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Lin C, Huang FY, Zhou SYD, Li H, Zhang X, Su JQ. HiLi-chip: A high-throughput library construction chip for comprehensive profiling of environmental microbial communities. ENVIRONMENTAL RESEARCH 2022; 213:113650. [PMID: 35690091 DOI: 10.1016/j.envres.2022.113650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Investigating the contribution and associations of environmental microbes to ecological health and human well-being is in great demand with the goal of One Health proposed. To achieve the goal, there is an urgent need for accurate approaches to obtaining a large amount of high-resolution molecular information from various microbes. In this study, we developed a high-throughput library construction chip (HiLi-Chip) for profiling environmental microbial communities and evaluated its performance. The HiLi-Chip showed high conformity with the conventional Pacbio method in terms of α-diversity, community composition of abundant bacteria (>83%), as well as rare taxa (>84%) and human pathogens detection (>67%), indicating its advantages of accuracy, high-throughput, cost-efficiency, and broad practicability. It is suggested that the optimal strategy of the HiLi-Chip was a 2.4 μL PCR mixture per sample (∼2.4 ng DNA) with a 216-sample × 24-replicate format. We have successfully applied the HiLi-Chip to the Jiulongjiang River and identified 51 potential human bacterial pathogens with a total relative abundance of 0.22%. Additionally, under limited nutrients and similar upstream environments, bacteria tended to impose competitive pressures, resulting in a more connected network at the downstream river confluence (RC). Whereas narrow niche breadth of bacteria and upstream environmental heterogeneity probably promoted niche complementary and environment selection leading to fewer links at RC in the midsection of the river. Core bacteria might represent the entire bacterial community and enhance network stability through synergistic interactions with other core bacteria. Collectively, our results demonstrate that the HiLi-Chip is a robust tool for rapid comprehensive profiling of microbial communities in environmental samples and has significant implications for a profound understanding of environmental microbial interactions.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, 510650, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xian Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
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Rapid DNA from a Disaster Victim Identification Perspective: is it a game changer? Forensic Sci Int Genet 2022; 58:102684. [DOI: 10.1016/j.fsigen.2022.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
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3
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Garcia-Cordero JL, Fan ZH. Sessile droplets for chemical and biological assays. LAB ON A CHIP 2017; 17:2150-2166. [PMID: 28561839 DOI: 10.1039/c7lc00366h] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Sessile droplets are non-movable droplets spanning volumes in the nL-to-μL range. The sessile-droplet-based platform provides a paradigm shift from the conventional, flow-based lab-on-a-chip philosophy, yet offering similar benefits: low reagent/sample consumption, high throughput, automation, and most importantly flexibility and versatility. Moreover, the platform relies less heavily on sophisticated fabrication techniques, often sufficient with a hydrophobic substrate, and no pump is required for operation. In addition, exploiting the physical phenomena that naturally arise when a droplet evaporates, such as the coffee-ring effect or Marangoni flow, can lead to fascinating applications. In this review, we introduce the physics of droplets, and then focus on the different types of chemical and biological assays that have been implemented in sessile droplets, including analyte concentration, particle separation and sorting, cell-based assays, and nucleic acid amplification. Finally, we provide our perspectives on this unique micro-scale platform.
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Affiliation(s)
- Jose L Garcia-Cordero
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Via del Conocimiento 201, Parque PIIT, Apodaca, NL, CP. 66628 Mexico.
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Eikmans M, van Halteren AGS, van Besien K, van Rood JJ, Drabbels JJM, Claas FHJ. Naturally acquired microchimerism: implications for transplantation outcome and novel methodologies for detection. CHIMERISM 2015; 5:24-39. [PMID: 24762743 DOI: 10.4161/chim.28908] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microchimerism represents a condition where one individual harbors genetically distinct cell populations, and the chimeric population constitutes <1% of the total number of cells. The most common natural source of microchimerism is pregnancy. The reciprocal cell exchange between a mother and her child often leads to the stable engraftment of hematopoietic and non-hematopoietic stem cells in both parties. Interaction between cells from the mother and those from the child may result in maternal immune cells becoming sensitized to inherited paternal alloantigens of the child, which are not expressed by the mother herself. Vice versa, immune cells of the child may become sensitized toward the non-inherited maternal alloantigens of the mother. The extent of microchimerism, its anatomical location, and the sensitivity of the techniques used for detecting its presence collectively determine whether microchimerism can be detected in an individual. In this review, we focus on the clinical consequences of microchimerism in solid organ and hematopoietic stem cell transplantation, and propose concepts derived from data of epidemiologic studies. Next, we elaborate on the latest molecular methodology, including digital PCR, for determining in a reliable and sensitive way the extent of microchimerism. For the first time, tools have become available to isolate viable chimeric cells from a host background, so that the challenges of establishing the biologic mechanisms and function of these cells may finally be tackled.
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Affiliation(s)
- Michael Eikmans
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
| | - Astrid G S van Halteren
- Immunology Laboratory; Willem Alexander Children's Hospital; Leiden University Medical Center; Leiden, the Netherlands
| | | | - Jon J van Rood
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands; Europdonor Foundation; Leiden, the Netherlands
| | - Jos J M Drabbels
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
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5
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Kim YT, Heo HY, Oh SH, Lee SH, Kim DH, Seo TS. Microchip-based forensic short tandem repeat genotyping. Electrophoresis 2015; 36:1728-37. [DOI: 10.1002/elps.201400477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/06/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyun Young Heo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Shin Hye Oh
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Seung Hwan Lee
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Do Hyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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6
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Sun Y, Zhou X, Yu Y. A novel picoliter droplet array for parallel real-time polymerase chain reaction based on double-inkjet printing. LAB CHIP 2014; 14:3603-10. [PMID: 25070461 DOI: 10.1039/c4lc00598h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We present a double-inkjet printing method for the generation of picoliter droplet-in-oil arrays on planar substrates, efficiently addressing droplet evaporation issues without the assistance of a humidifier or glycerol.
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Affiliation(s)
- Yingnan Sun
- State Key Laboratory on Integrated Optoelectronics
- Institute of Semiconductors
- Chinese Academy of Sciences
- Beijing, China
| | - Xiaoguang Zhou
- State Key Laboratory on Integrated Optoelectronics
- Institute of Semiconductors
- Chinese Academy of Sciences
- Beijing, China
- Joint Laboratory of Bioinformation Acquisition and Sensing Technology
| | - Yude Yu
- State Key Laboratory on Integrated Optoelectronics
- Institute of Semiconductors
- Chinese Academy of Sciences
- Beijing, China
- Joint Laboratory of Bioinformation Acquisition and Sensing Technology
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8
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Song Q, Yang H, Zou B, Kajiyama T, Kambara H, Zhou G. Improvement of LATE-PCR to allow single-cell analysis by pyrosequencing. Analyst 2013; 138:4991-7. [DOI: 10.1039/c3an00821e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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10
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DNA profiling of spermatozoa by laser capture microdissection and low volume-PCR. PLoS One 2011; 6:e22316. [PMID: 21853031 PMCID: PMC3154896 DOI: 10.1371/journal.pone.0022316] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/19/2011] [Indexed: 11/19/2022] Open
Abstract
Genetic profiling of sperm from complex biological mixtures such as sexual assault casework samples requires isolation of a pure sperm population and the ability to analyze low abundant samples. Current standard procedure for sperm isolation includes preferential lysis of epithelial contaminants followed by collection of intact sperm by centrifugation. While effective for samples where sperm are abundant, this method is less effective when samples contain few spermatozoa. Laser capture microdissection (LCM) is a proven method for the isolation of cells biological mixtures, even when found in low abundance. Here, we demonstrate the efficacy of LCM coupled with on-chip low volume PCR (LV-PCR) for the isolation and genotyping of low abundance sperm samples. Our results indicate that this method can obtain complete profiles (13-16 loci) from as few as 15 sperm cells with 80% reproducibility, whereas at least 40 sperm cells are required to profile 13-16 loci by standard 'in-tube' PCR. Further, LCM and LV-PCR of a sexual assault casework sample generated a DNA genotype that was consistent with that of the suspect. This method was unable, however, to analyze a casework sample from a gang rape case in which two or more sperm contributors were in a mixed population. The results indicate that LCM and LV-PCR is sensitive and effective for genotyping sperm from sperm/epithelial cell mixtures when epithelial lysis may be insufficient due to low abundance of sperm; LCM and LV-PCR, however, failed in a casework sample when spermatozoa from multiple donors was present, indicating that further study is necessitated.
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11
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Liu P, Li X, Greenspoon SA, Scherer JR, Mathies RA. Integrated DNA purification, PCR, sample cleanup, and capillary electrophoresis microchip for forensic human identification. LAB ON A CHIP 2011; 11:1041-8. [PMID: 21293830 DOI: 10.1039/c0lc00533a] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A fully integrated microdevice and process for forensic short tandem repeat (STR) analysis has been developed that includes sequence-specific DNA template purification, polymerase chain reaction (PCR), post-PCR cleanup and inline injection, and capillary electrophoresis (CE). Fragmented genomic DNA is hybridized with biotin-labeled capture oligos and pumped through a fluidized bed of magnetically immobilized streptavidin-coated beads in microchannels where the target DNA is bound to the beads. The bead-DNA conjugates are then transferred into a 250 nL PCR reactor for autosomal STR amplification using one biotin and one fluorescence-labeled primer. The resulting biotin-labeled PCR products are electrophoretically injected through a streptavidin-modified capture gel where they are captured to form a concentrated and purified injection plug. The thermally released sample plug is injected into a 14 cm long CE column for fragment separation and detection. The DNA template capture efficiency provided by the on-chip sequence-specific template purification is determined to be 5.4% using K562 standard DNA. This system can produce full 9-plex STR profiles from 2.5 ng input standard DNA and obtain STR profiles from oral swabs in about 3 hours. This fully integrated microsystem with sample-in-answer-out capability is a significant advance in the development of rapid, sensitive, and reliable micro-total analysis systems for on-site human identification.
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Affiliation(s)
- Peng Liu
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, CA 94720, USA
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12
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van Oorschot RAH, Ballantyne KN, Mitchell RJ. Forensic trace DNA: a review. INVESTIGATIVE GENETICS 2010; 1:14. [PMID: 21122102 PMCID: PMC3012025 DOI: 10.1186/2041-2223-1-14] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 12/01/2010] [Indexed: 11/10/2022]
Abstract
DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.
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Affiliation(s)
- Roland AH van Oorschot
- Forensic Services Department, Victoria Police, 31 Forensic Drive, Macleod 3085, Victoria, Australia
| | - Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - R John Mitchell
- Department of Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
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Woide D, Zink A, Thalhammer S. Technical note: PCR analysis of minimum target amount of ancient DNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:321-7. [PMID: 20229501 DOI: 10.1002/ajpa.21268] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The study of ancient DNA plays an important role in archaeological and palaeontological research as well as in pathology and forensics. Here, we present a new tool for ancient DNA analysis, which overcomes contamination problems, DNA degradation, and the negative effects of PCR inhibitors while reducing the amount of starting target material in the picogram range. Ancient bone samples from four Egyptian mummies were examined by combining laser microdissection, conventional DNA extraction, and low-volume PCR. Initially, several bone particles (osteons) in the micrometer range were extracted by laser microdissection. Subsequently, ancient DNA amplification was performed to verify our extraction method. Amelogenin and beta-actin gene specific fragments were amplified via low-volume PCR in a total reaction volume of 1 microl. Results of microdissected mummy DNA samples were compared to mummy DNA, which was extracted using a standard DNA extraction method based on pulverization of bone material. Our results highlight the combination of laser microdissection and low-volume PCR as a promising new technique in ancient DNA analysis.
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Affiliation(s)
- Daniela Woide
- Helmholtz Zentrum Munich, Institute of Radiation Protection, 85764 Neuherberg, Germany
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Brück S, Evers H, Heidorn F, Müller U, Kilper R, Verhoff MA. Single Cells for Forensic DNA Analysis-From Evidence Material to Test Tube. J Forensic Sci 2010; 56:176-80. [DOI: 10.1111/j.1556-4029.2010.01553.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vandewoestyne M, Deforce D. Laser capture microdissection in forensic research: a review. Int J Legal Med 2010; 124:513-21. [PMID: 20680318 PMCID: PMC2952761 DOI: 10.1007/s00414-010-0499-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/20/2010] [Indexed: 11/30/2022]
Abstract
In forensic sciences, short tandem repeat (STR) analysis has become the prime tool for DNA-based identification of the donor(s) of biological stains and/or traces. Many traces, however, contain cells and, hence, DNA, from more than a single individual, giving rise to mixed genotypes and the subsequent difficulties in interpreting the results. An even more challenging situation occurs when cells of a victim are much more abundant than the cells of the perpetrator. Therefore, the forensic community seeks to improve cell-separation methods in order to generate single-donor cell populations from a mixed trace in order to facilitate DNA typing and identification. Laser capture microdissection (LCM) offers a valuable tool for precise separation of specific cells. This review summarises all possible forensic applications of LCM, gives an overview of the staining and detection options, including automated detection and retrieval of cells of interest, and reviews the DNA extraction protocols compatible with LCM of cells from forensic samples.
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Affiliation(s)
- Mado Vandewoestyne
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000, Ghent, Belgium
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16
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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Schulz MM, Buschner MG, Leidig R, Wehner HD, Fritz P, Häbig K, Bonin M, Schütz M, Shiozawa T, Wehner F. A New Approach to the Investigation of Sexual Offenses-Cytoskeleton Analysis Reveals the Origin of Cells Found on Forensic Swabs. J Forensic Sci 2010; 55:492-8. [DOI: 10.1111/j.1556-4029.2009.01071.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Giese H, Lam R, Selden R, Tan E. Fast multiplexed polymerase chain reaction for conventional and microfluidic short tandem repeat analysis. J Forensic Sci 2009; 54:1287-96. [PMID: 19840207 DOI: 10.1111/j.1556-4029.2009.01200.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The time required for short tandem repeat (STR) amplification is determined by the temperature ramp rates of the thermal cycler, the components of the reaction mix, and the properties of the reaction vessel. Multiplex amplifications in microfluidic biochip-based and conventional tube-based thermal cyclers have been demonstrated in 17.3 and 19 min, respectively. Optimized 28-cycle amplification protocols generated alleles with signal strengths above calling thresholds, heterozygous peak height ratios of greater than 0.65, and incomplete nontemplate nucleotide addition and stutter of less than 15%. Full CODIS-compatible profiles were generated using the Profiler Plus ID, COfiler and Identifiler primer sets. PCR performance over a wide range of DNA template levels from 0.006 to 4 ng was characterized by separation and detection on a microfluidic electrophoresis system, Genebench-FX. The fast multiplex PCR approach has the potential to reduce process time and cost for STR analysis and enables development of a fully integrated microfluidic forensic DNA analysis system.
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Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes. Int J Legal Med 2009; 123:413-8. [DOI: 10.1007/s00414-009-0358-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
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Kroneis T, Gutstein-Abo L, Kofler K, Hartmann M, Hartmann P, Alunni-Fabbroni M, Walcher W, Dohr G, Petek E, Guetta E, Sedlmayr P. Automatic retrieval of single microchimeric cells and verification of identity by on-chip multiplex PCR. J Cell Mol Med 2009; 14:954-69. [PMID: 19453769 PMCID: PMC3823127 DOI: 10.1111/j.1582-4934.2009.00784.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The analysis of rare cells is not an easy task. This is especially true when cells representing a fetal microchimerism are to be utilized for the purpose of non-invasive prenatal diagnosis because it is both imperative and difficult to avoid contaminating the minority of fetal cells with maternal ones. Under these conditions, even highly specific biochemical markers are not perfectly reliable. We have developed a method to verify the genomic identity of rare cells that combines automatic screening for enriched target cells (based on immunofluorescence labelling) with isolation of single candidate microchimeric cells (by laser microdissection and subsequent laser catapulting) and low-volume on-chip multiplex PCR for DNA fingerprint analysis. The power of the method was tested using samples containing mixed cells of related and non-related individuals. Single-cell DNA fingerprinting was successful in 74% of the cells analysed (55/74), with a PCR efficiency of 59.2% (860/1452) for heterozygous loci. The identification of cells by means of DNA profiling was achieved in 100% (12/12) of non-related cells in artificial mixtures and in 86% (37/43) of cells sharing a haploid set of chromosomes and was performed on cells enriched from blood and cells isolated from tissue. We suggest DNA profiling as a standard for the identification of microchimerism on a single-cell basis.
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Affiliation(s)
- Thomas Kroneis
- Institute of Cell Biology, Histology and Embryology, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
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Cave CA, Hancock K, Schumm JW. Principles of STR multiplex amplification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Liu P, Yeung SHI, Crenshaw KA, Crouse CA, Scherer JR, Mathies RA. Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer. Forensic Sci Int Genet 2008; 2:301-9. [PMID: 19083840 DOI: 10.1016/j.fsigen.2008.03.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/10/2008] [Accepted: 03/31/2008] [Indexed: 11/19/2022]
Abstract
An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2h and 30min with <or=0.8bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful "mock" CODIS hit was generated on the suspect's sample within 6h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.
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Affiliation(s)
- Peng Liu
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, CA 94720, USA
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Lutz-Bonengel S, Sänger T, Parson W, Müller H, Ellwart JW, Follo M, Bonengel B, Niederstätter H, Heinrich M, Schmidt U. Single lymphocytes from two healthy individuals with mitochondrial point heteroplasmy are mainly homoplasmic. Int J Legal Med 2007; 122:189-97. [PMID: 17922134 DOI: 10.1007/s00414-007-0190-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 07/26/2007] [Indexed: 11/26/2022]
Abstract
The nature of mitochondrial DNA heteroplasmy is still unclear. It could either be caused by two mitochondrial DNA (mtDNA) haplotypes coexisting within a single cell or by an admixture of homoplasmic cells, each of which contains only one type of mtDNA molecule. To address this question, single lymphocytes were separated by flow cytometry assisted cell sorting and analyzed by cycle sequencing or minisequencing. To attain the required PCR sensitivity, the reactions were carried out on the surface of chemically structured glass slides in a reaction volume of 1-2 microl. In this study, blood samples from two healthy donors showing mitochondrial point heteroplasmy in direct sequencing (195Y and 234R, respectively) were analyzed. Nearly 96% of single lymphocytes tested were found to be in a homoplasmic state, but heteroplasmic cells were also detected. These results suggest that mitochondrial point heteroplasmy in blood may well be mainly due to the mixture of homoplasmic cells.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104 Freiburg, Germany.
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Horsman KM, Bienvenue JM, Blasier KR, Landers JP. Forensic DNA Analysis on Microfluidic Devices: A Review. J Forensic Sci 2007; 52:784-99. [PMID: 17553097 DOI: 10.1111/j.1556-4029.2007.00468.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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.
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Affiliation(s)
- Katie M Horsman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Lutz-Bonengel S, Sänger T, Heinrich M, Schön U, Schmidt U. Low volume amplification and sequencing of mitochondrial DNA on a chemically structured chip. Int J Legal Med 2006; 121:68-73. [PMID: 17093971 DOI: 10.1007/s00414-006-0125-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 08/29/2006] [Indexed: 10/23/2022]
Abstract
Low volume (LV) amplification (1 microL) of nuclear DNA (nucDNA) on a chemically structured chip is an appropriate and highly sensitive method to simultaneously amplify amelogenin and 15 forensically relevant short tandem repeats (STR). In this study, a combined method using on-chip LV amplification of mitochondrial DNA (mtDNA) and subsequent on-chip LV cycle sequencing was established to obtain a method, which is sensitive and robust enough to allow reliable analysis of DNA amounts representing the single cell level. All the necessary steps of the procedure--except for the purification of the sequencing products--were accomplished within the same final 2-microL reaction volume.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104, Freiburg, Germany.
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