1
|
Nakanishi H, Takada A, Yoneyama K, Hara M, Sakai K, Saito K. Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer. Forensic Sci Int 2024; 358:112010. [PMID: 38581825 DOI: 10.1016/j.forsciint.2024.112010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
We used a nanopore sequencer to quantify DNA fragments > 10,000 bp in size and then evaluated their relationship with short-term bloodstain age. Moreover, DNA degradation was investigated after bloodstains were wetted once with water. Bloodstain samples on cotton gauze were stored at room temperature and low humidity for up to 6 months. Bloodstains stored for 1 day were wetted with nuclease-free water, allowed to dry, and stored at room temperature and low humidity for up to 1 week. The proportion of fragments > 20,000 bp in dry bloodstains tended to decrease over time, particularly for fragments > 50,000 bp in size. This trend was modeled using a power approximation curve, with the highest R2 value (0.6475) noted for fragments > 50,000 bp in size; lower values were recorded for shorter fragments. The proportion of longer fragments was significantly reduced in bloodstains that were dried after being wetted once, and there was significant difference in fragments > 50,000 bp between dry conditions and once-wetted. This result suggests that even temporary exposure to water causes significant DNA fragmentation, but not extensive degradation. Thus, bloodstains that appear fresh but have a low proportion of long DNA fragments may have been wetted previously. Our results indicate that evaluating the proportion of long DNA fragments yields information on both bloodstain age and the environment in which they were stored.
Collapse
Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan.
| | - Aya Takada
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan
| | - Kentaro Sakai
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan; Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo 112-0012, Japan
| |
Collapse
|
2
|
Moura-Neto R, King JL, Mello I, Dias V, Crysup B, Woerner AE, Budowle B, Silva R. Evaluation of Promega PowerSeq™ Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies. Forensic Sci Int Genet 2021; 53:102516. [PMID: 33878618 DOI: 10.1016/j.fsigen.2021.102516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/06/2021] [Accepted: 03/29/2021] [Indexed: 02/01/2023]
Abstract
Forensic DNA typing typically relies on the length-based (LB) separation of PCR products containing short tandem repeat loci (STRs). Massively parallel sequencing (MPS) elucidates an additional level of STR motif and flanking region variation. Also, MPS enables simultaneous analysis of different marker-types - autosomal STRs, SNPs for lineage and identification purposes, reducing both the amount of sample used and the turn-around-time of analysis. Therefore, MPS methodologies are being considered as an additional tool in forensic genetic casework. The PowerSeq™ Auto/Y System (Promega Corp), a multiplex forensic kit for MPS, enables analysis of the 22 autosomal STR markers (plus Amelogenin) from the PowerPlex® Fusion 6C kit and 23 Y-STR markers from the PowerPlex® Y23 kit. Population data were generated from 140 individuals from an admixed sample from Rio de Janeiro, Brazil. All samples were processed according to the manufacturers' recommended protocols. Raw data (FastQ) were generated for each indexed sample and analyzed using STRait Razor v2s and PowerSeqv2.config file. The subsequent population data showed the largest increase in expected heterozygosity (23%), from LB to sequence-based (SB) analyses at the D5S818 locus. Unreported allele was found at the D21S11 locus. The random match probability across all loci decreased from 5.9 × 10-28 to 7.6 × 10-33. Sensitivity studies using 1, 0.25, 0.062 and 0.016 ng of DNA input were analyzed in triplicate. Full Y-STR profiles were detected in all samples, and no autosomal allele drop-out was observed with 62 pg of input DNA. For mixture studies, 1 ng of genomic DNA from a male and female sample at 1:1, 1:4, 1:9, 1:19 and 1:49 proportions were analyzed in triplicate. Clearly resolvable alleles (i.e., no stacking or shared alleles) were obtained at a 1:19 male to female contributor ratio. The minus one stutter (-1) increased with the longest uninterrupted stretch (LUS) allele size reads and according to simple or compound/complex repeats. The haplotype-specific stutter rates add more information for mixed samples interpretation. These data support the use of the PowerSeqTM Auto/Y systems prototype kit (22 autosomal STR loci, 23 Y-STR loci and Amelogenin) for forensic genetics applications.
Collapse
Affiliation(s)
- Rodrigo Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Isadora Mello
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
3
|
Jiang B, He W, Jin C, Liu Y, Wen D, Wang C, Zeye MMJ, Li J, Zha L. Developmental validation of the STRscan-17LC kit: a 6 Dye STR kit enhanced stability and ability to detect degraded samples. Int J Legal Med 2021; 135:431-440. [PMID: 33454809 DOI: 10.1007/s00414-020-02490-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/09/2020] [Indexed: 11/26/2022]
Abstract
Genotyping of short tandem repeat (STR) markers is the basic method of forensic science. Enhanced technologies are needed to meet the requirements of databasing and casework samples. The STRscan-17LC kit is a 6 Dye STR kit which amplifies 16 STR loci: D3S1358, TPOX, D16S539, vWA, D2S1338, CSF1PO, D19S433, D7S820, FGA, D8S1179, D5S818, D13S317, D18S51, TH01, D12S391, and D21S11 and the sex-determinant locus amelogenin. This kit is designed for better tolerance to PCR inhibitors and analysis of mildly degraded samples with all fragments smaller than 330 bases. In this study, the STRscan-17LC kit is validated according to the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines, including PCR-based studies, sensitivity, precision and accuracy, inhibitors, species specificity, DNA mixture studies, population, and concordance studies. The validation results suggest that the STRscan-17LC kit is a useful tool for forensic application.
Collapse
Affiliation(s)
| | | | - Chuan Jin
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, People's Republic of China
| | - Ying Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China.
| |
Collapse
|
4
|
Romsos EL, French JL, Smith M, Figarelli V, Harran F, Vandegrift G, Moreno LI, Callaghan TF, Brocato J, Vaidyanathan J, Pedroso JC, Amy A, Stoiloff S, Morillo VH, Czetyrko K, Johnson ED, de Tagyos J, Murray A, Vallone PM. Results of the 2018 Rapid DNA Maturity Assessment. J Forensic Sci 2020; 65:953-959. [PMID: 31985834 PMCID: PMC11034630 DOI: 10.1111/1556-4029.14267] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/25/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023]
Abstract
Three commercially available integrated rapid DNA instruments were tested as a part of a rapid DNA maturity assessment in July of 2018. The assessment was conducted with sets of blinded single-source reference samples provided to participants for testing on the individual rapid platforms within their laboratories. The data were returned to the National Institute of Standards and Technology (NIST) for review and analysis. Both FBI-defined automated review (Rapid DNA Analysis) and manual review (Modified Rapid DNA Analysis) of the datasets were conducted to assess the success of genotyping the 20 Combined DNA Index System (CODIS) core STR loci and full profiles generated by the instruments. Genotype results from the multiple platforms, participating laboratories, and STR typing chemistries were combined into a single analysis. The Rapid DNA Analysis resulted in a success rate of 80% for full profiles (85% for the 20 CODIS core loci) with automated analysis. Modified Rapid DNA Analysis resulted in a success rate of 90% for both the CODIS 20 core loci and full profiles (all attempted loci per chemistry). An analysis of the peak height ratios demonstrated that 95% of all heterozygous alleles were above 59% heterozygote balance. For base-pair sizing precision, the precision was below the standard 0.5 bp deviation for both the ANDE 6C System and the RapidHIT 200.
Collapse
Affiliation(s)
- Erica L Romsos
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
| | | | - Mark Smith
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Vincent Figarelli
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Frederick Harran
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Glenn Vandegrift
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Lilliana I Moreno
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Thomas F Callaghan
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Joanie Brocato
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Janaki Vaidyanathan
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Juan C Pedroso
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Andrea Amy
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Stephanie Stoiloff
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Victor H Morillo
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Karina Czetyrko
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Elizabeth D Johnson
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Jessica de Tagyos
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Ashley Murray
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
| |
Collapse
|
5
|
Abstract
Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2'-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.
Collapse
Affiliation(s)
- Madiha Sultan
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
| |
Collapse
|
6
|
Henry J, Scandrett L. Assessment of the Yfiler® Plus PCR amplification kit for the detection of male DNA in semen-negative sexual assault cases. Sci Justice 2019; 59:480-485. [PMID: 31472792 DOI: 10.1016/j.scijus.2019.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022]
Abstract
The ability to detect male epithelial cells deposited during digital penetration or penile penetration without ejaculation is limited by the sensitivity of the Y-STR profiling kit. In this study, the relative profiling success of the Thermofisher Yfiler® Plus kit was compared to its predecessor, AmpFlSTR Yfiler®, for 104 semen-negative sexual assault samples from casework at Forensic Science SA, Adelaide, South Australia. Yfiler Plus generated allele information in 25% more samples than Yfiler and gave a higher recovery of informative alleles in all but two samples where detectable male DNA was present. Where a profile was obtained in both kits, 92% of samples gave a higher percentage of informative loci with Yfiler Plus compared to Yfiler. Yfiler Plus also resolved DNA mixtures in 15 samples as compared to 1 sample with Yfiler. Detection of male DNA with the Quantifiler™ Trio DNA Quantification kit was shown to correlate with a successful profiling outcome with Yfiler Plus. The success of profiling with Yfiler Plus was independent of the time elapsed between the alleged offence and the sample being collected, the type of sexual penetration which occurred, and the anatomical origin of the sample.
Collapse
Affiliation(s)
- Julianne Henry
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia; College of Science and Engineering, Flinders University of South Australia, GPO Box 2100, Adelaide, South Australia 5001, Australia.
| | - Lenara Scandrett
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia.
| |
Collapse
|
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: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | | | - Tim Stakenborg
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| |
Collapse
|
8
|
Puri P, Kumar N, Sharma D, Shukla SK. Differential organic DNA extraction of semen sample contaminated with blood for the identification of a serial sexual offender: A case report. Med Leg J 2019; 87:32-35. [PMID: 30070156 DOI: 10.1177/0025817218789569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In many cases of sexual assault, traces of semen are left behind on the victim's body, clothes and the area in which the assault has taken place. The positive identification of semen is instrumental in supporting such cases. There are several methods of forensic examination of semen reported in literature, but the presence of blood complicates the identification of semen stains. This paper presents one such case study where the presence of blood makes DNA profiling more challenging as the PCR amplification becomes complicated, and the absolute differential isolation is the only way to get the clear profile using identifiler kits.
Collapse
Affiliation(s)
- Pooja Puri
- 1 Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Naresh Kumar
- 2 Biology Division, Forensic Science Laboratory, Home Department, GNCT of Delhi, Rohini, New Delhi, India
| | - Dhruv Sharma
- 2 Biology Division, Forensic Science Laboratory, Home Department, GNCT of Delhi, Rohini, New Delhi, India
| | - S K Shukla
- 1 Amity Institute of Forensic Sciences, Amity University, Noida, India
| |
Collapse
|
9
|
Yang J, Hurth C, Nordquist A, Smith S, Zenhausern F. Integrated Microfluidic System for Rapid DNA Fingerprint Analysis: A Miniaturized Integrated DNA Analysis System (MiDAS)-Swab Sample-In to DNA Profile-Out. Methods Mol Biol 2019; 1906:207-224. [PMID: 30488395 DOI: 10.1007/978-1-4939-8964-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A fully automated rapid DNA analysis system requires integrating several operational elements performing multiple steps onto one single microfluidic platform. The functions to include on the microfluidic platform consist of substrate lysis, lysate DNA extraction, single or multiplexed PCR amplification, amplicon separation, and product readout. Here we describe a fully automated integrated system for forensic short tandem repeat (STR) analysis of reference samples, achieving buccal swab-in and DNA profile-out.
Collapse
Affiliation(s)
- Jianing Yang
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| | - Cedric Hurth
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Alan Nordquist
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Stan Smith
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| |
Collapse
|
10
|
Mapes AA, Stoel RD, de Poot CJ, Vergeer P, Huyck M. Decision support for using mobile Rapid DNA analysis at the crime scene. Sci Justice 2018; 59:29-45. [PMID: 30654966 DOI: 10.1016/j.scijus.2018.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 04/17/2018] [Accepted: 05/02/2018] [Indexed: 11/17/2022]
Abstract
Mobile Rapid DNA technology is close to being incorporated into crime scene investigations, with the potential to identify a perpetrator within hours. However, the use of these techniques entails the risk of losing the sample and potential evidence, because the device not only consumes the inserted sample, it is also is less sensitive than traditional technologies used in forensic laboratories. Scene of Crime Officers (SoCOs) therefore will face a 'time/success rate trade-off' issue when making a decision to apply this technology. In this study we designed and experimentally tested a Decision Support System (DSS) for the use of Rapid DNA technologies based on Rational Decision Theory (RDT). In a vignette study, where SoCOs had to decide on the use of a Rapid DNA analysis device, participating SoCOs were assigned to either the control group (making decisions under standard conditions), the Success Rate (SR) group (making decisions with additional information on DNA success rates of traces), or the DSS group (making decisions supported by introduction to RDT, including information on DNA success rates of traces). This study provides positive evidence that a systematic approach for decision-making on using Rapid DNA analysis assists SoCOs in the decision to use the rapid device. The results demonstrated that participants using a DSS made different and more transparent decisions on the use of Rapid DNA analysis when different case characteristics were explicitly considered. In the DSS group the decision to apply Rapid DNA analysis was influenced by the factors "time pressure" and "trace characteristics" like DNA success rates. In the SR group, the decisions depended solely on the trace characteristics and in the control group the decisions did not show any systematic differences on crime type or trace characteristic. Guiding complex decisions on the use of Rapid DNA analyses with a DSS could be an important step towards the use of these devices at the crime scene.
Collapse
Affiliation(s)
- A A Mapes
- Amsterdam University of Applied Sciences (HvA), PO Box 1025, Amsterdam BA 1000, The Netherlands.
| | - R D Stoel
- Netherlands Forensic Institute, Postbus 24044, Den Haag 2490 AA, The Netherlands.
| | - C J de Poot
- Amsterdam University of Applied Sciences (HvA), PO Box 1025, Amsterdam BA 1000, The Netherlands.
| | - P Vergeer
- Netherlands Forensic Institute, Postbus 24044, Den Haag 2490 AA, The Netherlands.
| | - M Huyck
- New York Police Department, Forensic Investigative Division, United States.
| |
Collapse
|
11
|
Jin M, Ba HJ, Zhu AH, Ma J, Shi JW, Liu YN, Lin ZQ. [Effect of Benzidine Test on DNA Analysis of Bloodstain]. Fa Yi Xue Za Zhi 2018; 34:157-160. [PMID: 29923382 DOI: 10.3969/j.issn.1004-5619.2018.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Indexed: 06/08/2023]
Abstract
OBJECTIVES To explore the effect of benzidine test and related reagents on DNA analysis of bloodstain. METHODS A total of 970 bloodstain filter paper samples with 1 μL venous blood were collected, and 10 of them acted as control samples. After benzidine test and related reagent processing, DNA of 960 samples was extracted by Chelex-100 and silica bead methods and then multiplex amplified by AmpFℓSTR™ Identifiler™ Plus PCR kits. The results of STR typing were compared between different groups. RESULTS DNA were extracted immediately after benzidine test. Totally STR loci (3.80±1.34) were detected by silica bead method, while no STR loci were obtained by Chelex-100 method. Thirteen samples (21.7%) with whole STR typing results were obtained by drying after benzidine test, and the STR locus number (12.90±1.49) which obtained by silica bead method was much higher than by Chelex-100 method (4.70±1.96) (P<0.05). When DNA was extracted immediately after the addition of glacial acetic acid, the STR locus number was (9.40±2.09) by silica bead method, but no STR typing result was obtained by Chelex-100 method. All 15 STR loci could be obtained by only adding glacial acetic acid after drying and only adding tetramethylbenzidine alcoholization liquid or 3% hydrogen peroxide liquid. CONCLUSIONS Benzidine test has significant influence on DNA analysis of bloodstain. The Chelex-100 method is not suitable for the DNA extraction of bloodstain after benzidine test. Drying after benzidine test and silica bead methods can effectively enhance the STR locus number of bloodstain.
Collapse
Affiliation(s)
- M Jin
- Institute of Forensic Science, Changzhou Public Security Bureau, Changzhou 213003, China
| | - H J Ba
- Institute of Forensic Science, Changzhou Public Security Bureau, Changzhou 213003, China
| | - A H Zhu
- Institute of Forensic Science, Changzhou Public Security Bureau, Changzhou 213003, China
| | - J Ma
- Institute of Forensic Science, Changzhou Public Security Bureau, Changzhou 213003, China
| | - J W Shi
- Institute of Forensic Science, Changzhou Public Security Bureau, Changzhou 213003, China
| | - Y N Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Z Q Lin
- Department of Forensic Medicine, China Criminal Police College, Shenyang 110035, China
| |
Collapse
|
12
|
Zajac BK, Zehner R, Scheiper S, Weissenberger M. Kit-dependent discrepancy in D16S539 and general considerations for database matches. Forensic Sci Int Genet 2018; 34:148-151. [PMID: 29482104 DOI: 10.1016/j.fsigen.2018.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/12/2018] [Indexed: 01/20/2023]
Abstract
Throughout the last decade more companies have been offering multiplex PCR kits for forensic STR typing. As a consequence, it has been demonstrated, that an observed genotype may unexpectedly vary at a single locus when different STR kits have been used. Analysing STR profiles which have to be entered in a national database, unknown or undetected primer binding site mutations, insertions or deletions within the flanking region of STR loci may hinder matches and therefore have far-reaching consequences. The current study is a further example indicating that sequence variations in flanking regions are a common problem within STR typing which should not be underestimated. A deletion of 16 nucleotides close to the primer binding site downstream of the repeat sequence resulted in deviant genotypes at the D16S539 locus according to different STR kits used.
Collapse
Affiliation(s)
- Barbara Karolina Zajac
- Institute of Forensic Medicine and Traffic Medicine, Department for Forensic Genetics, University Hospital Heidelberg, Germany.
| | - Richard Zehner
- Institute of Legal Medicine, Department for Forensic Biology, University Hospital Frankfurt, Germany.
| | - Stefanie Scheiper
- Institute of Legal Medicine, Department for Forensic Biology, University Hospital Frankfurt, Germany.
| | - Melanie Weissenberger
- Institute of Forensic Medicine and Traffic Medicine, Department for Forensic Genetics, University Hospital Heidelberg, Germany.
| |
Collapse
|
13
|
Li B, Lü Z. [DNA Extraction from Old Bones by AutoMate Express™ System]. Fa Yi Xue Za Zhi 2017; 33:380-382. [PMID: 29219269 DOI: 10.3969/j.issn.1004-5619.2017.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To establish a method for extracting DNA from old bones by AutoMate Express™ system. METHODS Bones were grinded into powder by freeze-mill. After extraction by AutoMate Express™, DNA were amplified and genotyped by Identifiler®Plus and MinFiler™ kits. RESULTS DNA were extracted from 10 old bone samples, which kept in different environments with the postmortem interval from 10 to 20 years, in 3 hours by AutoMate Express™ system. Complete STR typing results were obtained from 8 samples. CONCLUSIONS AutoMate Express™ system can quickly and efficiently extract DNA from old bones, which can be applied in forensic practice.
Collapse
Affiliation(s)
- B Li
- Criminal Technology Agency of Fujian Province Public Security Department, Fuzhou 350003, China
| | - Z Lü
- Gulou District Public Security Bureau of Fuzhou City, Fuzhou 350003, China
| |
Collapse
|
14
|
Abstract
We report the findings of the evaluation of the InnoTyper® 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs. All loci presented biallelic patterns except the triallelic RG148 locus resulting from a variant insertion allele, named RG148I-1, observed exclusively in the Bantu. The InnoTyper® 21 kit was found to be highly discriminatory between the 507 unrelated individuals of the Afrikaaner, Asian Indian, Coloured, amaXhosa and amaZulu groups. The HID parameters: the CPD ranged between 0.99999987 and 0.9999999845, and the CMP between 1.0335×10-7 and 1.5506×10-8. The paternity parameters: the CPI ranged between 0.0202 and 0.3177, and the CPE between 0.9161 and 0.9749. There were no significant signs of deviations from HWE or linkage disequilibrium (LD) after applying a Bonferroni correction. This kit also showed minor levels of population structure which could differentiate between the African and non-African population groups. Finally, in challenging casework with severely degraded biological material, the InnoTyper® 21 genotyping kit was compatible with GlobalFiler® and Investigator DIPplex® to increase the HID parameters.
Collapse
Affiliation(s)
- Peter Gustav Ristow
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Nicole Barnes
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Gina Pineda Murphy
- InnoGenomics Technologies, 1441 Canal Street, Suite 307, New Orleans, LA, 70112, United States of America
| | - Hiromi Brown
- InnoGenomics Technologies, 1441 Canal Street, Suite 307, New Orleans, LA, 70112, United States of America
| | - Kevin Wesley Cloete
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa.
| |
Collapse
|
15
|
Crnjac J, Ozretić P, Merkaš S, Ratko M, Lozančić M, Rožić S, Špoljarić D, Korolija M, Popović M, Mršić G. Analysis of 12 X-chromosomal markers in the population of central Croatia. Leg Med (Tokyo) 2016; 21:77-84. [PMID: 27497338 DOI: 10.1016/j.legalmed.2016.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/12/2016] [Accepted: 07/01/2016] [Indexed: 02/05/2023]
Abstract
Investigator® Argus X-12 Kit is a commercially available set that allows simultaneous PCR amplification of 12 X-STR markers belonging to four linkage groups (LG). To assess the forensic efficiency of these markers for the population of central Croatia and consequent applicability in routine forensic casework, DNA from 200 blood samples of unrelated donors (100 female and 100 male) was amplified by Investigator® Argus X-12 Kit and analyzed by capillary electrophoresis. Statistical computations based on allele and haplotype frequencies for LG1 - LG4 were performed using Arlequin 3.5 software and on-line tool available at ChrX-STR.org. In female samples, all X-STR markers were in Hardy-Weinberg equilibrium (HWE). The most informative marker for central Croatia population was DXS10135 with polymorphism information content (PIC) 0.9296. The least polymorphic locus was DXS8378 (PIC=0.6363). Power of discrimination (PD) varied from 0.6968 to 0.9336 in male and from 0.8476 to 0.9916 in female samples. Combined PD exceeded 0.999999999 in both men and women. In male samples, linkage disequilibrium (LD) test revealed significant association (P=0.0000) of one marker pair in LG4 and two marker pairs in LG3. Portion of observed haplotypes in the number of possible haplotypes varied from 2.86% to 7.47% across all LGs. LG1 was the most informative with haplotype diversity (H) 0.9972. High PD of all analyzed markers exhibited for central Croatia population confirms suitability of Investigator® Argus X-12 for forensic pertinence. Moreover, results of this study will be included in establishing a national reference X-STR database based on 12 X-STR loci, which is necessary for the correct interpretation of the forensic casework results.
Collapse
Affiliation(s)
- Josip Crnjac
- University Department for Forensic Sciences, University of Split, Split, Croatia
| | | | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Martina Ratko
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
| | | | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Daniel Špoljarić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia.
| |
Collapse
|
16
|
Wang SC, Ding MM, Wei XL, Zhang T, Yao F. Recognition of Y Fragment Deletion by Genotyping Graphs after Amplified by PowerPlex ® 21 Detection Kit. Fa Yi Xue Za Zhi 2016; 32:193-195. [PMID: 29171738 DOI: 10.3969/j.issn.1004-5619.2016.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To recognize the possibility of Y fragment deletion of Amelogenin gene intuitively and simply according to the genotyping graphs. METHODS By calculating the ratio of total peak height of genotyping graphs, the statistics of equilibrium distribution between Amelogenin and D3S1358 loci, Amelogenin X-gene and Amelogenin Y-gene, and different alleles of D3S1358 loci from 1 968 individuals was analyzed after amplified by PowerPlex® 21 detection kit. RESULTS Sum of peak height of Amelogenin X allele was not less than 60% that of D3S1358 loci alleles in 90.8% female samples, and sum of peak height of Amelogenin X allele was not higher than 70% that of D3S1358 loci alleles in 94.9% male samples. CONCLUSIONS The result of genotyping after amplified by PowerPlex® 21 detection kit shows that the possibility of Y fragment deletion should be considered when only Amelogenin X-gene of Amelogenin is detected and the peak height of Amelogenin X-gene is not higher than 70% of the total peak height of D3S1358 loci.
Collapse
Affiliation(s)
- S C Wang
- DNA Lab of Criminal Investigation Detachment, Jiaxing Public Security Bureau, Jiaxing 314001, China
| | - M M Ding
- DNA Lab of Criminal Investigation Detachment, Jiaxing Public Security Bureau, Jiaxing 314001, China
| | - X L Wei
- DNA Lab of Criminal Investigation Detachment, Jiaxing Public Security Bureau, Jiaxing 314001, China
| | - T Zhang
- Criminal Investigation Team, Nanhu District Branch Bureau, Jiaxing Public Security Bureau, Jiaxing 314000, China
| | - F Yao
- DNA Lab of Criminal Investigation Detachment, Jiaxing Public Security Bureau, Jiaxing 314001, China
| |
Collapse
|
17
|
Sołtyszewski I, Szeremeta M, Skawrońska M, Niemcunowicz-Janica A, Pepiński W. Typeability of DNA in Touch Traces Deposited on Paper and Optical Data Discs. ADV CLIN EXP MED 2015; 24:437-40. [PMID: 26467131 DOI: 10.17219/acem/34474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Nucleated epithelial cells that are transferred by casual touching and handling of objects are the primary source of biological evidence that is found in high-volume crimes. Cellular material associated with touch traces usually contains low levels of DNA template making it challenging to acquire an informative profile. OBJECTIVES The main purpose of this study was to examine the efficacy of DNA typing in fingerprints deposited on optical data discs and the office paper. MATERIAL AND METHODS Latent fingerprints were made by 60 subjects of both sexes (30 males and 30 females). A highly effective DNA extraction method with QIAamp DNA Mini Kit (Qiagen) and an increased sensitivity PCR by AmpFlSTR® NGM™ Amplification Kit (Applied Biosystems) carried out at standard 30 cycles and at increased 34 cycles were used. RESULTS The mean value of total DNA recovery was 0.4 ng from CDs/DVDs and 0.3 ng from the office paper. Amplification of Low Template DNA (LT-DNA) resulted in improved analytical success by increasing the number of PCR cycles from standard 30 to 34. On the other hand, the increased PCR cycles resulted in allele drop-ins showing additional peaks, the majority of which were outside the stutter positions. CONCLUSIONS Rigorous procedures and interpretation guidelines are required during LT-DNA for producing reliable and reproducible DNA profiles for forensic purposes.
Collapse
Affiliation(s)
- Ireneusz Sołtyszewski
- Department of Criminalistics and Forensic Medicine, University of Warmia and Mazury in Olsztyn, Poland
| | - Michał Szeremeta
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | | | - Witold Pepiński
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| |
Collapse
|
18
|
Kalogianni DP, Bazakos C, Boutsika LM, Targem MB, Christopoulos TK, Kalaitzis P, Ioannou PC. Olive oil DNA fingerprinting by multiplex SNP genotyping on fluorescent microspheres. J Agric Food Chem 2015; 63:3121-8. [PMID: 25754746 DOI: 10.1021/jf5054657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Olive oil cultivar verification is of primary importance for the competitiveness of the product and the protection of consumers and producers from fraudulence. Single-nucleotide polymorphisms (SNPs) have emerged as excellent DNA markers for authenticity testing. This paper reports the first multiplex SNP genotyping assay for olive oil cultivar identification that is performed on a suspension of fluorescence-encoded microspheres. Up to 100 sets of microspheres, with unique "fluorescence signatures", are available. Allele discrimination was accomplished by primer extension reaction. The reaction products were captured via hybridization on the microspheres and analyzed, within seconds, by a flow cytometer. The "fluorescence signature" of each microsphere is assigned to a specific allele, whereas the signal from a reporter fluorophore denotes the presence of the allele. As a model, a panel of three SNPs was chosen that enabled identification of five common Greek olive cultivars (Adramytini, Chondrolia Chalkidikis, Kalamon, Koroneiki, and Valanolia).
Collapse
Affiliation(s)
| | - Christos Bazakos
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
| | | | - Mehdi Ben Targem
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
| | | | - Panagiotis Kalaitzis
- §Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute, Chania (MAICh), Chania, Crete, Greece 73100
| | | |
Collapse
|
19
|
Thomas JT, Berlin RM, Barker JM, Dawson Cruz T. Qiagen's Investigator™ Quantiplex Kit as a predictor of STR amplification success from low-yield DNA samples. J Forensic Sci 2013; 58:1306-1309. [PMID: 23786239 DOI: 10.1111/1556-4029.12171] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/25/2012] [Accepted: 07/14/2012] [Indexed: 11/29/2022]
Abstract
Qiagen's Investigator™ Quantiplex kit, a total human DNA quantitation kit, has a 200-base pair internal control, fast cycling time, and scorpion molecules containing a covalently linked primer, probe, fluorophore, and quencher. The Investigator™ Quantiplex kit was evaluated to investigate a value under which complete short tandem repeat (STR) failure was consistently obtained. Buccal swabs were extracted using the Qiagen QIAamp(®) DNA Blood Mini Kit, quantified with the Investigator™ Quantiplex kit using a tested half-volume reaction, amplified with the ABI AmpFlSTR(®) Identifiler kit, separated on the 3100Avant Genetic Analyzer, and data analyzed with GeneMapper(®) ID v.3.2. While undetected samples were unlikely to produce sufficient data for statistical calculations or CODIS upload (2.00 alleles and 0.82 complete loci on average), data may be useful for exclusionary purposes. Thus, the Investigator™ Quantiplex kit may be useful for predicting STR success. These findings are comparable with previously reported data from the Quantifiler™ Human kit.
Collapse
Affiliation(s)
- Jacqueline T Thomas
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Rebecca M Berlin
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Jessica M Barker
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
- Department of Biology, Virginia Commonwealth University, P.O. Box 843079, 1020 W. Main Street, Room 2015, Richmond, VA 23284
| |
Collapse
|
20
|
Olarte A, Mantri N, Nugent G, Pang ECK. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species. PLoS One 2013; 8:e70347. [PMID: 23940565 PMCID: PMC3734018 DOI: 10.1371/journal.pone.0070347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 06/18/2013] [Indexed: 01/01/2023] Open
Abstract
Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.
Collapse
Affiliation(s)
- Alexandra Olarte
- School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
| | - Nitin Mantri
- School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
- * E-mail:
| | - Gregory Nugent
- School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
| | - Edwin C. K. Pang
- School of Applied Sciences, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
| |
Collapse
|
21
|
Dereviagina EO, Kuklev MI, Lapenkov MI, Plakhina NV. [Comparison of the effectiveness of DNA isolation from nail plates with the use of commercial kits]. Sud Med Ekspert 2013; 56:27-29. [PMID: 24428053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We compared the effectiveness of DNA isolation from nail plates using three commercial kits from different manufacturers. The results of the study give reason to recommend the use of PrepFiler BTA Forensic DNA Extraction Kits and QIAamp DNA Investigator Kit for the work with nail microfragments.
Collapse
|
22
|
Gao LL, Xu NL, Xie W, Ding SC, Wang DJ, Ma LQ, Li YY. [DNA extraction from bones and teeth using AutoMate Express forensic DNA extraction system]. Fa Yi Xue Za Zhi 2013; 29:127-129. [PMID: 23930509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To explore a new method in order to extract DNA from bones and teeth automatically. METHODS Samples of 33 bones and 15 teeth were acquired by freeze-mill method and manual method, respectively. DNA materials were extracted and quantified from the triturated samples by AutoMate Express forensic DNA extraction system. RESULTS DNA extraction from bones and teeth were completed in 3 hours using the AutoMate Express forensic DNA extraction system. There was no statistical difference between the two methods in the DNA concentration of bones. Both bones and teeth got the good STR typing by freeze-mill method, and the DNA concentration of teeth was higher than those by manual method. CONCLUSION AutoMate Express forensic DNA extraction system is a new method to extract DNA from bones and teeth, which can be applied in forensic practice.
Collapse
Affiliation(s)
- Lin-Lin Gao
- Institute of Criminal Science and Technology, Hangzhou Public Security Bureau, Hangzhou 310004, China.
| | | | | | | | | | | | | |
Collapse
|
23
|
Keller E, Looser M, Bieri HP, Kübler E, Balitzki B. [Recovery of blood traces with scenesafe FAST tape]. Arch Kriminol 2012; 230:166-176. [PMID: 23367791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Affiliation(s)
- Eva Keller
- Institut für Rechtsmedizin der Universität Basel
| | | | | | | | | |
Collapse
|
24
|
Drabik J, Jagiełło A, Niemcunowicz-Janica A, Pepiński W. [Validation and evaluation of a five miniSTRs kit in forensic genetics]. Arch Med Sadowej Kryminol 2011; 61:153-160. [PMID: 22390129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Affiliation(s)
- Jacek Drabik
- Z Wydziału Biologii Centralnego Laboratorium Kryminalistycznego KGP w Warszawie
| | | | | | | |
Collapse
|
25
|
Gu LH, Dong Y, Zhang C, Xu Y, Chen RH, Hu W, Chen LK, Zhou HG. [Forensic analysis of LCN DNA using sample concentration methods followed by miniSTR genotyping]. Fa Yi Xue Za Zhi 2010; 26:361-363. [PMID: 21287741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To optimize low copy number (LCN) DNA analysis methods for forensic STR genotyping. METHODS Two groups of DNA sample, extracted using either Magnetic bead method or Chelex-100 methods, were previously amplified with a Identifiler PCR Amplification kit, but no genotype was detected. The DNA samples were concentrated using either a drying method or the Microcon-100 method, then amplified using an miniFiler PCR Amplification kit and genotyped. RESULTS Among the 127 DNA samples, 47 samples, previously extracted using the Magnetic bead method, were genotyped with 36% success rate. Eighty samples, previously extracted using the Chelex-100 method, were genotyped with 30% success rate. CONCLUSION The application of sample concentration methods and miniFiler kit can improve the success rate of LCN STR analysis.
Collapse
Affiliation(s)
- Li-Hua Gu
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
In this work, a number of performance checks were carried out to evaluate the efficacy of commercial Y-short tandem repeats (Y-STR) kits for casework applications. The study evaluated the sensitivity, specificity and stability of the Y-STR markers used and the ability to obtain a male profile from postcoital samples taken at various time points after intercourse. All systems performed well with 1-3 ng of male DNA as recommended by the manufacturers. All systems gave full profiles at 100 pg of input DNA, which is within the realm of low copy number DNA analysis. Moreover all, except Y-Plex12, gave full profiles with 30-50 pg of male DNA. No increased performance was obtained with any of the systems by increasing the cycle number beyond that recommended by the various manufacturers. When up to 1 microg of female DNA was used (in the absence of male DNA) no female DNA cross reactivity was observed with the Y-Plex 12 and Y-Filer systems. PowerPlex Y produced female DNA derived products near the DYS438 and within the DYS392 loci at a rare allele position with high input DNA levels (300 ng and 1 microg, respectively). Male/female DNA admixture experiments indicated the particularly high specificity of the Y-Filer and PowerPlex Y systems under conditions of several thousand fold female DNA excess. All systems were able to detect the minor alleles in male/male DNA admixtures at a 1:5 dilution with the PowerPlex Y and Y-Filer being able to detect some minor alleles at 1:20. Species testing indicated some limited, minor cross reactivity of the commercial systems with some domestic male mammals although it is easily recognizable and would not pose any problems in casework analysis. As expected a significant number of cross-reacting products were obtained with nonhuman primate species. All Y-STR multiplex systems tested were able to produce complete Y-STR profiles from bloodstains and semen stains exposed up to 6 weeks when the samples were protected against precipitation and sunlight. However, exposure of the samples to precipitation either in the presence or absence of sunlight resulted in Y-STR profile loss over time, with total profile loss occurring with all systems after 3 weeks or more. Complete Y-STR profiles of the male donors up to 72 h postcoitus were obtained with all of the multiplex systems tested, except for Y-Plex12, which gave partial profiles.
Collapse
Affiliation(s)
- Kathleen A Mayntz-Press
- Forensic Biochemistry Track, Graduate Program in Chemistry, University of Central Florida, PO Box 162366, Orlando, FL 32816-2366, USA
| | | |
Collapse
|
27
|
Abstract
Accurate quantification of DNA samples is an important step in obtaining accurate and reproducible short tandem repeat (STR) profiles. Quantitative real-time-PCR has improved the speed and accuracy of DNA quantification over earlier methods, albeit at significantly greater cost per reaction. Here, the performance of reduced volume (10 microL) DNA quantification assays using the Quantifiler Human DNA Quantification Kit was evaluated using commercial standards and single source biological stains (e.g., venous blood, saliva, and semen). In addition, casework-type samples including those subjected to environmental contaminants containing PCR inhibitors and samples having undergone extensive DNA degradation were also quantified. The concentration of DNA in various forensic samples ranged from 0 to 2.9 ng/microL depending on sample source and/or environmental insult. Compared to full-scale reactions, reduced volume assays displayed equivalent to improved amplification efficiency and sample-to-sample reproducibility (+/-0.01-0.17 C(T FAM)). Furthermore, the use of data from reduced-scale Quantifiler reactions facilitated the accurate determination of the amount of sample DNA extract needed to generate quality STR profiles. The use of 10 microL-scale Quantifiler reaction volumes has the practical benefit of increasing the effective number of reactions per kit by 250%; thereby reducing the cost per assay by 60% while consuming less sample. This is particularly advantageous in cases of consumptive testing.
Collapse
Affiliation(s)
- Christian G Westring
- Department of Biological Sciences, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA.
| | | | | | | |
Collapse
|
28
|
Tang JP, Wu D, Zhang C, Zhou HG. [Application of MiniFiler kit in forensic DNA testing of low copy number template]. Fa Yi Xue Za Zhi 2007; 23:304-6. [PMID: 17896528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To detect low copy number of DNA samples by using a newly launched commercial miniSTR detection kit (MiniFiler) in forensic practice. METHODS Low concentration and/or challenged forensic DNA samples were analyzed according to protocols provided by the manufacturer (Applied Biosystems, Foster City, USA). RESULTS DNA samples as low as 10 pg could be amplified by MiniFiler kit, and the optimal DNA quantity was 40 pg or above. CONCLUSION MiniFiler kit can be used for analysis of low copy number STR.
Collapse
Affiliation(s)
- Jian-ping Tang
- Institute of Forensic Science, Shanghai Municipal Public Security Bureau, Shanghai 200083, China
| | | | | | | |
Collapse
|
29
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
30
|
Abstract
The advent of microfluidic technology for genetic analysis has begun to impact forensic science. Recent advances in microfluidic separation of short-tandem-repeat (STR) fragments has provided unprecedented potential for improving speed and efficiency of DNA typing. In addition, the analytical processes associated with sample preparation--which include cell sorting, DNA extraction, DNA quantitation, and DNA amplification--can all be integrated with the STR separation in a seamless manner. The current state of these microfluidic methods as well as their advantages and potential shortcomings are detailed. Recent advances in microfluidic device technology, as they pertain to forensic DNA typing, are discussed with a focus on the forensic community.
Collapse
Affiliation(s)
- Katie M Horsman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | | | | | | |
Collapse
|
31
|
Yu PH, Wallace MM. Effect of 1,2-indanedione on PCR-STR typing of fingerprints deposited on thermal and carbonless paper. Forensic Sci Int 2007; 168:112-8. [PMID: 16876350 DOI: 10.1016/j.forsciint.2006.06.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 06/24/2006] [Accepted: 06/24/2006] [Indexed: 10/24/2022]
Abstract
1,2-Indanedione treated fingerprints deposited on two substrates (thermal and carbonless paper) were swabbed and tested to determine the effect of the chemical on PCR-STR DNA typing. Samples from 10 post-treatment intervals were analyzed. Two extraction methods, Chelex and Qiamp, were used to determine the effect of extraction procedure on the quality of the DNA profiles. The LCN DNA samples were concentrated using Microcon 100 and amplified using the Profiler Plus amplification kit. 1,2-Indanedione did not adversely affect the DNA profiles obtained from the treated fingerprints. Partial DNA profiles were obtained at all post-development time frames. Both extraction methods produced comparable profiles although more "drop-ins" were observed with the Qiamp method. More "drop-outs" occurred in the DNA profiles from samples deposited on the thermal substrate compared with carbonless substrate.
Collapse
Affiliation(s)
- Pei-Hua Yu
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 445 West 59th Street, New York, NY, United States
| | | |
Collapse
|
32
|
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: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Affiliation(s)
- Peng Liu
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | | | | |
Collapse
|
33
|
Barkham T. BioRobot EZ1 workstation compares well with manual spin kits for extraction of viral RNA from sera and saves substantial staff time. J Clin Microbiol 2006; 44:1598. [PMID: 16597907 PMCID: PMC1448687 DOI: 10.1128/jcm.44.4.1598.2006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Timothy Barkham
- Department of Pathology and Laboratory MedicineTan Tock Seng Hospital11 Jalan Tan Tock SengSingapore 308433Phone: 65-63578957, Fax: 65-62536507, E-mail:
| |
Collapse
|
34
|
Yeung SHI, Greenspoon SA, McGuckian A, Crouse CA, Emrich CA, Ban J, Mathies RA. Rapid and High-Throughput Forensic Short Tandem Repeat Typing Using a 96-Lane Microfabricated Capillary Array Electrophoresis Microdevice*. J Forensic Sci 2006; 51:740-7. [PMID: 16882214 DOI: 10.1111/j.1556-4029.2006.00153.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A 96-channel microfabricated capillary array electrophoresis (muCAE) device was evaluated for forensic short tandem repeat (STR) typing using PowerPlex 16 and AmpFlSTR Profiler Plus multiplex PCR systems. The high-throughput muCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the muCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.
Collapse
Affiliation(s)
- Stephanie H I Yeung
- UCSF/UCB Joint Graduate Group in Bioengineering, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | |
Collapse
|
35
|
Guerasimova A, Nyarsik L, Liu JP, Schwartz R, Lange M, Lehrach H, Janitz M. Liquid-based hybridization assay with real-time detection in miniaturized array platforms. ACTA ACUST UNITED AC 2006; 23:35-40. [PMID: 16298548 DOI: 10.1016/j.bioeng.2005.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 09/26/2005] [Accepted: 09/26/2005] [Indexed: 11/18/2022]
Abstract
An assay for the fluorescent detection of short oligonucleotide probe hybridization in miniaturized high-density array platforms is presented. It combines hybridization in solution with real-time fluorescent detection, which involves measurement of fluorescence increase by means of an induced fluorescence resonance energy transfer. The feasibility of this approach using DNA or RNA as a target, and short DNA- as well as LNA (locked nucleic acid)-modified oligonucleotides as probes is shown. The presented approach could potentially contribute to a significant increase in the throughput of large-scale genomic applications, such as oligofingerprinting and genotyping, and also reduce material consumption.
Collapse
|
36
|
Schmidt U, Lutz-Bonengel S, Weisser HJ, Sänger T, Pollak S, Schön U, Zacher T, Mann W. Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit. Int J Legal Med 2005; 120:42-8. [PMID: 16231187 DOI: 10.1007/s00414-005-0041-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Accepted: 08/03/2005] [Indexed: 10/25/2022]
Abstract
In forensic DNA analysis, improvement of DNA typing technologies has always been an issue. It has been shown that DNA amplification in low volumes is a suitable way to enhance the sensitivity and efficiency of amplification. In this study, DNA amplification was performed on a flat, chemically structured glass slide in 1-microl reaction volumes from cell line DNA contents between 1,000 and 4 pg. On-chip DNA amplification reproducibly yielded full allelic profiles from as little as 32 pg of template DNA. Applicability on the simultaneous amplification of 15 short tandem repeats and of a segment of the Amelogenin gene, which are routinely used in forensic DNA analysis, is shown. The results are compared to conventional in-tube amplification carried out in 25-microl reaction volumes.
Collapse
Affiliation(s)
- Ulrike Schmidt
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104, Freiburg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
With the recent expansion of DNA database laws in many states, there is a critical need for the rapid and simple collection of DNA samples and streamlined processing for downstream applications. The Buccal DNA Collector was developed to address the need for a reliable, practical alternative to blood collection that is compatible with high-throughput operations. The collection area consists of filter paper that is placed against the inside of the cheek, and the sample is taken by swiping the cheek several times while pulling the device out of the mouth. Using this method, DNA profiles have been obtained from samples stored for 2 years at room temperature. Cells are collected on all regions of the filter paper, with the maximum DNA recovery from the tip. The processing of DNA for DNA typing is accomplished with BodeElute™, a new product that prepares DNA for amplification in a single 30-min heating step. Extracted DNA samples were successfully amplified with four commonly used multiplex short tandem repeat (STR) amplification kits. These products provide simplified approaches for collecting and processing buccal cell samples.
Collapse
|
38
|
Anslinger K, Bayer B, Rolf B, Keil W, Eisenmenger W. Application of the BioRobot EZ1 in a forensic laboratory. Leg Med (Tokyo) 2005; 7:164-8. [PMID: 15847824 DOI: 10.1016/j.legalmed.2005.01.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 11/22/2004] [Accepted: 01/11/2005] [Indexed: 11/26/2022]
Abstract
In a forensic laboratory, the routine application of an automated DNA extraction and purification robot has to fulfil several conditions, like producing reproducible DNA's of sufficient quantity and quality from all the different forensic biological stains relevant to various carrier materials. In this study, the suitability of the BioRobot EZ1 system from QIAGEN (Hilden, Germany), which offers fully automated extraction and purification of nucleic acids using magnetic bead technology, was tested. In summary, the DNA's obtained from the BioRobot EZ1 for different forensic relevant biological materials showed a quantity and quality comparable to those of the forensic standard protocols normally used in our laboratory. The system saves time, because there is no need of any further purification or concentration step after the automated DNA extraction. It can also be used as a replacement for time consuming organic extractions. A disadvantage of the system was the unsteady quality of the chemical regencies used by the robot. Nineteen different lots were tested with a self designed test system.
Collapse
Affiliation(s)
- Katja Anslinger
- Institute of Legal Medicine, Ludwig-Maximilians-University of Munich, Frauenlobstrasse 7a, D-80337 München, Germany.
| | | | | | | | | |
Collapse
|
39
|
Mansour L, Cheikali C, Desaunais P, Coulon JP, Daubin J, Hassine OKB, Vivarès CP, Jeanjean J, Cornillot E. Description of an ultrathin multiwire proportional chamber-based detector and application to the characterization of theSpraguea lophii(Microspora) two-dimensional genome fingerprint. Electrophoresis 2004; 25:3365-77. [PMID: 15490460 DOI: 10.1002/elps.200406089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiwire proportional chamber is a useful technology to build detectors that supersede the lack of interactivity of autoradiography in molecular biology experiments. Some drawbacks still limited the diffusion of existing instruments in biological laboratories. The major competitors are storage phosphor imaging systems. The simplified description of a radio-chromato-imager prototype (RCI) based on an original ultrathin multiwire proportional chamber is presented. It combines the advantage of the different existing technologies to present competitive properties in terms of efficiency, spatial resolution, robustness, manipulation easiness and production cost. Application of the RCI detector to molecular biology was performed by the analysis of karyotype and restriction display two-dimensional pulsed-field gel electrophoresis (KARD 2-D PFGE) data which are used to describe small eukaryotic genome structures. The comparative analysis with autoradiography was performed with the PDQuest software on Spraguea lophii (Microspora) genome fingerprints. The spot detection procedure applied to the different images leads to a similar conclusion considering the genome structure of S. lophii which appeared to be composed of 15 chromosomes for 13 karyotypic bands (200-880 kbp).
Collapse
Affiliation(s)
- Lamjed Mansour
- Parasitologie Moléculaireet Cellulaire, Université Blaise Pascal, Aubière, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Salvador JM, De Ungria MCA. Isolation of DNA from saliva of betel quid chewers using treated cards. J Forensic Sci 2003; 48:794-7. [PMID: 12877294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Betel quid (BQ) chewing, a common tradition in tropical areas, often poses a problem during collection and DNA analysis of buccal samples from many indigenous communities for population genetic studies and in forensic analysis of chewed BQ residues. This study evaluated the use of FTA card, a chemically treated filter paper, in collecting buccal samples from long-term BQ users and subsequent PCR-based analysis using nine STR markers. A low overall success rate of amplification was observed in the samples extracted using a standard organic extraction procedure (7%) as compared with those prepared using the FTA card (89%). The presence of inhibitors in liquid DNA samples was verified when control DNA failed to amplify in the presence of an equal volume of liquid BQ samples. The use of the FTA card is more practical during field sampling than handling tubes containing buccal swabs.
Collapse
Affiliation(s)
- Jazelyn M Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, Miranda Hall, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | | |
Collapse
|
41
|
Abstract
As the Iraqis discover a mass grave in a village south of Baghdad, scientists in Bosnia are still undertaking the painstaking task of trying to identify bodies found in mass graves in the former Yugoslavia
Collapse
|
42
|
Abstract
The recovery of DNA from teeth is usually associated with the destruction of the evidential tooth using, for instance a special grinding mill. In some cases, however, a minimal invasive method of DNA retrieval with a high recovery is required particularly when historical material has to be investigated. A tooth attributed to the German Emperor Wilhelm II was the only source of DNA in an analysis of a possible paternity and the DNA had to be extracted without destroying the appearance of the tooth. Here, the results of the DNA analysis are presented.
Collapse
Affiliation(s)
- H Pfeiffer
- Institute of Legal Medicine Münster, Röntgenstrasse 23, 48149 Münster, Germany
| | | | | | | |
Collapse
|
43
|
Aimi T, Kano S, Yotsutani Y, Morinaga T. Telomeric fingerprinting of the white root rot fungus, Rosellinia necatrix: a useful tool for strain identification. FEMS Microbiol Lett 2002; 217:95-101. [PMID: 12445651 DOI: 10.1111/j.1574-6968.2002.tb11461.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The telomere associated DNA sequence pTel46, which was isolated from Coprinus cinereus, was hybridized with Rosellinia necatrix genomic DNA. The DNA fragments hybridized with pTel46 were more sensitive to Bal31 nuclease. This result suggests that the DNA fragments hybridized with pTel46 were located at the end of chromosomes in R. necatrix. Telomere-linked restriction fragment length polymorphism (RFLP) was found in strains of R. necatrix isolated from various field and single ascospores. Thus, this marker appears to be an excellent tool to show the great polymorphism of R. necatrix. However, RFLP could not be found among several field isolated strains belonging to the same mycelial compatibility group (MCG) isolated in the same field. Therefore the strains belonging to the same MCG might be the same strain that could be anastomosed with each other without cell death except for strain W718 carrying a double-stranded RNA (dsRNA) virus. Therefore the RFLP corresponded to a MCG group, and none of the strains belonging to the same MCG group showed different RFLP in R. necatrix. Moreover, the presence of a kind of dsRNA virus might imply anastomosis between compatible strains.
Collapse
Affiliation(s)
- Tadanori Aimi
- Department of Bioresource Development, Hiroshima Prefectural University, Nanatsukahara, Shobara-shi, 727-0023, Hiroshima, Japan
| | | | | | | |
Collapse
|
44
|
Rutty GN. An investigation into the transference and survivability of human DNA following simulated manual strangulation with consideration of the problem of third party contamination. Int J Legal Med 2002; 116:170-3. [PMID: 12111321 DOI: 10.1007/s00414-001-0279-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Amplification was performed on human DNA material transferred during a model of manual strangulation. A total of 29 separate experiments were performed using a single male offender-female victim combination to observe whether DNA was transferred both from the offender's fingers to the victim's neck and vice versa and to consider the period of time after the event during which the material could potentially be recovered and amplified. DNA was amplified from either the victim's neck or the offender's fingers for at least 10 days after the contact although it is discussed whether this is potentially due to primary contact or a secondary/tertiary transfer event. The study highlights the problem of contamination of the offender's hands and victim's neck with third party DNA, the presence of which could have a significant outcome for both the investigating authority and the third party.
Collapse
Affiliation(s)
- G N Rutty
- Division of Forensic Pathology, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, PO Box 65, Leicester, LE2 7LX.
| |
Collapse
|
45
|
Mellon JN. Manufacturing convictions: why defendants are entitled to the data underlying forensic DNA kits. Duke Law J 2001; 51:1097-1137. [PMID: 11944660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|
46
|
Terefework Z, Kaijalainen S, Lindström K. AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officinalis. J Biotechnol 2001; 91:169-80. [PMID: 11566388 DOI: 10.1016/s0168-1656(01)00338-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AFLP fingerprints of Rhizobium galegae strains that infect Galega orientalis and Galega officinalis obtained from different geographical sources, and of taxonomically diverse rhizobia representing the recognized species, were generated. Comparisons of the fingerprints from fluorescent labeled AFLP products using capillary electrophoresis on ABI prism 310, slab gel electrophoresis on ABI prism 377 genetic analyzers and silver staining were in good agreement. All methods delineated the G. orientalis strains from G. officinalis strains, the G. orientalis strains formed a tight cluster whereas the G. officinalis strains seem to show a greater level of genetic diversity. Comparison of fluorescent AFLP with other detection methods revealed that fluorescent labeling is more sensitive and practical, in addition, the deleterious effect of radioactivity associated with 32P-labeling, the delicate process of blotting polyacrylamide gels or the tedious procedure of silver staining can be avoided. The automated system facilitated a large number of runs at a time and the subsequent analysis of the data by generating exportable raw data. The congruency of the experiments was analyzed using the Bionumerics software.
Collapse
Affiliation(s)
- Z Terefework
- Division of Microbiology, Department of Applied Chemistry and Microbiology, Biocenter 1, P.O. Box 56, Vikinkaari 9, FIN-00014 University of Helsinki, Helsinki, Finland.
| | | | | |
Collapse
|
47
|
Abstract
Distribution of allele frequencies for 12 STR loci (CSFIPO, TPOX, THO1, F13A01, FESFPS, vWA, D16S539, D7S820, D13S317, HPRTB, F13B and LPL) has been studied for the first time in unrelated Tamil (south India) population.
Collapse
Affiliation(s)
- S Panneerchelvam
- Forensic Sciences Department, 30A Kamarajar Salai, Mylapore, 600004, Chennai, India
| | | | | | | | | |
Collapse
|
48
|
Abstract
Allele frequencies for the 13 STRs included in the AmpFl/STR Profiler Plus and Cofiler kits were determined for an Andalusian population (southern Spain).
Collapse
Affiliation(s)
- P Sanz
- Instituto Nacional de Toxicología, P.O. Box 863, 41080, Sevilla, Spain
| | | | | | | | | | | |
Collapse
|
49
|
Abstract
Allele frequencies for twelve STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and GenePrint CTTv kit (VWA, TH01, TPO and CSF1PO) were estimated from a sample of 110 unrelated individuals from Mozambique.
Collapse
Affiliation(s)
- C Alves
- IPATIMUP, R. Roberto Frias, s/n, 4200, Porto, Portugal
| | | | | |
Collapse
|
50
|
Rerkamnuaychoke B, Chantratita W, Jomsawat U, Thanakitgosate J, Ruangvithayanon T, Rojanasunan P. Database of nine tetrameric STR loci--D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 in Thai population. Forensic Sci Int 2001; 119:123-5. [PMID: 11348805 DOI: 10.1016/s0379-0738(00)00415-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Allele distributions for the nine STR loci included in the AmpFlSTR Profiler Plus kit were evaluated in a Thai population of 300 unrelated individuals.
Collapse
Affiliation(s)
- B Rerkamnuaychoke
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | | | | | | | | | | |
Collapse
|