short Tandem Repeat Typing. Anal Chem 2007; 79:1881-9. [PMID: 17269794 DOI: 10.1021/ac061961k] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A portable forensic genetic analysis system consisting of a microfluidic device for amplification and separation of short tandem repeat (STR) fragments as well as an instrument for chip operation and four-color fluorescence detection has been developed. The microdevice performs polymerase chain reaction (PCR) in a 160-nL chamber and capillary electrophoresis (CE) in a 7-cm-long separation channel. The instrumental design integrates PCR thermal cycling, electrophoretic separation, pneumatic valve fluidic control, and four-color laser excited fluorescence detection. A quadruplex Y-chromosome STR typing system consisting of amelogenin and three Y STR loci (DYS390, DYS393, DYS439) was developed and used for validation studies. The multiplex amplification of these 4 loci with 35 PCR cycles followed by CE separation and 4-color fluorescence detection was completed in 1.5 h. All the amplicons can be detected with a limit of detection of 20 copies of male standard DNA in the reactor. Real-world forensic analyses of oral swab and human bone extracts from case evidence were also successfully performed. Mixture analysis demonstrated that a balanced profile can be obtained even at a male-to-female template ratio of 1:10. The successful development and operation of this portable PCR-CE system establishes the feasibility of rapid point-of-analysis DNA typing of forensic casework, of mass disaster samples or of individuals at a security checkpoint.
Collapse
|
|
18 |
130 |
2
|
Lounsbury JA, Karlsson A, Miranian DC, Cronk SM, Nelson DA, Li J, Haverstick DM, Kinnon P, Saul DJ, Landers JP. From sample to PCR product in under 45 minutes: a polymeric integrated microdevice for clinical and forensic DNA analysis. LAB ON A CHIP 2013; 13:1384-1393. [PMID: 23389252 DOI: 10.1039/c3lc41326h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The extraction and amplification of DNA from biological samples is laborious and time-consuming, requiring numerous instruments and sample handling steps. An integrated, single-use, poly(methyl methacrylate) (PMMA) microdevice for DNA extraction and amplification would benefit clinical and forensic communities, providing a completely closed system with rapid sample-in-PCR-product-out capability. Here, we show the design and simple flow control required for enzyme-based DNA preparation and PCR from buccal swabs or liquid whole blood samples with an ~5-fold reduction in time. A swab containing cells or DNA could be loaded into a novel receptacle together with the DNA liberation reagents, heated using an infrared heating system, mixed with PCR reagents for one of three different target sets under syringe-driven flow, and thermally-cycled in less than 45 min, an ~6-fold reduction in analysis time as compared to conventional methods. The 4 : 1 PCR reagents : DNA ratio required to provide the correct final concentration of all PCR components for effective amplification was verified using image analysis of colored dyes in the PCR chamber. Novel single-actuation, 'normally-open' adhesive valves were shown to effectively seal the PCR chamber during thermal cycling, preventing air bubble expansion. The effectiveness of the device was demonstrated using three target sets: the sex-typing gene Amelogenin, co-amplification of the β-globin and gelsolin genes, and the amplification of 15 short tandem repeat (STR) loci plus Amelogenin. The use of the integrated microdevice was expanded to the analysis of liquid blood samples which, when incubated with the DNA liberation reagents, form a brown precipitate that inhibits PCR. A simple centrifugation of the integrated microchips (on a custom centrifuge), mobilized the precipitate away from the microchannel entrance, improving amplification of the β-globin and gelsolin gene fragments by ~6-fold. This plastic integrated microdevice represents a microfluidic platform with potential for evolution into point-of-care prototypes for application to both clinical and forensic analyses, providing a 5-fold reduction from conventional analysis time.
Collapse
|
|
12 |
47 |
3
|
Perlin MW, Dormer K, Hornyak J, Schiermeier-Wood L, Greenspoon S. TrueAllele casework on Virginia DNA mixture evidence: computer and manual interpretation in 72 reported criminal cases. PLoS One 2014; 9:e92837. [PMID: 24667531 PMCID: PMC3965478 DOI: 10.1371/journal.pone.0092837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 02/26/2014] [Indexed: 12/03/2022] Open
Abstract
Mixtures are a commonly encountered form of biological evidence that contain DNA from two or more contributors. Laboratory analysis of mixtures produces data signals that usually cannot be separated into distinct contributor genotypes. Computer modeling can resolve the genotypes up to probability, reflecting the uncertainty inherent in the data. Human analysts address the problem by simplifying the quantitative data in a threshold process that discards considerable identification information. Elevated stochastic threshold levels potentially discard more information. This study examines three different mixture interpretation methods. In 72 criminal cases, 111 genotype comparisons were made between 92 mixture items and relevant reference samples. TrueAllele computer modeling was done on all the evidence samples, and documented in DNA match reports that were provided as evidence for each case. Threshold-based Combined Probability of Inclusion (CPI) and stochastically modified CPI (mCPI) analyses were performed as well. TrueAllele's identification information in 101 positive matches was used to assess the reliability of its modeling approach. Comparison was made with 81 CPI and 53 mCPI DNA match statistics that were manually derived from the same data. There were statistically significant differences between the DNA interpretation methods. TrueAllele gave an average match statistic of 113 billion, CPI averaged 6.68 million, and mCPI averaged 140. The computer was highly specific, with a false positive rate under 0.005%. The modeling approach was precise, having a factor of two within-group standard deviation. TrueAllele accuracy was indicated by having uniformly distributed match statistics over the data set. The computer could make genotype comparisons that were impossible or impractical using manual methods. TrueAllele computer interpretation of DNA mixture evidence is sensitive, specific, precise, accurate and more informative than manual interpretation alternatives. It can determine DNA match statistics when threshold-based methods cannot. Improved forensic science computation can affect criminal cases by providing reliable scientific evidence.
Collapse
|
Comparative Study |
11 |
16 |
4
|
Cortellini V, Cerri N, Verzeletti A. Genetic variation at 5 new autosomal short tandem repeat markers (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in a population-based sample from Maghreb region. Croat Med J 2011; 52:368-71. [PMID: 21674833 PMCID: PMC3118715 DOI: 10.3325/cmj.2011.52.368] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/02/2011] [Indexed: 11/11/2022] Open
Abstract
AIM To investigate allele distribution and genetic parameters of a population-based sample from Maghreb region. METHODS Allele frequencies for 5 new autosomal short tandem repeat (STR) markers (D10S1248, D22S1045, D2S441, D1S1656, and D12S391) and several forensic parameters were determined for 95 unrelated individuals. RESULTS The combined power of discrimination and power of exclusion for the 5 loci were high (0.9999991 and 0.9954757, respectively). Allele frequencies were compared with previously published population data. Significant differences were found between Maghreb population and all other populations at the locus D2S441. Also, significant differences were found between the Maghreb and the African American population at the D22S1045, D1S1656, and D12S391 loci, between Maghreb and Caucasian population at the D1S1656 locus, and between Maghreb and Hispanic population at the D22S1045 locus. CONCLUSIONS Typing of the 5 new STR loci may provide a useful addition to the previously established sets of autosomal STRs.
Collapse
|
Comparative Study |
14 |
13 |
5
|
Anazawa T, Uchiho Y, Yokoi T, Chalkidis G, Yamazaki M. A simple and highly sensitive spectroscopic fluorescence-detection system for multi-channel plastic-microchip electrophoresis based on side-entry laser-beam zigzag irradiation. LAB ON A CHIP 2017; 17:2235-2242. [PMID: 28585967 DOI: 10.1039/c7lc00448f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A five-color fluorescence-detection system for eight-channel plastic-microchip electrophoresis was developed. In the eight channels (with effective electrophoretic lengths of 10 cm), single-stranded DNA fragments were separated (with single-base resolution up to 300 bases within 10 min), and seventeen-loci STR genotyping for forensic human identification was successfully demonstrated. In the system, a side-entry laser beam is passed through the eight channels (eight A channels), with alternately arrayed seven sacrificial channels (seven B channels), by a technique called "side-entry laser-beam zigzag irradiation." Laser-induced fluorescence from the eight A channels and Raman-scattered light from the seven B channels are then simultaneously, uniformly, and spectroscopically detected, in the direction perpendicular to the channel array plane, through a transmission grating and a CCD camera. The system is therefore simple and highly sensitive. Because the microchip is fabricated by plastic-injection molding, it is inexpensive and disposable and thus suitable for actual use in various fields.
Collapse
|
|
8 |
4 |
6
|
Talavera Bustamante I, Silva Mata F, Hernández González N, González Gazapo R, Palau J, Ferreira MMC. Application of chemometric tools for automatic classification and profile extraction of DNA samples in forensic tasks. Anal Chim Acta 2007; 595:43-50. [PMID: 17605982 DOI: 10.1016/j.aca.2007.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 12/23/2006] [Accepted: 01/08/2007] [Indexed: 11/26/2022]
Abstract
In this paper a method for the automatic DNA spots classification and extraction of profiles associated in DNA polyacrylamide gel electrophoresis is presented and it integrates the use of image processing techniques and chemometrics tools. A software which implements this method was developed; for feature extraction a combination of a PCA analysis and a C4.5 decision tree were used. To obtain good results in the profile extraction only DNA spots are useful; therefore, it was necessary to solve a two-class classification problem among DNA spots and no-DNA spots. In order to perform the classification process with high velocity, effectiveness and robustness, comparative classification studies among support vector machine (SVM), K-NN and PLS-DA classifiers were made. The best results obtained with the SVM classifier demonstrated the advantages attributed to it in the literature as a two-class classifier. A Sequential Cluster Leader Algorithm and another one developed for the restoration of pattern missing spots were needed to conclude the profiles extraction step. The experimental results show that this method has a very effective computational behavior and effectiveness, and provide a very useful tool to decrease the time and increase the quality of the specialist responses.
Collapse
|
Comparative Study |
18 |
4 |
7
|
Cornelis S, Tytgat O, Fauvart M, Gansemans Y, Vander Plaetsen AS, Wiederkehr RS, Deforce D, Van Nieuwerburgh F, Stakenborg T. Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves. Sci Rep 2019; 9:7341. [PMID: 31089203 PMCID: PMC6517373 DOI: 10.1038/s41598-019-43946-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
Collapse
|
research-article |
6 |
4 |
8
|
Turrina S, De Leo D. Resizing reaction volumes for the ForenSeq™ DNA Signature Prep kit library preparation. MEDICINE, SCIENCE, AND THE LAW 2021; 61:92-95. [PMID: 33591883 DOI: 10.1177/0025802420923163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The introduction of next generation sequencing (NGS; also known as massively parallel sequencing) technology in the field of forensic genetics has been welcomed by the scientific community, above all because it complements the weaknesses of capillary electrophoresis (CE) in the analysis of genetic markers, such as single nucleotide polymorphism (SNP) typing. However, one of the main obstacles to its adoption does not seem to be the cost of the instrumentation, but rather the cost of the NGS library preparation kits. With the aim of reducing the cost of library preparation without compromising the quality of the results, we tried to scale down reaction volumes for the first two polymerase chain reactions in the amplification and enrichment phases of the targeted loci of library preparation using the ForenSeq™ DNA Signature Prep kit. We used 1 µL templated DNA input to a concentration of 1 ng/µL, instead of the 5 µL at 0.2 ng/µL recommended by the manufacturer. Our findings indicate that reduction of the library preparation volume using the ForenSeq™ DNA Signature Prep kit did not interfere with the quality and reproducibility of the DNA profiles obtained and can help lower the overall cost of NGS.
Collapse
|
|
4 |
3 |
9
|
Dekhanov DV, Vlaskova NV. [The use of modern high-intensity radiation sources for the discovery and identification of the traces in the biological and molecular-genetic expertise]. Sud Med Ekspert 2011; 54:44-45. [PMID: 22384709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
|
|
14 |
|
10
|
Fesenko DO, Mitiaeva ON, Nasedkina TV, Rubtsov PM, Lysov IP, Zasedatelev AS. [HLA-DQA1, AB0 and AMEL genotyping of biological material by biochips]. Mol Biol (Mosk) 2010; 44:456-462. [PMID: 20608169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A genotyping method of biological material for ABO, HLA-DQA1 and AMEL loci is described. The method is based on allele-specific SNP determination using the hydrogel biochips technology. The amplified fluorescently labeled fragments of the genes were hybridized with specific DNA probes immobilized on a biochip. The allele/genotype assignment was done according to the distribution of fluorescent signal. The minimal amount of biological material is corresponded to 100 pg of DNA. The method was proved using control samples with known genotype. Using biochips 442 DNA samples belonging to the East Slavic population group were genotyped. The allele frequencies of ABO and HLA-DQA1 loci were determined. The possibility of genotyping of biological traces, including the stubs of filter cigarettes, material from the lip of the glass was demonstrated. This method can be used for genetic testing in forensic studies. The probability that the determined genotype belongs to a concrete individual was estimated as 99.6%.
Collapse
|
English Abstract |
15 |
|
11
|
Ivanov PL, Leonov SN, Zemskova EI. [The estimation of possibilities for the application of the laser capture microdissection technology for the molecular-genetic expert analysis (genotyping) of human chromosomal DNA]. Sud Med Ekspert 2012; 55:34-37. [PMID: 23272562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present study was designed to estimate the possibilities of application of the laser capture microdissection (LCM) technology for the molecular-genetic expert analysis (genotyping) of human chromosomal DNA. The experimental method employed for the purpose was the multiplex multilocus analysis of autosomal DNA polymorphism in the preparations of buccal epitheliocytes obtained by LCM. The key principles of the study were the application of physical methods for contrast enhancement of the micropreparations (such as phase-contrast microscopy and dark-field microscopy) and PCR-compatible cell lysis. Genotyping was carried out with the use of AmpFISTR Minifiler TM PCR Amplification Kits ("Applied Biosynthesis", USA). It was shown that the technique employed in the present study ensures reliable genotyping of human chromosomal DNA in the pooled preparations containing 10-20 dissected diploid cells each. This result fairly well agrees with the calculated sensitivity of the method. A few practical recommendations are offered.
Collapse
|
English Abstract |
13 |
|
12
|
Han JP, Wang YX, Liu C, Liu F, Guo JR, Zhu W, Tang GF, Li CX, Wang X, Jiao ZP. Test and Evaluation of the Made-in-China Quick TargSeq Fully Integrated Automated On-site Rapid DNA Detection Instrument. FA YI XUE ZA ZHI 2024; 40:461-467. [PMID: 39992338 DOI: 10.12116/j.issn.1004-5619.2023.530601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
OBJECTIVES To verify the stability and accuracy of the made-in-China Quick TargSeq Fully Integrated Automated On-site Rapid DNA Detection Instrument (hereinafter referred to as Quick TargSeq DNA detection instrument) and evaluate its forensic application prospects. METHODS A total of 74 blind samples provided by the expert group of Criminal Investigation Bureau of the Ministry of Public Security (4 individuals, 20 samples) and five participating institutions (54 samples) were used to test on 5 Quick TargSeq DNA detection instruments and the accompanying microfluidic chip cartridges. The results were compared with the known genotypes to calculate the samples' detection rate and genotyping accuracy. RESULTS The results of reproducibility obtained from 20 samples provided by the expert group on the 5 Quick TargSeq DNA detection instruments were all consistent with the known genotypes. The detection rate of the 74 samples was 100%, and the genotyping accuracy was 97.33%. CONCLUSIONS The Quick TargSeq DNA detection instrument has good stability and high genotyping accuracy.
Collapse
|
Evaluation Study |
1 |
|
13
|
Drabik J, Jagiełło A, Niemcunowicz-Janica A, Pepiński W. [Validation and evaluation of a five miniSTRs kit in forensic genetics]. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2011; 61:153-160. [PMID: 22390129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
The newly designed and optimized miniplex contains the following markers: D3S3053, D6S474, D9S2157, D20S482 and sex-determining marker - amelogenin. The target amplicon lengths for the developed multiplex are 71-135 bp. Amplification products were detected in a fluorescence based automated genetic analyzer. A minimal DNA sample required to obtain full genetic profiles was 250 pg. The usefulness of these miniSTRs in genotyping of severely degraded forensic samples, such as stains of blood and semen, saliva on cigarette butts and telogen hair has been confirmed in validation studies. The designed pentaplex offers a new potential screening tool in cases of old crime scenes, mass disasters, mass graves, etc., where DNA degradation, body fragmentation or large numbers of victims occur. The use of additional non-CODIS markers may increase typeability of severely degraded samples and ensure a higher potential for genetic discrimination.
Collapse
|
Evaluation Study |
14 |
|
14
|
Keller E, Looser M, Bieri HP, Kübler E, Balitzki B. [Recovery of blood traces with scenesafe FAST tape]. ARCHIV FUR KRIMINOLOGIE 2012; 230:166-176. [PMID: 23367791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
For complete and conclusive DNA profiling a sufficient amount of DNA must be available. For that, biological traces are recovered from crime scenes using special trace recovery material. The current method to collect biological traces for DNA analysis is to wipe them off with cotton swabs. However, for a few years the use of adhesive tapes has also been described for the recovery of evidence. In 2009, an adhesive tape was launched which was specially developed for the collection of biological traces. This product called Scenesafe FAST Tape (SSF) was investigated in this work to give recommendations for its use in evidence recovery. The results of this work show that the DNA can be extracted from the SSF very well. However, the tapes seem less suitable for direct use at the crime scene, as they are not flexible enough for adaptation to different crime scene conditions and the risk of contamination is higher than when collecting evidence with cotton swabs. Neither SSF nor cotton swabs are optimal for all requirements. The best method to recover biological evidence is still dependent on the surface material and the circumstances at the crime scene.
Collapse
|
English Abstract |
13 |
|