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Shrinet G, Chhabra R, Sharma A, Batra K, Talukdar SJ, Maan S. High throughput Luminex beads based multiplex assay for identification of six major bacterial pathogens of mastitis in dairy animals. Front Cell Infect Microbiol 2023; 13:1125562. [PMID: 37533933 PMCID: PMC10390833 DOI: 10.3389/fcimb.2023.1125562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction Bovine mastitis is caused by over 150 different microorganisms. Specific identification and quantification of multiple bacteria in a single milk sample becomes essential for rapid intervention. Methods In the present study a Luminex beads based multiplex assay emphasizing on the precise identification of six major bacterial pathogens of mastitis was developed. Assay was developed in two triplex sets, triplex 1 comprised of Streptococcus agalactiae, Streptococcus dysgalactiae and Streptococcus uberis while triplex 2 consisted of Staphylococcus aureus, E. coli and Klebsiella pneumoniae. Results The analytical sensitivity was 10 6 copies per reaction mixture for all the six bacteria. A 100% analytical specificity was observed for simultaneous detection of these bacteria. Clinical milk samples from 100 bovine quarters were tested for validation. Discussion The analytical sensitivity was similar to the findings reported earlier in real time PCR multiplex assay targeting the DNA of the 11 most common bacterial species or groups in mastitis. The analytical specificity of the optimized assay was 100% similar to reported earlier for simultaneous detection of Mycoplasma spp. and for seven entric viruses of humans.The developed assay indicates a concept proof of a rapid, cost effective high throughput diagnostic tool for identification of major bacteria causing mastitis.
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Affiliation(s)
- Garima Shrinet
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Rajesh Chhabra
- College Central Laboratory, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Archana Sharma
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Kanisht Batra
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Saurabh Jyoti Talukdar
- College Central Laboratory, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Sushila Maan
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Single Nucleotide Polymorphisms in XMN1-HBG2, HBS1L-MYB, and BCL11A and Their Relation to High Fetal Hemoglobin Levels That Alleviate Anemia. Diagnostics (Basel) 2022; 12:diagnostics12061374. [PMID: 35741184 PMCID: PMC9221560 DOI: 10.3390/diagnostics12061374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023] Open
Abstract
Anemia is a condition in which red blood cells and/or hemoglobin (Hb) concentrations are decreased below the normal range, resulting in a lack of oxygen being transported to tissues and organs. Those afflicted with this condition may feel lethargic and weak, which reduces their quality of life. The condition may be manifested in inherited blood disorders, such as thalassemia and sickle cell disease, whereas acquired disorders include aplastic anemia, chronic disease, drug toxicity, pregnancy, and nutritional deficiency. The augmentation of fetal hemoglobin (HbF) results in the reduction in clinical symptoms in beta-hemoglobinopathies. Several transcription factors as well as medications such as hydroxyurea may help red blood cells produce more HbF. HbF expression increases with the downregulation of three main quantitative trait loci, namely, the XMN1-HBG2, HBS1L-MYB, and BCL11A genes. These genes contain single nucleotide polymorphisms (SNPs) that modulate the expression of HbF differently in various populations. Allele discrimination is important in SNP genotyping and is widely applied in many assays. In conclusion, the expression of HbF with a genetic modifier is crucial in determining the severity of anemic diseases, and genetic modification of HbF expression may offer clinical benefits in diagnosis and disease management.
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Burg S, Roth S, Cohen M, Avivi-Mintz S, Margulis M, Rohana H, Peretz A, Danielli A. High throughput optical modulation biosensing for highly sensitive and rapid detection of biomarkers. Talanta 2022; 248:123624. [PMID: 35660998 DOI: 10.1016/j.talanta.2022.123624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/24/2022]
Abstract
Rapid, highly sensitive, and high-throughput detection of biomarkers at low concentrations is invaluable for early diagnosis of various diseases. In many highly sensitive immunoassays, magnetic beads are used to capture fluorescently labeled target molecules. The target molecules are then quantified by detecting the fluorescent signal from individual beads, which is time consuming and requires a complicated and expensive detection system. Here, we demonstrate a high-throughput optical modulation biosensing (ht-OMB) system, which uses a small permanent magnet to aggregate the beads into a small detection volume and eliminates background noise by steering a laser beam in and out of the cluster of beads. Shortening the aggregation, acquisition, and well-to-well scanning transition times enables reading a 96-well plate within 10 min. Using the ht-OMB system to detect human Interleukin-8, we demonstrated a limit of detection of 0.14 ng/L and a 4-log dynamic range. Testing 94 RNA extracts from 36 confirmed RT-qPCR SARS-CoV-2-positive patients (Ct≤40) and 58 confirmed RT-qPCR SARS-CoV-2-negative individuals resulted in 100% sensitivity and 100% specificity.
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Affiliation(s)
- Shmuel Burg
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Shira Roth
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Meir Cohen
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Shira Avivi-Mintz
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Michael Margulis
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel
| | - Hanan Rohana
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel; Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, 1528001, Israel
| | - Amos Danielli
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan, 5290002, Israel.
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4
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Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 2021; 7:e08093. [PMID: 34765757 PMCID: PMC8569399 DOI: 10.1016/j.heliyon.2021.e08093] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.
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Affiliation(s)
- Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing (NARP), Graduate School of Nuclear and Allied Sciences (SNAS), College of Basic and Applied Sciences, University of Ghana, P. O. Box AE 1, Accra, Ghana
- Biotechnology Centre, Biotechnology and Nuclear Agriculture Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), P. O. Box AE 50, Accra, Ghana
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Reslova N, Huvarova V, Hrdy J, Kasny M, Kralik P. A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay. Sci Rep 2019; 9:2719. [PMID: 30804418 PMCID: PMC6389906 DOI: 10.1038/s41598-019-40035-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/06/2019] [Indexed: 12/28/2022] Open
Abstract
Multiplex oligonucleotide ligation-PCR (MOL-PCR) is a rapid method for simultaneous detection of multiple molecular markers within a single reaction. MOL-PCR is increasingly employed in microbial detection assays, where its ability to facilitate identification and further characterization via simple analysis is of great benefit and significantly simplifies routine diagnostics. When adapted to microsphere suspension arrays on a MAGPIX reader, MOL-PCR has the potential to outperform standard nucleic acid-based diagnostic assays. This study represents the guideline towards in-house MOL-PCR assay optimization using the example of foodborne pathogens (bacteria and parasites) with an emphasis on the appropriate choice of crucial parameters. The optimized protocol focused on specific sequence detection utilizes the fluorescent reporter BODIPY-TMRX and self-coupled magnetic microspheres and allows for a smooth and brisk workflow which should serve as a guide for the development of MOL-PCR assays intended for pathogen detection.
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Affiliation(s)
- Nikol Reslova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic. .,Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Veronika Huvarova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jakub Hrdy
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Martin Kasny
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petr Kralik
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic
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Manley W, Moreau MP, Azaro M, Siecinski SK, Davis G, Buyske S, Vieland V, Bassett AS, Brzustowicz L. Validation of a microRNA target site polymorphism in H3F3B that is potentially associated with a broad schizophrenia phenotype. PLoS One 2018. [PMID: 29529098 PMCID: PMC5847241 DOI: 10.1371/journal.pone.0194233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite much progress, few genetic findings for schizophrenia have been assessed by functional validation experiments at the molecular level. We previously reported evidence for genetic linkage of broadly defined schizophrenia to chromosome 17q25 in a sample of 24 multiplex families. 2,002 SNPs under this linkage peak were analyzed for evidence of linkage disequilibrium using the posterior probability of linkage (PPL) framework. SNP rs1060120 produced the strongest evidence for association, with a PPLD|L score of 0.21. This SNP is located within the 3'UTR of the histone gene H3F3B and colocalizes with potential gene target miR-616. A custom miRNA target prediction program predicted that the binding of miR-616 to H3F3B transcripts would be altered by the allelic variants of rs1060120. We used dual luciferase assays to experimentally validate this interaction. The rs1060120 A allele significantly reduced luciferase expression, indicating a stronger interaction with miR-616 than the G allele (p = 0.000412). These results provide functional validation that this SNP could alter schizophrenia epigenetic mechanisms thereby contributing to schizophrenia-related disease risk.
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Affiliation(s)
- William Manley
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
| | - Michael P. Moreau
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
| | - Marco Azaro
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
| | - Stephen K. Siecinski
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
| | - Gillian Davis
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
- Department of Statistics & Biostatistics, Rutgers University, Piscataway, NJ, United States of America
| | - Veronica Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Linda Brzustowicz
- Department of Genetics, Rutgers University, Piscataway, NJ, United States of America
- * E-mail:
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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8
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Dwivedi A, Khim N, Reynes C, Ravel P, Ma L, Tichit M, Bourchier C, Kim S, Dourng D, Khean C, Chim P, Siv S, Frutos R, Lek D, Mercereau-Puijalon O, Ariey F, Menard D, Cornillot E. Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia. Malar J 2016; 15:319. [PMID: 27301553 PMCID: PMC4908689 DOI: 10.1186/s12936-016-1370-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/02/2016] [Indexed: 11/25/2022] Open
Abstract
Background Western Cambodia is recognized as the epicentre of emergence of Plasmodium falciparum multi-drug resistance. The emergence of artemisinin resistance has been observed in this area since 2008–2009 and molecular signatures associated to artemisinin resistance have been characterized in k13 gene. At present, one of the major threats faced, is the possible spread of Asian artemisinin resistant parasites over the world threatening millions of people and jeopardizing malaria elimination programme efforts. To anticipate the diffusion of artemisinin resistance, the identification of the P. falciparum population structure and the gene flow among the parasite population in Cambodia are essential. Methods To this end, a mid-throughput PCR-LDR-FMA approach based on LUMINEX technology was developed to screen for genetic barcode in 533 blood samples collected in 2010–2011 from 16 health centres in malaria endemics areas in Cambodia. Results Based on successful typing of 282 samples, subpopulations were characterized along the borders of the country. Each 11-loci barcode provides evidence supporting allele distribution gradient related to subpopulations and gene flow. The 11-loci barcode successfully identifies recently emerging parasite subpopulations in western Cambodia that are associated with the C580Y dominant allele for artemisinin resistance in k13 gene. A subpopulation was identified in northern Cambodia that was associated to artemisinin (R539T resistant allele of k13 gene) and mefloquine resistance. Conclusions The gene flow between these subpopulations might have driven the spread of artemisinin resistance over Cambodia. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1370-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ankit Dwivedi
- Institut de Biologie Computationnelle (IBC), Montpellier, France.,IRCM-INSERM U1194, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,Université de Montpellier, Montpellier, France.,ICM, Institut régional du Cancer Montpellier, Montpellier, France
| | - Nimol Khim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Christelle Reynes
- Laboratoire de Biostatistiques, Informatique et Physique Pharmaceutique, UFR Pharmacie, Université de Montpellier, Montpellier, France.,Institut de Génomique Fonctionnelle, Montpellier, France
| | - Patrice Ravel
- IRCM-INSERM U1194, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,Université de Montpellier, Montpellier, France.,ICM, Institut régional du Cancer Montpellier, Montpellier, France
| | - Laurence Ma
- Genopole Sequencing Platform, Institut Pasteur, Paris, France
| | - Magali Tichit
- Genopole Sequencing Platform, Institut Pasteur, Paris, France
| | | | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Dany Dourng
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Chanra Khean
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Pheaktra Chim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Sovannaroth Siv
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Roger Frutos
- UMR 17, Intertryp, Cirad-IRD, Campus International de Baillarguet, Montpellier, France.,IES-UMR 5214, Institut d'Electronique et des Systèmes, Université de Montpellier-CNRS, Montpellier, France
| | - Dysoley Lek
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | | | - Frédéric Ariey
- Parasite Molecular Immunology Unit, Institut Pasteur, Paris, France
| | - Didier Menard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia.
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), Montpellier, France. .,IRCM-INSERM U1194, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France. .,Université de Montpellier, Montpellier, France. .,ICM, Institut régional du Cancer Montpellier, Montpellier, France.
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Jung C, Ellington AD. A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). Anal Bioanal Chem 2016; 408:8583-8591. [PMID: 27032410 DOI: 10.1007/s00216-016-9479-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/01/2022]
Abstract
There are various ways that priming can occur in nucleic acid amplification reactions. While most reactions rely on a primer to initiate amplification, a mechanism for DNA amplification has been developed in which hairpin sequences at the 3' terminus of a single-stranded oligonucleotide fold on themselves to initiate priming. Unfortunately, this method is less useful for diagnostic applications because the self-folding efficiency is low and only works over a narrow range of reaction temperatures. In order to adapt this strategy for analytical applications we have developed a variant that we term phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). In PS-THSP a phosphorothioate (PS) modification is incorporated into the DNA backbone, leading to a reduction in the thermal stability of dsDNA and increased self-folding of terminal hairpins. By optimizing the number of PS linkages that are included in the initial template, we greatly increased self-folding efficiency and the range of reaction temperatures, ultimately achieving a detection limit of 1 pM. This improved method was readily adapted to the detection of single nucleotide polymorphisms and to the detection of non-nucleic acid analytes, such as alkaline phosphatase, which was quantitatively detected at a limit of 0.05 mU/mL, approximately 10-fold better than commercial assays. Graphical abstract Efficient self-folding by phosphorothioate (PS) modification.
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Affiliation(s)
- Cheulhee Jung
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway MBB 3.424, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway MBB 3.424, Austin, TX, 78712, USA.
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10
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Huang CW, Lin YT, Ding ST, Lo LL, Wang PH, Lin EC, Liu FW, Lu YW. Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection. ACTA ACUST UNITED AC 2015; 4:570-95. [PMID: 27600241 PMCID: PMC4996412 DOI: 10.3390/microarrays4040570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.
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Affiliation(s)
- Chao-Wei Huang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Tsung Lin
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Torng Ding
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Ling-Ling Lo
- Department of Animal Science, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pei-Hwa Wang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - En-Chung Lin
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Fang-Wei Liu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yen-Wen Lu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
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11
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Blair C, Sulik M, Willoughby M, Mills-Koonce R, Petrill S, Bartlett C, Greenberg M. Catechol-O-methyltransferase Val158met polymorphism interacts with early experience to predict executive functions in early childhood. Dev Psychobiol 2015; 57:833-41. [PMID: 26251232 PMCID: PMC5241672 DOI: 10.1002/dev.21332] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/26/2015] [Indexed: 12/14/2022]
Abstract
Numerous studies demonstrate that the Methionine variant of the catechol-O-methyltransferase Val158Met polymorphism, which confers less efficient catabolism of catecholamines, is associated with increased focal activation of prefrontal cortex (PFC) and higher levels of executive function abilities. By and large, however, studies of COMT Val158Met have been conducted with adult samples and do not account for the context in which development is occurring. Effects of early adversity on stress response physiology and the inverted U shape relating catecholamine levels to neural activity in PFC indicate the need to take into account early experience when considering relations between genes such as COMT and executive cognitive ability. Consistent with this neurobiology, we find in a prospective longitudinal sample of children and families (N = 1292) that COMT Val158Met interacts with early experience to predict executive function abilities in early childhood. Specifically, the Valine variant of the COMT Val158Met polymorphism, which confers more rather than less efficient catabolism of catecholamines is associated with higher executive function abilities at child ages 48 and 60 months and with faster growth of executive function for children experiencing early adversity, as indexed by cumulative risk factors in the home at child ages 7, 15, 24, and 36 months. Findings indicate the importance of the early environment for the relation between catecholamine genes and developmental outcomes and demonstrate that the genetic moderation of environmental risk is detectable in early childhood.
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Affiliation(s)
- Clancy Blair
- Department of Applied Psychology, NYU, 246 Greene St, Kimball Hall, 8th floor, New York, NY 10003.
| | - Michael Sulik
- Department of Applied Psychology, NYU, 246 Greene St, Kimball Hall, 8th floor, New York, NY 10003
| | - Michael Willoughby
- Frank Porter Graham Child Development Center, 521 S. Greensboro Street, CB 8185, NC 27599
| | - Roger Mills-Koonce
- Frank Porter Graham Child Development Center, 521 S. Greensboro Street, CB 8185, NC 27599
| | - Stephen Petrill
- Department of Psychology, The Ohio State University, 1835 Neil Avenue, Columbus, OH 43210
| | - Christopher Bartlett
- The Research Institute at Nationwide Children's Hospital & The Ohio State University, 575 Children's Crossroad WB5149, Columbus, OH 43215
| | - Mark Greenberg
- Department of HDFS, 110 Henderson South, Pennsylvania State University, University Park, PA 16802
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Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Bartlett CW, Hou L, Flax JF, Hare A, Cheong SY, Fermano Z, Zimmerman-Bier B, Cartwright C, Azaro MA, Buyske S, Brzustowicz LM. A genome scan for loci shared by autism spectrum disorder and language impairment. Am J Psychiatry 2014; 171:72-81. [PMID: 24170272 PMCID: PMC4431698 DOI: 10.1176/appi.ajp.2013.12081103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The authors conducted a genetic linkage study of families that have both autism spectrum disorder (ASD) and language-impaired probands to find common communication impairment loci. The hypothesis was that these families have a high genetic loading for impairments in language ability, thus influencing the language and communication deficits of the family members with ASD. Comprehensive behavioral phenotyping of the families also enabled linkage analysis of quantitative measures, including normal, subclinical, and disordered variation in all family members for the three general autism symptom domains: social, communication, and compulsive behaviors. METHOD The primary linkage analysis coded persons with either ASD or specific language impairment as "affected." The secondary linkage analysis consisted of quantitative metrics of autism-associated behaviors capturing normal to clinically severe variation, measured in all family members. RESULTS Linkage to language phenotypes was established at two novel chromosomal loci, 15q23-26 and 16p12. The secondary analysis of normal and disordered quantitative variation in social and compulsive behaviors established linkage to two loci for social behaviors (at 14q and 15q) and one locus for repetitive behaviors (at 13q). CONCLUSION These data indicate shared etiology of ASD and specific language impairment at two novel loci. Additionally, nonlanguage phenotypes based on social aloofness and rigid personality traits showed compelling evidence for linkage in this study group. Further genetic mapping is warranted at these loci.
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Affiliation(s)
- Christopher W. Bartlett
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Liping Hou
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Judy F. Flax
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Abby Hare
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Soo Yeon Cheong
- The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Zena Fermano
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Barbie Zimmerman-Bier
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Department of Pediatrics, Saint Peter's University Hospital, New Brunswick, NJ
| | - Charles Cartwright
- Department of Psychiatry, University of Medicine and Dentistry of New Jersey – New Jersey Medical School, Newark, NJ
| | - Marco A. Azaro
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Steven Buyske
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Department of Statistics and Biostatistics, Rutgers University, Rutgers University, Piscataway, NJ
| | - Linda M. Brzustowicz
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ,Corresponding Author:
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A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis. J Microbiol Methods 2013; 95:357-65. [DOI: 10.1016/j.mimet.2013.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 10/06/2013] [Indexed: 11/24/2022]
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15
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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Ellis GM, Vlaskin TA, Koth A, Vaz LE, Dross SE, Beck IA, Frenkel LM. Simultaneous and sensitive detection of human immunodeficiency virus type 1 (HIV) drug resistant genotypes by multiplex oligonucleotide ligation assay. J Virol Methods 2013; 192:39-43. [PMID: 23660583 DOI: 10.1016/j.jviromet.2011.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 11/10/2011] [Accepted: 11/14/2011] [Indexed: 11/29/2022]
Abstract
Oligonucleotide ligation assay (OLA) is a highly specific and relatively simple method to detect point mutations encoding HIV-1 drug-resistance, which can detect mutants comprising ≥2-5% of the viral population. Nevirapine (NVP), tenofovir (TDF) and lamivudine (3TC) are antiretroviral (ARV) drugs used worldwide for treatment of HIV infection and prevention of mother-to-child-transmission. Adapting the OLA to detect multiple mutations associated with HIV resistance to these ARV simultaneously would provide an efficient tool to monitor drug resistance in resource-limited settings. Known proportions of mutant and wild-type plasmids were used to optimize a multiplex OLA for detection of K103N, Y181C, K65R, and M184V in HIV subtypes B and C, and V106M and G190A in subtype C. Simultaneous detection of two mutations was impaired if probes annealed to overlapping regions of the viral template, but was sensitive to ≥2-5% when testing codons using non-overlapping probes. PCR products from HIV-subtype B- and C-infected individuals were tested by multiplex-OLA and compared to results of single-codon OLA. Multiplex-OLA detected mutations at codon pairs 103/181, 106/190 and 65/184 reliably when compared to singleplex-OLA in clinical specimens. The multiplex-OLA is sensitive and specific and reduces the cost of screening for NVP, TDF and/or 3TC resistance.
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Affiliation(s)
- Giovanina M Ellis
- Seattle Children's Research Institute, 1900 9th Avenue, Mailstop C9S-8, Seattle, WA 98101, USA
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Chen JY, Xu H, Shi P, Culbertson A, Meslin EM. Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Integrative analysis and modeling of the omics data using systems biology have led to growing interests in the development of predictive and personalized medicine. Personalized medicine enables future physicians to prescribe the right drug to the right patient at the right dosage, by helping them link each patient’s genotype to their specific disease conditions. This chapter shares technological, ethical, and social perspectives on emerging personalized medicine applications. First, it examines the history and research trends of pharmacogenomics, systems biology, and personalized medicine. Next, it presents bioethical concerns that arise from dealing with the increasing accumulation of biological samples in many biobanking projects today. Lastly, the chapter describes growing concerns over patient privacy when large amount of individuals’ genetic data and clinical data are managed electronically and accessible online.
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Affiliation(s)
- Jake Y. Chen
- Indiana Center for Systems Biology and Personalized Medicine, USA, Indiana University, USA & Purdue University, USA
| | - Heng Xu
- The Pennsylvania State University, USA
| | - Pan Shi
- The Pennsylvania State University, USA
| | | | - Eric M. Meslin
- Indiana University Center for Bioethics, USA & Indiana University, USA
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Park S, Moon HS, Lee DS, Kim HC, Chun H. High-throughput on-chip leukemia diagnosis. Int J Lab Hematol 2013; 35:480-90. [PMID: 23414350 DOI: 10.1111/ijlh.12054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/18/2012] [Indexed: 01/04/2023]
Abstract
Advances in lab-on-a-chip technologies enabled programmable, reconfigurable, and scalable manipulation of a variety of laboratory procedures. Samples, reagents, and fluids can be precisely controlled; buffer temperature, pH, and concentration control systems as well as a variety of detection systems can be integrated on a small chip. These advantages have attracted attention in various fields of clinical application including leukemia diagnosis and research. A lot of research on lab-on-a-chip based diagnosis has been reported and the field is rapidly expanding. This review describes recent developments of lab-on-a-chip technologies as solutions to challenges for high-throughput leukemia diagnosis.
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Affiliation(s)
- S Park
- Interdisciplinary Program, Bioengineering Major, Graduate School, Seoul National University, Seoul, Korea
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Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams PD, Singh AK. A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres. Chem Commun (Camb) 2013; 49:5441-3. [DOI: 10.1039/c3cc39155h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Spierings G, Dunbar SA. Pharmacogenetics using Luminex® xMAP® technology: a method for developing a custom multiplex single nucleotide polymorphism mutation assay. Methods Mol Biol 2013; 1015:115-26. [PMID: 23824852 DOI: 10.1007/978-1-62703-435-7_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sequence variations in the human genome can affect the development of diseases and provide markers for the identification of genetic diseases and drug susceptibility. Single Nucleotide Polymorphisms (SNPs), the most abundant sequence variations in the genome, are used in pharmacogenetics as indicators of drug therapy efficacy in individuals and are important road maps in the route to personalized medicine. This chapter describes the development of PCR based custom multiplex SNP mutation analysis assays using Luminex(®) Multi-Analyte Profiling (xMAP(®)) Technology. Up to 500 different mutations can be detected in a single well and up to 384 samples can be analyzed per run.
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21
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Meldgaard M, Szecsi PB, Carlsen BC, Thyssen JP, Johansen JD, Menné T, Stender S. A novel multiplex analysis of filaggrin polymorphisms: a universally applicable method for genotyping. Clin Chim Acta 2012; 413:1488-92. [PMID: 22705401 DOI: 10.1016/j.cca.2012.06.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/24/2012] [Accepted: 06/07/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND The filaggrin protein is expressed as profilaggrin mainly in stratum granulosum cells of the epidermis. The profilaggrin gene codes for 10-12 filaggrin repeats. The filaggrin protein is important for skin barrier function. Filaggrin deficiency due to functional null-polymorphisms affects 8-10% of the people in Northern Europe and is a strong risk factor for several diseases. Here, we describe a novel method for efficient, multiplexed genotyping of variations in the profilaggrin gene. METHODS Five known techniques were combined: i) allele-specific PCR, ii) PCR with tagged primers, iii) asymmetric PCR, iv) multiplex PCR, and v) hybridization of single-stranded PCR products to spectrally coded microbeads carrying tag sequences as capture probes. Asymmetry of PCR was accomplished by having the tagged and allele-specific forward primers present in limiting concentrations. Asymmetry ensured that the later PCR cycles generated only single-stranded reverse-strand products. This greatly improved the assay sensitivity and allowed for simple optimization. RESULTS The specificity of the tags was verified with single PCR in wildtype and homozygous samples. Only the PCR products with the appropriate anti-tag hybridized to the corresponding beads, demonstrating the specificity of the signal. The hybridization signal is strongly dependent on single-stranded PCR products. After 46 PCR cycles, double-stranded products are clearly present, but only the single-stranded products generated in later cycles hybridize to the beads and elicit the strong signals that allow for unambiguous genotyping. CONCLUSIONS We have tested 17,000 samples for three filaggrin polymorphisms using this method, with a call rate exceeding 99% and a reagent cost of US $ 0.75 per sample. The method is universally applicable for multiplex genotyping of e.g. hereditary hemochromatosis, lactose intolerance, or cystic fibrosis.
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Affiliation(s)
- Michael Meldgaard
- Department of Clinical Biochemistry, Gentofte Hospital, University of Copenhagen, Denmark.
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22
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Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol 2011; 11:80. [PMID: 21831278 PMCID: PMC3224242 DOI: 10.1186/1472-6750-11-80] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.
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Affiliation(s)
- Joseph R Dobosy
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 5224, USA
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Hou L, Phillips C, Azaro M, Brzustowicz LM, Bartlett CW. Validation of a cost-efficient multi-purpose SNP panel for disease based research. PLoS One 2011; 6:e19699. [PMID: 21611176 PMCID: PMC3096622 DOI: 10.1371/journal.pone.0019699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/13/2011] [Indexed: 12/04/2022] Open
Abstract
Background Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA “barcoding” to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies. Principal Findings Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the “barcode.” Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel. Conclusion The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists.
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Affiliation(s)
- Liping Hou
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Christopher Phillips
- Forensic Genetics Department, Genomic Medicine Group, University of Santiago de Compostela and Centro Nacional de Genotipado (CeGen), Genomic Medicine Group, Hospital Clínico Universitario, Galicia, Spain
| | - Marco Azaro
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Christopher W. Bartlett
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Simmons TR, Flax JF, Azaro MA, Hayter JE, Justice LM, Petrill SA, Bassett AS, Tallal P, Brzustowicz LM, Bartlett CW. Increasing genotype-phenotype model determinism: application to bivariate reading/language traits and epistatic interactions in language-impaired families. Hum Hered 2010; 70:232-44. [PMID: 20948219 PMCID: PMC3085518 DOI: 10.1159/000320367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 08/13/2010] [Indexed: 11/19/2022] Open
Abstract
While advances in network and pathway analysis have flourished in the era of genome-wide association analysis, understanding the genetic mechanism of individual loci on phenotypes is still readily accomplished using genetic modeling approaches. Here, we demonstrate two novel genotype-phenotype models implemented in a flexible genetic modeling platform. The examples come from analysis of families with specific language impairment (SLI), a failure to develop normal language without explanatory factors such as low IQ or inadequate environment. In previous genome-wide studies, we observed strong evidence for linkage to 13q21 with a reading phenotype in language-impaired families. First, we elucidate the genetic architecture of reading impairment and quantitative language variation in our samples using a bivariate analysis of reading impairment in affected individuals jointly with language quantitative phenotypes in unaffected individuals. This analysis largely recapitulates the baseline analysis using the categorical trait data (posterior probability of linkage (PPL) = 80%), indicating that our reading impairment phenotype captured poor readers who also have low language ability. Second, we performed epistasis analysis using a functional coding variant in the brain-derived neurotrophic factor (BDNF) gene previously associated with reduced performance on working memory tasks. Modeling epistasis doubled the evidence on 13q21 and raised the PPL to 99.9%, indicating that BDNF and 13q21 susceptibility alleles are jointly part of the genetic architecture of SLI. These analyses provide possible mechanistic insights for further cognitive neuroscience studies based on the models developed herein.
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Affiliation(s)
- Tabatha R Simmons
- Battelle Center for Mathematical Medicine, Research Institute at Nationwide Children's Hospital and Department of Pediatrics, Ohio State University, Columbus, OH 43205, USA
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Song Y, Roumagnac P, Weill FX, Wain J, Dolecek C, Mazzoni CJ, Holt KE, Achtman M. A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. J Antimicrob Chemother 2010; 65:1631-41. [PMID: 20511368 PMCID: PMC2904664 DOI: 10.1093/jac/dkq175] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Objectives Decreased susceptibility to fluoroquinolones has become a major problem for the successful therapy of human infections caused by Salmonella enterica, especially the life-threatening typhoid and paratyphoid fevers. Methods By using Luminex xTAG beads, we developed a rapid, reliable and cost-effective multiplexed genotyping assay for simultaneously detecting 11 mutations in gyrA, gyrB and parE of S. enterica serovars Typhi and Paratyphi A that result in nalidixic acid resistance (NalR) and/or decreased susceptibility to fluoroquinolones. Results This assay yielded unambiguous single nucleotide polymorphism calls on extracted DNA from 292 isolates of Salmonella Typhi (NalR = 223 and NalS = 69) and 106 isolates of Salmonella Paratyphi A (NalR = 24 and NalS = 82). All of the 247 NalRSalmonella Typhi and Salmonella Paratyphi A isolates were found to harbour at least one of the target mutations, with GyrA Phe-83 as the most common one (143/223 for Salmonella Typhi and 18/24 for Salmonella Paratyphi A). We also identified three GyrB mutations in eight NalSSalmonella Typhi isolates (six for GyrB Phe-464, one for GyrB Leu-465 and one for GyrB Asp-466), and mutations GyrB Phe-464 and GyrB Asp-466 seem to be related to the decreased ciprofloxacin susceptibility phenotype in Salmonella Typhi. This assay can also be used directly on boiled single colonies. Conclusions The assay presented here would be useful for clinical and reference laboratories to rapidly screen quinolone-resistant isolates of Salmonella Typhi and Salmonella Paratyphi A, and decipher the underlying genetic changes for epidemiological purposes.
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Affiliation(s)
- Yajun Song
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
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Kissel HD, Galipeau PC, Li X, Reid BJ. Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity. Cancer Biomark 2009; 5:143-58. [PMID: 19407369 DOI: 10.3233/cbm-2009-0618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss of heterozygosity (LOH) has been shown to be a promising biomarker of cancer risk in patients with premalignant conditions. In this study we describe analytical validation in clinical biopsy samples of a SNP-based pyrosequencing panel targeting regions of LOH on chromosomes 17p and 9p including TP53 and CDKN2A tumor suppressor genes. Assays were tested for analytic specificity, sensitivity, efficiency, and reproducibility. Accuracy was evaluated by comparing SNP-based LOH results to those obtained by previously well-studied short tandem repeat polymorphisms (STRs) in DNA derived from different tissue sources including fresh-frozen endoscopic biopsies, samples from surgical resections, and formalin-fixed paraffin-embedded sections. A 17p/9p LOH panel comprised of 43 SNPs was designed to amplify with universal assay conditions in a two-step PCR and sequence-by-synthesis reaction that can be completed in two hours and 10 minutes. The methods presented can be a model for developing a SNP-based LOH approach targeted to any chromosomal region of interest for other premalignant conditions and this panel could be incorporated as part of a biomarker for cancer risk prediction, early detection, or as entry criteria for randomized trials.
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Affiliation(s)
- Heather D Kissel
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Wratten NS, Memoli H, Huang Y, Dulencin AM, Matteson PG, Cornacchia MA, Azaro MA, Messenger J, Hayter JE, Bassett AS, Buyske S, Millonig JH, Vieland VJ, Brzustowicz LM. Identification of a schizophrenia-associated functional noncoding variant in NOS1AP. Am J Psychiatry 2009; 166:434-41. [PMID: 19255043 PMCID: PMC3295829 DOI: 10.1176/appi.ajp.2008.08081266] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The authors previously demonstrated significant association between markers within NOS1AP and schizophrenia in a set of Canadian families of European descent, as well as significantly increased expression in schizophrenia of NOS1AP in unrelated postmortem samples from the dorsolateral prefrontal cortex. In this study the authors sought to apply novel statistical methods and conduct additional biological experiments to isolate at least one risk allele within NOS1AP. METHOD Using the posterior probability of linkage disequilibrium (PPLD) to measure the probability that a single nucleotide polymorphism (SNP) is in linkage disequilibrium with schizophrenia, the authors evaluated 60 SNPs from NOS1AP in 24 Canadian families demonstrating linkage and association to this region. SNPs exhibiting strong evidence of linkage disequilibrium were tested for regulatory function by luciferase reporter assay. Two human neural cell lines (SK-N-MC and PFSK-1) were transfected with a vector containing each allelic variant of the SNP, the NOS1AP promoter, and a luciferase gene. Alleles altering expression were further assessed for binding of nuclear proteins by electrophoretic mobility shift assay. RESULTS Three SNPs produced PPLDs >40%. One of them, rs12742393, demonstrated significant allelic expression differences in both cell lines tested. The allelic variation at this SNP altered the affinity of nuclear protein binding to this region of DNA. CONCLUSIONS The A allele of rs12742393 appears to be a risk allele associated with schizophrenia that acts by enhancing transcription factor binding and increasing gene expression.
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Affiliation(s)
- Naomi S Wratten
- Rutgers University Department of Genetics, 145 Bevier Road, Piscataway, NJ 08854, USA
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