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Qu W, Wang F, Sun D, Liu Y, Jin X, Gong Z, Liu J, Zhang N, Wen D, Wang C, Jia H, Xu R, Tang X, Chen S, Fu X, Li X, Rong H, Zhang T, Jin C, Chen L, Li J, Liu Y, Cai J, Jiang B, Zha L. Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification. Int J Legal Med 2024; 138:361-373. [PMID: 37843624 DOI: 10.1007/s00414-023-03106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.
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Affiliation(s)
- Weifeng Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Feng Wang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Sun
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Yi Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xin Jin
- Public Security Department of Hainan Province, No. 9. Binya Road, Hainan, 570203, China
| | - Zheng Gong
- Criminal Technology Detachment, Public Security Bureau of Harbin, No. 35. Dongfeng Road, Harbin, 150010, China
| | - Jinjie Liu
- Criminal Investigation Detachment, Public Security Bureau of Beijing, No. 44. Banbuqiao Road, Beijing, 102611, China
| | - Ningjie Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Hongtao Jia
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ruyi Xu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xuan Tang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Siqi Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xiaoyi Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xue Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Haibo Rong
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Tao Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Chuan Jin
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Li Chen
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ying Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Bowei Jiang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China.
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China.
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Soldati G, Turrina S, Treccani M, Saccardo C, Ausania F, De Leo D. Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system. Mol Biol Rep 2023; 50:9779-9789. [PMID: 37812349 PMCID: PMC10676315 DOI: 10.1007/s11033-023-08808-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Massively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses. METHODS AND RESULTS DNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened. CONCLUSIONS Although the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.
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Affiliation(s)
- Giulia Soldati
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy.
| | - Stefania Turrina
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Mirko Treccani
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Chiara Saccardo
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Francesco Ausania
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Evaluating the effects of whole genome amplification strategies for amplifying trace DNA using capillary electrophoresis and massive parallel sequencing. Forensic Sci Int Genet 2021; 56:102599. [PMID: 34656831 DOI: 10.1016/j.fsigen.2021.102599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/04/2022]
Abstract
To draw robust conclusions when trace DNA samples are detected in complex cases, it is essential to successfully recover and genotype short tandem repeats (STRs) from trace DNA. However, obtaining complete STR profiles by the conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) method is generally difficult as trace DNA is often less than 100 pg. Previous studies have proven that through whole-genome amplification (WGA), the yield of DNA from trace DNA samples could be improved. In this study, we used two WGA kits, namely, REPLI-g® Single Cell kit and MALBAC® Single Cell DNA Quick-Amp Kit (hereafter referred to as REPLI and MALBAC), to amplify DNA samples with a series of dilutions (from 5.00 ng/μL to 0.391 pg/μL). Typing of STR markers in samples with and without WGA were then performed on a CE platform by the application of Goldeneye® DNA ID System 20 A kit, as well as directly calling sequences from massive parallel sequencing (MPS) for WGA samples with 1.00 ng, 125 pg and 25.0 pg as DNA inputs. Quantification results demonstrated that the yield of samples with WGA could reach the microgram level. The amplification fold was at least > 2000 and > 200 for REPLI and MALBAC, respectively. CE results showed that the number of correctly called loci was improved for trace DNA after WGA when the DNA inputs were lower than 25.0 pg for REPLI and 6.25 pg for MALBAC, respectively. WGA remarkably improved the percentage of called loci with DNA inputs lower than 50.0 pg, although poor performance in repeatability was observed. MPS results suggested that the correctly called loci calculated by MPS reads were mostly more than those calculated by CE, particularly for those of short length, implying MPS of samples after WGA is worth testing in the future. In conclusion, WGA has the potential usability for forensic trace DNA analysis at the single-cell level with good fidelity, although its repeatability requires further improvement.
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Affiliation(s)
- Qiannan Xu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Qianqian Kong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, PR China
| | - Xiaoxiao Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, PR China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
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Roy D, Tomo S, Purohit P, Setia P. Microbiome in Death and Beyond: Current Vistas and Future Trends. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.
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5
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Barrio PA, García Ó, Phillips C, Prieto L, Gusmão L, Fernández C, Casals F, Freitas JM, González-Albo MDC, Martín P, Mosquera A, Navarro-Vera I, Paredes M, Pérez JA, Pinzón A, Rasal R, Ruiz-Ramírez J, Trindade BR, Alonso A. The first GHEP-ISFG collaborative exercise on forensic applications of massively parallel sequencing. Forensic Sci Int Genet 2020; 49:102391. [PMID: 32957016 DOI: 10.1016/j.fsigen.2020.102391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/17/2023]
Abstract
One of the main goals of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. The GHEP-ISFG supports several Working Commissions which develop different scientific activities. One of them, the Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications", organized its first collaborative exercise on forensic applications of MPS technology in 2019. The aim of this exercise was to assess the concordance between the MPS results and those obtained with conventional technologies (capillary electrophoresis and Sanger sequencing), as well as to compare the results obtained within the different MPS platforms and/or the different kits/panels and analysis software packages (commercial and open-access) available on the market. The seven participating laboratories analyzed some samples of the annual GHEP-ISFG proficiency test (EIADN No. 27 (2019)), using Ion Torrent™ or MiSeq FGx® platforms. Six of them sent autosomal STR sequence data, five laboratories performed MPS analysis of individual identification SNPs, four laboratories reported MPS data of Y-chromosomal STRs, and X-chromosomal STRs, three laboratories performed MPS analysis of ancestry informative SNPs and phenotype informative SNPs, two labs performed MPS analysis of the mitochondrial DNA control region, and only one lab produced MPS data of lineage informative SNPs. Autosomal STR sequencing results were highly concordant to the consensus obtained by capillary electrophoresis in the EIADN No. 27 (2019) exercise. Furthermore, in general, a high level of concordance was observed between the results of the participating laboratories, regardless of the platform used. The main discordances were due to errors during the analysis process or from sequence data obtained with low depth of coverage. In this paper we highlight some issues that still arise, such as standardization of the nomenclature for STRs analyzed by sequencing with MPS, the universal uptake of a nomenclature framework by the analysis software, and well established validation and accreditation of the new MPS platforms for use in routine forensic case-work.
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Affiliation(s)
- Pedro A Barrio
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain.
| | - Óscar García
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Christopher Phillips
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Lourdes Prieto
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain; Comisaría General de Policía Científica, Madrid, Spain
| | - Leonor Gusmão
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; DNA Diagnostics Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Coro Fernández
- Quality Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jorge M Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brazil
| | | | - Pablo Martín
- Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ana Mosquera
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | | | - Manuel Paredes
- Subdirección de Investigación Científica, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Juan Antonio Pérez
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Andrea Pinzón
- Grupo Nacional de Ciencias Forenses, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Raquel Rasal
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Antonio Alonso
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
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Hasap L, Chotigeat W, Pradutkanchana J, Vongvatcharanon U, Kitpipit T, Thanakiatkrai P. A novel, 4-h DNA extraction method for STR typing of casework bone samples. Int J Legal Med 2020; 134:461-471. [PMID: 31897668 DOI: 10.1007/s00414-019-02232-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Bones are often found in mass grave crime scene. To increase DNA identification success rates, a highly efficient DNA extraction method should be selected. Several DNA extraction methods for human bones have been published yet never been systematically compared, and some are time-consuming or complex. As such, a quick and highly efficient DNA extraction method was developed and compared with three published methods (Hi-Flow silica-based, total demineralization (TD) and PrepFiler BTA) using 70 fresh and 22 casework bones from different body parts. The highest median DNA concentrations were obtained from developed method (135.85 ng/μL and 0.224 ng/μL for fresh and casework bones, respectively). For residual PCR inhibitors, the threshold cycle (Ct) of the internal positive control (IPC) showed that developed method and PrepFiler BTA removed most PCR inhibitors. Similarly, 95.45% of casework STR profiles obtained using the developed protocol meet the standard requirements for Australian National Criminal Investigative DNA Database (NCIDD) entry, followed by 86.35% using TD, 81.82% using PrepFiler BTA, and 45.45% using Hi-Flow. Additionally, DNA extracts from seven different bones revealed that the 1st distal phalange of the hand contained the highest DNA concentration of 338.43 ng/μL, which was three times higher than the tibia and femur. Our findings suggest that developed method was highly efficient for casework bone analysis. It significantly reduced the extraction processing time down to 4 h and is two to four times cheaper compared with other methods. In practice, both the extraction method and the bone sampling must be considered by a forensic DNA analyst to increase the chances of successful identification.
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Affiliation(s)
- Laila Hasap
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wilaiwan Chotigeat
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Jintana Pradutkanchana
- Forensic Medicine and Toxicology Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Uraporn Vongvatcharanon
- Department of Anatomy, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand.
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Chen T, Jia Y, Dong C, Gao J, Mak PI, Martins RP. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device. LAB ON A CHIP 2016; 16:743-752. [PMID: 26781669 DOI: 10.1039/c5lc01533b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis.
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Affiliation(s)
- Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
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8
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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9
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De Wilde B, Lefever S, Dong W, Dunne J, Husain S, Derveaux S, Hellemans J, Vandesompele J. Target enrichment using parallel nanoliter quantitative PCR amplification. BMC Genomics 2014; 15:184. [PMID: 24612714 PMCID: PMC4234423 DOI: 10.1186/1471-2164-15-184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Next generation targeted resequencing is replacing Sanger sequencing at high pace in routine genetic diagnosis. The need for well validated, high quality enrichment platforms to complement the bench-top next generation sequencing devices is high. RESULTS We used the WaferGen Smartchip platform to perform highly parallelized PCR based target enrichment for a set of known cancer genes in a well characterized set of cancer cell lines from the NCI60 panel. Optimization of PCR assay design and cycling conditions resulted in a high enrichment efficiency. We provide proof of a high mutation rediscovery rate and have included technical replicates to enable SNP calling validation demonstrating the high reproducibility of our enrichment platform. CONCLUSIONS Here we present our custom developed quantitative PCR based target enrichment platform. Using highly parallel nanoliter singleplex PCR reactions makes this a flexible and efficient platform. The high mutation validation rate shows this platform's promise as a targeted resequencing method for multi-gene routine sequencing diagnostics.
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Affiliation(s)
- Bram De Wilde
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Wes Dong
- WaferGen Biosystems Inc, Fremont, USA
| | | | | | | | | | - Jo Vandesompele
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
- Biogazelle, Zwijnaarde, Belgium
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Jabbar A, Gasser RB. Mutation scanning analysis of genetic variation within and among Echinococcus species: implications and future prospects. Electrophoresis 2014; 34:1852-62. [PMID: 23977679 DOI: 10.1002/elps.201300078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid-filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
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11
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Jex AR, Gasser RB. Diagnostic and analytical mutation scanning ofCryptosporidium: utility and advantages. Expert Rev Mol Diagn 2014; 9:179-85. [DOI: 10.1586/14737159.9.2.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Diaw L, Youngblood V, Taylor JG. Introduction to next-generation nucleic acid sequencing in cardiovascular disease research. Methods Mol Biol 2013; 1027:157-79. [PMID: 23912986 DOI: 10.1007/978-1-60327-369-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The identification of new genomic paradigms in lipoprotein and cardiovascular diseases will be accelerated by the application of the recent technological advances in nucleic acid sequencing. Presently, large-scale genomics facilities are equipped to accomplish this objective with a combination of "next-generation" DNA sequencing chemistries, largely focused on assembling massively parallel sequence reads corresponding to complete genes, entire exomes, or whole genomes from populations of individuals. In the future, individual laboratories will also use this emerging technology for focused genomic studies with the use of a combination of next-generation sequencing and automated Sanger sequencing. In particular, -next-generation sequencing will play an increasingly important role when applied to chromatin -immunoprecipitation, RNA transcriptome analysis, and studies of human genetic variation and mutation in carefully phenotyped healthy and disease populations. In this chapter, a brief overview of recent technological advances in next-generation nucleic acid sequencing is presented, with emphasis on practical -application to clinical studies in cardiovascular diseases.
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Affiliation(s)
- Lena Diaw
- Pulmonary and Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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13
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Mao R, Bayrak-Toydemir P, Lyon E. Capillary electrophoresis for the detection of Fragile X expanded alleles. Methods Mol Biol 2012; 919:275-85. [PMID: 22976108 DOI: 10.1007/978-1-62703-029-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Capillary electrophoresis is an analytical technique that separates ions based on their electrophoresis mobility with the use of an applied voltage. Capillary electrophoresis is used most predominantly in nuclear acid fragment analysis as well as DNA sequencing because it gives faster results and provides high resolution separation. Here we describe an application using capillary electrophoreses for screening the Fragile X expanded alleles to demonstrate the application.
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Affiliation(s)
- Rong Mao
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT, USA.
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14
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Morinha F, Cabral J, Bastos E. Molecular sexing of birds: A comparative review of polymerase chain reaction (PCR)-based methods. Theriogenology 2012; 78:703-14. [DOI: 10.1016/j.theriogenology.2012.04.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/18/2012] [Accepted: 04/26/2012] [Indexed: 02/08/2023]
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15
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Cheng HL, Chiou SS, Liao YM, Chen YL, Wu SM. Genotyping of single nucleotide polymorphism in γ-glutamyl hydrolase gene by capillary electrophoresis. Electrophoresis 2011; 32:2021-7. [DOI: 10.1002/elps.201000422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/03/2010] [Accepted: 11/16/2010] [Indexed: 12/14/2022]
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16
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Wang H, Knobel G, Wilson WB, Calimag-Williams K, Campiglia AD. Gold nanoparticles deposited capillaries for in-capillary microextraction capillary zone electrophoresis of monohydroxy-polycyclic aromatic hydrocarbons. Electrophoresis 2011; 32:720-7. [DOI: 10.1002/elps.201000516] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 01/03/2011] [Accepted: 01/03/2011] [Indexed: 11/10/2022]
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17
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Lien KY, Lee GB. Miniaturization of molecular biological techniques for gene assay. Analyst 2010; 135:1499-518. [PMID: 20390199 DOI: 10.1039/c000037j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.
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Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, National Cheng Kung University, Tainan, 701, Taiwan
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18
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Jex AR, Smith HV, Monis PT, Campbell BE, Gasser RB. Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation. Biotechnol Adv 2008; 26:304-17. [PMID: 18430539 DOI: 10.1016/j.biotechadv.2008.02.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 01/29/2008] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
Abstract
Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.
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Affiliation(s)
- A R Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
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19
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Tempels FWA, Underberg WJM, Somsen GW, de Jong GJ. Design and applications of coupled SPE-CE. Electrophoresis 2008; 29:108-28. [DOI: 10.1002/elps.200700149] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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Abstract
Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.
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Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria 3030, Australia.
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22
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Schindler AR, Abs El-Osta YG, Stevens M, Sinclair MI, Gasser RB. Capillary electrophoretic analysis of fragment length polymorphism in ribosomal markers of Cryptosporidium from humans. Mol Cell Probes 2005; 19:394-9. [PMID: 16169706 DOI: 10.1016/j.mcp.2005.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 07/05/2005] [Indexed: 11/16/2022]
Abstract
Cryptosporidium oocyst DNA samples (n=80) from humans with cryptosporidiosis in Australia and the UK were characterized genetically and categorized by capillary electrophoretic (CE) analysis of part of the small subunit gene (pSSU; approximately 300bp) and second internal transcribed spacer (pITS-2; approximately 230bp) of nuclear ribosomal DNA. The amplicons were heat denatured and subjected to capillary electrophoresis in LPA matrix (Amersham) in a MegaBACEtrade mark 1000 system (Amersham). The chromatograms captured were stored electronically and then analysed using MegaBACEtrade mark Fragment Profiler software. Using reference DNA control samples representing Cryptosporidium hominis and Cryptosporidium parvum, particular peaks in the profiles were defined for their specific identification and differentiation. The two species could be readily differentiated based on their profile in the pSSU, the peak differences being associated with a nucleotide difference of <1.7%. While no variation was detectable in the pSSU profiles within each species, significant intraspecific variability in the positions of peaks in the pITS-2 chromatograms was displayed. For the 80 samples subjected to CE analysis of the pITS-2, four different genetic variants (genotypes) were detected within C. hominis and seven within C. parvum. Based on CE analysis of either pSSU and pITS-2 amplicons, it was readily possible to detect both species in 'mixed samples'. This CE method is time- and cost-effective, and may find applicability as a tool for the high throughput analysis of oocyst DNA samples for epidemiological surveys and for the monitoring of cryptosporidiosis outbreaks.
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Affiliation(s)
- A Regina Schindler
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria. 3030, Australia
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Abstract
Clinical analysis often requires rapid, automated, and high-throughput analytical systems. Microchip capillary electrophoresis (CE) has the potential to achieve very rapid analysis (typically seconds), easy integration of multiple analytical steps, and parallel operation. Although it is currently still in an early stage of development, there are already many reports in the literature describing the applications of microchip CE in clinical analysis. At the same time, more fully automated and higher throughput commercial instruments for microchip CE are becoming available and are expected to further enhance the development of applications of microchip CE in routine clinical testing. To put into perspective its potential, we briefly compare microchip CE with conventional CE and review developments in this technique that may be useful in diagnosis of major diseases.
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Affiliation(s)
- Sam F Y Li
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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24
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Gasser RB, Skinner R, Fadavi R, Richards G, Morris G. High-throughput capillary electrophoresis for the identification and differentiation of seven species ofEimeria from chickens. Electrophoresis 2005; 26:3479-85. [PMID: 16110460 DOI: 10.1002/elps.200500103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A capillary electrophoretic approach has been evaluated for the identification of seven currently recognised species of Eimeria infecting chickens. The second internal transcribed spacer of ribosomal DNA is PCR-amplified from any of the seven species using a single set of oligonucleotide primers (one of which is fluorescently labelled). The amplicons are heat-denatured and subjected to capillary electrophoresis in a MegaBACE 1000 (Amersham). The chromatograms captured are stored electronically and then analysed using MegaBACE Fragment Profiler software. Using control DNA samples representing monospecific lines of Eimeria, specific peaks in the chromatograms were defined for the unequivocal identification of each of the seven species and their differentiation. Electrophoretic reading and analysis are carried out automatically, thus making it a time- and cost-effective method. This procedure should find applicability as a tool for the quality control of Eimeria vaccines, the monitoring of coccidiosis outbreaks and the high-throughput analysis of oocyst samples for epidemiological surveys.
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Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
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25
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Csako G. Present and future of rapid and/or high-throughput methods for nucleic acid testing. Clin Chim Acta 2005; 363:6-31. [PMID: 16102738 DOI: 10.1016/j.cccn.2005.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/03/2005] [Accepted: 07/03/2005] [Indexed: 12/21/2022]
Abstract
BACKGROUND Behind the success of 'completing' the human genome project was a more than 30-year history of technical innovations for nucleic acid testing. METHODS Discovery of specific restriction endonucleases and reverse transcriptase was followed shortly by the development of the first diagnostic nucleic acid tests in the early 1970s. Introduction of Southern, Northern and dot blotting and DNA sequencing later in the 1970s considerably advanced the diagnostic capabilities. Nevertheless, it was the discovery of the polymerase chain reaction (PCR) in 1985 that led to an exponential growth in molecular biology and the introduction of practicable nucleic acid tests in the routine laboratory. The past two decades witnessed a continuing explosion of technological innovations in molecular diagnostics. In addition to classic PCR and reverse transcriptase PCR, numerous variations of PCR and alternative amplification techniques along with an ever-increasing variety of detection chemistries, closed tube (homogeneous) assays, and automated systems were developed. Discovery of real-time quantitative PCR and the development of oligonucleotide microarrays, the 'DNA chip', in the 1990s heralded the beginning of another revolution in molecular biology and diagnostics that is still in progress.
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Affiliation(s)
- Gyorgy Csako
- Department of Laboratory Medicine, W.G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892-1508, USA.
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26
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Affiliation(s)
- Wes W C Quigley
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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