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Saidi LK, Md Rani ZZ, Sulaiman SA, Jamal R, Ismail A, Alim AA, Ayob SNSA, Dee CF, Hamzah AA, Abdul Murad NA. Development of DNA-Based Lateral Flow Assay for Detection of LDLR Gene Mutation for Familial Hypercholesterolemia. Malays J Med Sci 2024; 31:92-106. [PMID: 38984253 PMCID: PMC11229576 DOI: 10.21315/mjms2024.31.3.6] [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: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2024] Open
Abstract
Background The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Methods Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Results Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. Conclusion The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection.
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Affiliation(s)
- Lina Khalida Saidi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zam Zureena Md Rani
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Siti Aishah Sulaiman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kelantan, Malaysia
| | - Anis Amirah Alim
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sharipah Nadzirah Syed Ahmad Ayob
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Perlis, Malaysia
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Ünsal SG, Yeni O, Büyük U, Özden Çiftçi Y. A novel method of multiplex SNP genotyping assay through variable fragment length allele-specific polymerase chain reaction: Multiplex VFLASP-ARMS. Mol Cell Probes 2024; 75:101960. [PMID: 38583643 DOI: 10.1016/j.mcp.2024.101960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
Variable Fragment Length Allele-Specific Polymerase Chain Reaction (VFLASP) and Amplification Refractory Mutation System (ARMS) are reliable methods for detecting allelic variations resulting from single base changes within the genome. Due to their widespread application, allele variations caused by Single Nucleotide Polymorphisms (SNPs) can be readily detected using allele-specific primers. In the context of the current study, VFLASP was combined with ARMS method as a novel strategy to enhance the efficacy of both techniques. Clinically important base variations within SNP regions used in the study were detected by a fragment analysis method. To validate the accuracy of the developed VFLASP-ARMS method, specifically designed synthetic sequences were tested using a capillary electrophoresis system. Allele-specific primers exhibit differences solely at the 3' end based on the sequence of the SNP. Additionally, to increase the specificity of the primers, a base was intentionally added for incompatibility. Therefore, allele discrimination on fragment analysis has been made possible through the 3-6 bp differences in the amplicons. With the optimization of the system, designed synthetic sequences provided reliable and reproducible results in wild-type, heterozygous, and homozygous genotypes using the VFLASP-ARMS method. Hence, our results demonstrated that VFLASP-ARMS method, offers a novel design methodology that can be included in the content of SNP genotyping assays.
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Affiliation(s)
- Selin Gül Ünsal
- Department of Molecular Biology and Genetics, Institute of Science, Gebze Technical University, 41400, Gebze, Turkey.
| | - Oğuzhan Yeni
- Department of Molecular Biotechnology and Genetics, Institute of Science, Istanbul University, 34452, Istanbul, Turkey
| | - Umut Büyük
- Department of Molecular Biotechnology and Genetics, Institute of Science, Istanbul University, 34452, Istanbul, Turkey
| | - Yelda Özden Çiftçi
- Department of Molecular Biology and Genetics, Institute of Science, Gebze Technical University, 41400, Gebze, Turkey; Smart Agriculture Research and Application Center, Gebze Technical University, 41400, Gebze, Turkey; Central Research Laboratory (GTU-MAR), Gebze Technical University, 41400, Gebze, Turkey
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Zhang L, Luo Y, Zhong X, Jia G, Chen H, Wang Y, Zhou J, Ma C, Li X, Huang K, Yang S, Wang J, Han D, Ren Y, Cai L, Zhou X. Genome-wide QTL mapping for agronomic traits in the winter wheat cultivar Pindong 34 based on 90K SNP array. FRONTIERS IN PLANT SCIENCE 2024; 15:1369440. [PMID: 38638350 PMCID: PMC11024375 DOI: 10.3389/fpls.2024.1369440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Introduction Agronomic traits are key components of wheat yield. Exploitation of the major underlying quantitative trait loci (QTLs) can improve the yield potential in wheat breeding. Methods In this study, we constructed a recombinant inbred line (RIL) population from Mingxian 169 (MX169) and Pindong 34 (PD34) to determine the QTLs for grain length (GL), grain width (GW), grain length-to-width ratio (LWR), plant height (PH), spike length (SL), grain number per spike (GNS), and the thousand grain weight (TGW) across four environments using wheat 90K SNP array. Results A QTL associated with TGW, i.e., QTGWpd.swust-6BS, was identified on chromosome 6B, which explained approximately 14.1%-16.2% of the phenotypic variation. In addition, eight QTLs associated with GL were detected across six chromosomes in four different test environments. These were QGLpd.swust-1BL, QGLpd.swust-2BL, QGLpd.swust-3BL.1, QGLpd.swust-3BL.2, QGLpd.swust-5DL, QGLpd.swust-6AL, QGLpd.swust-6DL.1, and QGLpd.swust-6DL.2. They accounted for 9.0%-21.3% of the phenotypic variation. Two QTLs, namely, QGWpd.swust-3BS and QGWpd.swust-6DL, were detected for GW on chromosomes 3B and 6D, respectively. These QTLs explained 12.8%-14.6% and 10.8%-15.2% of the phenotypic variation, respectively. In addition, two QTLs, i.e., QLWRpd.swust-7AS.1 and QLWRpd.swust-7AS.2, were detected on chromosome 7A for the grain LWR, which explained 10.9%-11.6% and 11.6%-11.2% of the phenotypic variation, respectively. Another QTL, named QGNSpd-swust-6DS, was discovered on chromosome 6D, which determines the GNS and which accounted for 11.4%-13.8% of the phenotypic variation. Furthermore, five QTLs associated with PH were mapped on chromosomes 2D, 3A, 5A, 6B, and 7B. These QTLs were QPHpd.swust-2DL, QPHpd.swust-3AL, QPHpd.swust-5AL, QPHpd.swust-6BL, and QPHpd.swust-7BS, which accounted for 11.3%-19.3% of the phenotypic variation. Lastly, a QTL named QSLpd.swust-3AL, conferring SL, was detected on chromosome 3A and explained 16.1%-17.6% of the phenotypic variation. All of these QTLs were defined within the physical interval of the Chinese spring reference genome. Discussion The findings of this study have significant implications for the development of fine genetic maps, for genomic breeding, and for marker-assisted selection to enhance wheat grain yield.
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Affiliation(s)
- Liangqi Zhang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yuqi Luo
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiao Zhong
- Chongqing Banan District Agricultural Technology Promoting Station, Chongqing, China
| | - Guoyun Jia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Chen
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yuqi Wang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jianian Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Chunhua Ma
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kebing Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Suizhuang Yang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shanxi, China
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, Sichuan, China
| | - Lin Cai
- College of Tobacco Science of Guizhou University, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, Guiyang, China
| | - Xinli Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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Daprà V, Giraudo I, Zaniol E, Galliano I, Calvi C, Montanari P, Alliaudi C, Saracco P, Bergallo M. Evaluation of the FCGR2B polymorphism in children with immune thrombocytopenia. Minerva Pediatr (Torino) 2024; 76:93-99. [PMID: 34859644 DOI: 10.23736/s2724-5276.21.05888-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Childhood immune thrombocytopenia (ITP) is an immune-mediated disease characterized by an isolated low platelet count. Pathogenesis of ITP is complex but many patients have platelet specific autoantibodies leading to accelerated clearance of opsonized platelets by Fc-gamma receptor (FcγR) bearing phagocytes, particularly in the spleen. In humans, there are three main types of Fcγ receptors: high-affinity FcγRI and low-affinity FcγRII and FcγRIII. About FcγRII, genetic variation of FCGR2B is associated with response to IVIg treatment in patients with Kawasaki disease and ITP. METHODS We used a TaqMAMA genotyping assay for detection of rs1050501 FCGR2B polymorphism in children with chronic ITP. A SNP rs1050501 (GenBank access number NG_023318.1, Homo sapiens Fc fragment of IgG receptor IIb [FCGR2B]) on chromosome 1 showing a T/C transition in position 15894 on FCGRB2 gene was chosen in this study. A series of experiments was conducted to evaluate the performance of the FCGR2B-MAMAPCR real time on a QuantStudio™ 5 Real-Time PCR System as compared to the 7500 Real-Time PCR System. RESULTS Background noise, genotypes discrimination, variability, allele and genotype frequencies and concordance were obtained. About clinical validation, all 60 samples collected from chronic ITP patients were analyzed. We found 53 on the 60 patients (88.4%) were homozygotes (52 TT and 1 CC) and 7/60 (11.6%) heterozygotes (TC). CONCLUSIONS The ability of the FCGR2B-MAMAPCR real time to detect rs1050501 FCGR2B polymorphism in children with chronic ITP on the QuantStudio™ 5 System is comparable to that on the 7500 System.
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Affiliation(s)
- Valentina Daprà
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
- BioMole srl, Turin, Italy
| | - Isaac Giraudo
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
- Unit of Hematology, Department of Pediatrics, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Elena Zaniol
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
| | - Carla Alliaudi
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy
| | - Paola Saracco
- Unit of Hematology, Department of Pediatrics, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatrics, University of Turin, School of Medicine, Turin, Italy -
- BioMole srl, Turin, Italy
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5
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Xu X, Hu X, Ma G, Wang T, Wu J, Zhu X, Chen G, Zhao L, Chen J. Detecting fa leptin receptor mutation in Zucker rats with tetra-primer amplification-refractory mutation system (ARMS)-PCR. Heliyon 2023; 9:e20159. [PMID: 37809507 PMCID: PMC10559934 DOI: 10.1016/j.heliyon.2023.e20159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Due to the genetic mutation (fa) in the gene encoding for leptin receptor, homozygous Zucker rats (fa-/-) develop excessive adiposity and become an experimental animal model in obesity and metabolic-related diseases research. Based on tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), we developed a method to quickly genotype Zucker rats with a mutated fa allele from their wildtype littermates. The three genotypes are clearly discriminated on 2.0% agarose gel. Our method can be used as a reliable tool to set up and maintain the breeding colony in animal facilities as well as assign animals to control and treatment groups based on their genotypes for animal studies.
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Affiliation(s)
- Xinyun Xu
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Xinge Hu
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Guodong Ma
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Tiannan Wang
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, The University of Tennessee Knoxville, TN, 37996, United States
| | - Xiaojuan Zhu
- Office of Information Technology, The University of Tennessee Knoxville, TN, 37996, United States
| | - Guoxun Chen
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Ling Zhao
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Jiangang Chen
- Department of Public Health, The University of Tennessee Knoxville, TN, 37996, United States
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Wang L, Yeo S, Lee M, Endah S, Alhuda NA, Yue GH. Combination of GWAS and F ST-based approaches identified loci associated with economic traits in sugarcane. Mol Genet Genomics 2023:10.1007/s00438-023-02040-2. [PMID: 37289230 DOI: 10.1007/s00438-023-02040-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Shadame Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - S Endah
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - N A Alhuda
- Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia
| | - G H Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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7
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López-Nevado M, Ortiz-Martín J, Serrano C, Pérez-Saez MA, López-Lorenzo JL, Gil-Etayo FJ, Rodríguez-Frías E, Cabrera-Marante O, Morales-Pérez P, Rodríguez-Pinilla MS, Manso R, Salgado-Sánchez RN, Cerdá-Montagud A, Quesada-Espinosa JF, Gómez-Rodríguez MJ, Paz-Artal E, Muñoz-Calleja C, Arranz-Sáez R, Allende LM. Novel Germline TET2 Mutations in Two Unrelated Patients with Autoimmune Lymphoproliferative Syndrome-Like Phenotype and Hematologic Malignancy. J Clin Immunol 2023; 43:165-180. [PMID: 36066697 DOI: 10.1007/s10875-022-01361-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
Somatic mutations in the ten-eleven translocation methylcytosine dioxygenase 2 gene (TET2) have been associated to hematologic malignancies. More recently, biallelic, and monoallelic germline mutations conferring susceptibility to lymphoid and myeloid cancer have been described. We report two unrelated autoimmune lymphoproliferative syndrome-like patients who presented with T-cell lymphoma associated with novel germline biallelic or monoallelic mutations in the TET2 gene. Both patients presented a history of chronic lymphoproliferation with lymphadenopathies and splenomegaly, cytopenias, and immune dysregulation. We identified the first compound heterozygous patient for TET2 mutations (P1) and the first ALPS-like patient with a monoallelic TET2 mutation (P2). P1 had the most severe form of autosomal recessive disease due to TET2 loss of function resulting in absent TET2 expression and profound increase in DNA methylation. Additionally, the immunophenotype showed some alterations in innate and adaptive immune system as inverted myeloid/plasmacytoid dendritic cells ratio, elevated terminally differentiated effector memory CD8 + T-cells re-expressing CD45RA, regulatory T-cells, and Th2 circulating follicular T-cells. Double-negative T-cells, vitamin B12, and IL-10 were elevated according to the ALPS-like suspicion. Interestingly, the healthy P1's brother carried a TET2 mutation and presented some markers of immune dysregulation. P2 showed elevated vitamin B12, hypergammaglobulinemia, and decreased HDL levels. Therefore, novel molecular defects in TET2 confirm and expand both clinical and immunological phenotype, contributing to a better knowledge of the bridge between cancer and immunity.
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Affiliation(s)
- Marta López-Nevado
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
| | | | - Cristina Serrano
- Immunology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - María A Pérez-Saez
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - José L López-Lorenzo
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Francisco J Gil-Etayo
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Edgar Rodríguez-Frías
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Oscar Cabrera-Marante
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Pablo Morales-Pérez
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Rebeca Manso
- Pathology Department, Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | | | - Ana Cerdá-Montagud
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Juan F Quesada-Espinosa
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - María J Gómez-Rodríguez
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Immunology Department, University Hospital La Princesa, Madrid, Spain
- School of Medicine, University Autónoma de Madrid, Madrid, Spain
- Research Institute Hospital de La Princesa, Madrid, Spain
| | - Reyes Arranz-Sáez
- Hematology Department, University Hospital La Princesa, Madrid, Spain
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
- School of Medicine, Complutense University of Madrid, Madrid, Spain.
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8
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Bergallo M, Montanari P, Loiacono E, Galliano I. A novel TaqMAMA assay for allelic discrimination of immunoproteasome subunit PSMB8 in pediatric patients. Minerva Pediatr (Torino) 2022; 74:301-307. [DOI: 10.23736/s2724-5276.16.04675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Bai C, Klimkowski P, Jin C, Kuchlyan J, El-Sagheer AH, Brown T. A new phosphoramidite enables orthogonal double labelling to form combination oligonucleotide probes. Org Biomol Chem 2022; 20:8618-8622. [DOI: 10.1039/d2ob01899c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A novel phosphoramidite (AP-C3 dT) containing an alkyne and amine has been synthesized, enabling orthogonal labelling for combination oligonucleotides probes.
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Affiliation(s)
- Chunsen Bai
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Piotr Klimkowski
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Cheng Jin
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jagannath Kuchlyan
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H. El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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10
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Wang G, Li M, Zhou J, An X, Bai F, Gao Y, Yu J, Li H, Lei C, Dang R. A novel A > G polymorphism in the intron 2 of TBX3 gene is significantly associated with body size in donkeys. Gene 2021; 785:145602. [PMID: 33766712 DOI: 10.1016/j.gene.2021.145602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
T-box transcription factor 3 (TBX3) gene encodes a transcriptional suppressor and plays an important role in embryonic development, which belongs to the T-box family. TBX3 also has been found to be associated with body size traits in horse that is a relative of donkey. Therefore, TBX3 is considered as a promising candidate gene for economic traits of donkey. This study aimed to reveal the significant variation of TBX3 gene in Dezhou donkey and explores the relationship between genotypes and body sizes. In this study, an A > G mutation was found in the intron 2 of TBX3 gene by sequencing, and three genotypes (AA, GG and AG) were identified in 380 Dezhou donkey individuals with Tm-shift method. Association analysis illustrated that there were significant differences between AA and GG genotype in body length, body height, chest depth, chest circumference, body weight, hucklebone width and rump length. Our results demonstrated that the polymorphism of TBX3 is significantly associated with body size traits, which can serve as a marker to improve donkey production performance.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Jun Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Xiaoya An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China; National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No. 78, E-jiao Street, Done-E Country, Shandong Province 252201, China.
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No. 78, E-jiao Street, Done-E Country, Shandong Province 252201, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
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11
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Identification of Echinococcus granulosus Genotypes G1 and G3 by SNPs Genotyping Assays. Pathogens 2021; 10:pathogens10020125. [PMID: 33530642 PMCID: PMC7910869 DOI: 10.3390/pathogens10020125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 11/25/2022] Open
Abstract
Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis in animals and humans. Different E. granulosuss.l. genotypes exhibit great diversity in their life cycle, host selectivity and pathogenicity. For this reason, the study of genetic variation within Echinococcus species is of importance for their epidemiological implication. We employed two SNP genotyping technologies to distinguish G1 and G3 E. granulosus sensu stricto (s.s.). genotypes. The genotypes of DNA samples (n = 28) extracted from hydatid cysts of different animal species were identified by amplification and sequencing of a fragment of the mitochondrial nad5 gene. Two SYBR green and three TaqMan real time PCR assays were developed for targeting of three nad5 informative positions (SNP758, 1123, and 1380) known to be able to discriminate G1 from G3. Genotyping by SYBR Green PCR based on cycle threshold (Ct) with melting temperature (Tm) analysis and performed on SNP1123 and SNP1380 failed to identify one DNA sample. TaqMan assays for SNP758, 1123 and 1380 effectively confirmed genotype identification obtained by Sanger sequencing. Our results demonstrated that the combination of the three Taqman assays developed in this study represents a valuable and cost effective tool alternative to DNA sequencing for E. granulosus s.s. genotyping.
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12
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Siamoglou S, Karamperis K, Mitropoulou C, Patrinos GP. Costing Methods as a Means to Measure the Costs of Pharmacogenomics Testing. J Appl Lab Med 2020; 5:1005-1016. [PMID: 32916714 DOI: 10.1093/jalm/jfaa113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/24/2020] [Indexed: 12/26/2022]
Abstract
Clinical implementation of pharmacogenomics and personalized medicine interventions relies on addressing important financial aspects of the delivery of genetic testing to the patients, be it from public or private providers. Details on how to determine the cost items of the genetic testing are often limited. The goal of this study is to present a costing methodology in order to estimate and measure the costs as far as the technical process of pharmacogenomics testing is concerned. Moreover, an overall cost mindset strategy based on the selective genotyping workflow to guide specialized laboratories of interest effectively is provided. We particularly accounted for the resources consumed within the laboratory premises such as cost of reagents for DNA isolation, cost of consumables, cost of personnel, while costs associated with patient recruitment, blood sample collection and maintenance, administration costs in the hospital, and costs of blood sample shipment were not taken into consideration. Our article presents the first-time detailed information on a costing framework for pharmacogenomic testing that could be employed to laboratories involved in routine clinical implementation of pharmacogenomics.
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Affiliation(s)
- Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Kariofyllis Karamperis
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,The Golden Helix Foundation, London, UK
| | | | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE
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13
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Daprà V, Galliano I, Alliaudi C, Zaniol E, Graziano E, Calvi C, Montanari P, Bergallo M. Evaluation of the polymorphism NUDT15c.415C>T real-time PCR on the CFX96 real-time PCR system and 7500 real-time PCR system. MINERVA BIOTECNOL 2020. [DOI: 10.23736/s1120-4826.20.02620-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Contreras R, van den Brink L, Burgos B, González M, Gacitúa S. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060744. [PMID: 32545703 PMCID: PMC7355918 DOI: 10.3390/plants9060744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 05/25/2023]
Abstract
The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.
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Affiliation(s)
- Roberto Contreras
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Av. Copayapu 485, 1530000 Copiapó, Chile
| | - Liesbeth van den Brink
- Department of Evolution and Ecology, Plant Ecology Group, Universität Tübingen, 72076 Tübingen, Germany;
| | - Boris Burgos
- Corporación Nacional Forestal (CONAF), Región de Atacama, Juan Martínez 55, 1530000 Copiapó, Chile;
| | - Marlene González
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| | - Sandra Gacitúa
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
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15
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Saady A, Steinman NY, Wojtyniak M, Ducho C, Fischer B. Synthesis of 2'-Deoxyuridine Modified with a 3,5-Difluoro-4-Methoxybenzylidene Imidazolinone Derivative for Incorporation into Oligonucleotide Probes for Detection of HER2 Breast Cancer Marker. ACTA ACUST UNITED AC 2020; 80:e104. [PMID: 32032480 DOI: 10.1002/cpnc.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleoside intercalator conjugates (NICs) describe an innovative methodology developed in our research group for preparation of fluorescence turn-on DNA hybridization probes targeting specific mRNA sequences (e.g., breast cancer markers). In this methodology, we conjugate a non-fluorescent intercalator to the base of a nucleic acid (e.g., uracil) via a flexible spacer. This modified monomer can be incorporated into oligonucleotides by solid-phase synthesis and a large fluorescence enhancement is observed when the modified oligonucleotide is hybridized with its complementary strand due to intercalation of the fluorophore between the two strands. 5-(6-p-Methoxybenzylidene imidazolinone-1-hexene)-2'-deoxyuridine (dUMBI ) is a synthetic monomer to which 4-methoxybenzylidene imidazolinone (MBI), the fluorescent chromophore of green fluorescent protein (GFP), has been conjugated via a flexible spacer. The detection of human epidermal growth factor receptor 2 (HER2) mRNA by this probe has already been established by our group. The fluorescent intensity of the single-strand DNA can be considered as negligible due to the free rotation of the fluorophore. Upon hybridization, however, the flexible spacer allows for the intercalation of the fluorophore between the hybridized strands, giving rise to enhanced fluorescence and indicating the presence of target mRNA. 3,5-Difluoro-4-methoxybenzylidene (DFMBI) has enhanced photophysical properties compared to MBI fluorophore. This protocol describes a simple, reliable, efficient, and general method for the synthesis of improved derivative dUDFMBI as a monomer of fluorescent turn-on DNA hybridization probe with application for detection of HER2 mRNA. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Synthesis of 5-[(6)-3,5-difluoro-4-methoxybenzylidene imidazolinone-1-hexene]-2'-deoxyuridine.
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Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| | - Noam Y Steinman
- Institute of Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
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16
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Galliano I, Daprà V, Ciferri F, Montanari P, Calvi C, Alliaudi C, Savino F, Bergallo M. TaqMAMA assay polymerase chain reaction real time for allelic discrimination of Macrophage receptor with collagenous structure rs1318645 polymorphism. MINERVA BIOTECNOL 2020. [DOI: 10.23736/s1120-4826.19.02567-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Iglesias MS, Grzelczak M. Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:263-284. [PMID: 32082965 PMCID: PMC7006498 DOI: 10.3762/bjnano.11.20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/21/2020] [Indexed: 05/02/2023]
Abstract
The possibility of detecting genetic mutations rapidly in physiological media through liquid biopsy has attracted the attention within the materials science community. The physical properties of nanoparticles combined with robust transduction methods ensure an improved sensitivity and specificity of a given assay and its implementation into point-of-care devices for common use. Covering the last twenty years, this review gives an overview of the state-of-the-art of the research on the use of gold nanoparticles in the development of colorimetric biosensors for the detection of single-nucleotide polymorphism as cancer biomarker. We discuss the main mechanisms of the assays that either are assisted by DNA-based molecular machines or by enzymatic reactions, summarize their performance and provide an outlook towards future developments.
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Affiliation(s)
- María Sanromán Iglesias
- Centro de Física de Materiales CSIC-UPV/EHU and Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 5, 20018 Donostia-Sebastián, Spain
| | - Marek Grzelczak
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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18
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Li L, Li S, Wu N, Wu J, Wang G, Zhao G, Wang J. HOLMESv2: A CRISPR-Cas12b-Assisted Platform for Nucleic Acid Detection and DNA Methylation Quantitation. ACS Synth Biol 2019; 8:2228-2237. [PMID: 31532637 DOI: 10.1021/acssynbio.9b00209] [Citation(s) in RCA: 362] [Impact Index Per Article: 72.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The next-generation CRISPR-based molecular diagnostics has the merits of rapidness, accuracy, and portability. We discovered the Cas12a trans-cleavage activity against collateral single-stranded DNA (ssDNA) and employed the activity to develop a rapid nucleic acid detection system, namely HOLMES (one-hour low-cost multipurpose highly efficient system). Here, with the employment of thermophilic CRISPR-Cas12b, we create HOLMESv2 for four different applications: (1) specifically discriminating single nucleotide polymorphism (SNP); (2) simply detecting virus RNA, human cell mRNA and circular RNA; (3) conveniently quantitating target nucleic acids with a one-step system combined with LAMP amplification in a constant temperature, thus avoiding cross-contamination; (4) accurately quantitating target DNA methylation degree with the combination of Cas12b detection and bisulfite treatment. These results highlight the potential of HOLMESv2 as a promising platform for both molecular diagnostics and epigenetics applications.
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Affiliation(s)
- Linxian Li
- University of Chinese Academy of Sciences , Beijing , 100049 , China
- Key Laboratory of Synthetic Biology , Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200032 , China
- State Key Laboratory of Cotton Biology, School of Life Sciences , Henan University , Kaifeng , Henan 475004 , China
| | - Shiyuan Li
- Shanghai Tolo Biotechnology Company Limited , Shanghai , 200233 , China
| | - Na Wu
- University of Chinese Academy of Sciences , Beijing , 100049 , China
- Key Laboratory of Synthetic Biology , Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200032 , China
- School of Life Science and Technology , Shanghai Tech University , Shanghai , 201210 , China
| | - Jiacheng Wu
- School of Life Science and Technology , Shanghai Tech University , Shanghai , 201210 , China
| | - Gang Wang
- State Key Laboratory of Cotton Biology, School of Life Sciences , Henan University , Kaifeng , Henan 475004 , China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology , Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200032 , China
- Department of Microbiology and Li KaShing Institute of Health Sciences , The Chinese University of Hong Kong, Prince of Wales Hospital , Shatin, New Territories, Hong Kong SAR , China
| | - Jin Wang
- College of Life Sciences , Shanghai Normal University , Shanghai , 200234 , China
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19
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Han J, Wu J, Du J. Fluorescent DNA Biosensor for Single-Base Mismatch Detection Assisted by Cationic Comb-Type Copolymer. Molecules 2019; 24:E575. [PMID: 30764576 PMCID: PMC6384784 DOI: 10.3390/molecules24030575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/03/2019] [Accepted: 02/04/2019] [Indexed: 11/16/2022] Open
Abstract
Simple and rapid detection of DNA single base mismatch or point mutation is of great significance for the diagnosis, treatment, and detection of single nucleotide polymorphism (SNP) in genetic diseases. Homogeneous mutation assays with fast hybridization kinetics and amplified discrimination signals facilitate the automatic detection. Herein we report a quick and cost-effective assay for SNP analysis with a fluorescent single-labeled DNA probe. This convenient strategy is based on the efficient quenching effect and the preferential binding of graphene oxide (GO) to ssDNA over dsDNA. Further, a cationic comb-type copolymer (CCC), poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly accelerates DNA hybridization and strand-exchange reaction, amplifying the effective distinction of the kinetic barrier between a perfect matched DNA and a mismatched DNA. Moreover, in vitro experiments indicate that RAW 264.7 cells cultured on PLL-g-Dex exhibits excellent survival and proliferation ability, which makes this mismatch detection strategy highly sensitive and practical.
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Affiliation(s)
- Jialun Han
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of materials and chemical engineering, Hainan University, Haikou 570228, China.
| | - Jincai Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of materials and chemical engineering, Hainan University, Haikou 570228, China.
| | - Jie Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of materials and chemical engineering, Hainan University, Haikou 570228, China.
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20
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Bergallo M, Galliano I, Montanari P, Calvi C, Rassu M, Daprà V. Toll-like receptor 9 gene polymorphisms rs352140 confer susceptibility to graft-versus-host disease in allogenic hematopoietic stem cell transplantation. MINERVA BIOTECNOL 2019. [DOI: 10.23736/s1120-4826.18.02484-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Zhao J, Xu Z, Chen A, You X, Zhao Y, He W, Zhao L, Yang S. Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method. Meat Sci 2018; 148:120-126. [PMID: 30388476 DOI: 10.1016/j.meatsci.2018.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 07/22/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Correct species identification is necessary for meat product quality assurance. Genetic markers are useful tools to accurately determine the animal source of meat products. To better protect yak meat and its products, ten single nucleotide polymorphism (SNP) loci from bovine meat-related genes and one positive control primer set were selected to discriminate meat sourced from yak or cattle. A multiplex allele-specific polymerase chain reaction and capillary electrophoresis method was employed for SNP genotyping. The samples were identified as from yak or cattle based on the number of amplicons. Yak samples generally produced one to three amplicon peaks, and the cattle samples yielded five or more peaks in the electropherogram. This method could be useful to distinguish yak meat from cattle beef, and would protect consumers and yak meat producers.
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Affiliation(s)
- Jie Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Xinyong You
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Yan Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Wenjing He
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Luyao Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Shuming Yang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China.
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22
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Zhang T, Guo L, Shi M, Xu L, Chen Y, Zhang L, Gao H, Li J, Gao X. Selection and effectiveness of informative SNPs for paternity in Chinese Simmental cattle based on a high-density SNP array. Gene 2018; 673:211-216. [PMID: 29933017 DOI: 10.1016/j.gene.2018.06.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022]
Abstract
Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%-39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle.
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Affiliation(s)
- Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Liping Guo
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mingyan Shi
- College of Life Science, Luoyang Normal University, Jiqing Road, 471934 Luoyang, PR China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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23
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Shen T, You Y, Joseph C, Mirzaei M, Klistorner A, Graham SL, Gupta V. BDNF Polymorphism: A Review of Its Diagnostic and Clinical Relevance in Neurodegenerative Disorders. Aging Dis 2018; 9:523-536. [PMID: 29896439 PMCID: PMC5988606 DOI: 10.14336/ad.2017.0717] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has a unique role in the neuronal development, differentiation, and survival in the developing and adult nervous system. A common single-nucleotide polymorphism in the pro-region of the human BDNF gene, resulting in a valine to methionine substitution (Val66Met), has been associated with the susceptibility, incidence, and clinical features of several neurodegenerative disorders. Much research has been dedicated to evaluating the effects of polymorphism in the past decade, and functional effects of this genetic variation. A better understanding of how this naturally occurring polymorphism associates with or influences physiology, anatomy, and cognition in both healthy and diseased adults in neurodegenerative conditions will help understand neurochemical mechanisms and definable clinical outcomes in humans. Here we review the role and relevance of the BDNF Val66Met polymorphism in neurodegenerative diseases, with particular emphasis on glaucoma, multiple sclerosis (MS), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Several controversies and unresolved issues, including small effect sizes, possible ethnicity, gender, and age effects of the BDNF Val66Met are also discussed with respect to future research.
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Affiliation(s)
- Ting Shen
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Yuyi You
- 2Save Sight Institute, Sydney University, Sydney, Australia
| | - Chitra Joseph
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Mehdi Mirzaei
- 3Faculty of Science and Engineering, Macquarie University, Australia
| | - Alexander Klistorner
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Stuart L Graham
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Vivek Gupta
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
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Genotyping and Sequencing Technologies in Population Genetics and Genomics. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2017_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Ott A, Liu S, Schnable JC, Yeh CT‘E, Wang KS, Schnable PS. tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res 2017; 45:e178. [PMID: 29036322 PMCID: PMC5716196 DOI: 10.1093/nar/gkx853] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only double-digested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3'-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (>97-99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci.
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Affiliation(s)
- Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | - James C. Schnable
- Data2Bio LLC, Ames, IA 50011-3650, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Cheng-Ting ‘Eddy’ Yeh
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | | | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
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Guo X, Seela F. Anomeric 2′-Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α-dC. Chemistry 2017; 23:11776-11779. [DOI: 10.1002/chem.201703017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
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27
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Mangin B, Pouilly N, Boniface MC, Langlade NB, Vincourt P, Vear F, Muños S. Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1099-1112. [PMID: 28255669 DOI: 10.1007/s00122-017-2872-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/04/2017] [Indexed: 05/20/2023]
Abstract
SNP genotyping of 114 cultivated sunflower populations showed that the multiplication process and the main traits selected during breeding of sunflower cultivars drove molecular diversity of the populations. The molecular diversity in a set of 114 cultivated sunflower populations was studied by single-nucleotide polymorphism genotyping. These populations were chosen as representative of the 400 entries in the INRA collection received or developed between 1962 and 2011 and made up of land races, open-pollinated varieties, and breeding pools. Mean allele number varied from 1.07 to 1.90. Intra-population variability was slightly reduced according to the number of multiplications since entry but some entries were probably largely homozygous when received. A principal component analysis was used to study inter-population variability. The first 3 axes accounted for 17% of total intra-population variability. The first axis was significantly correlated with seed oil content, more closely than just the distinction between oil and confectionary types. The second axis was related to the presence or absence of restorer genes and the third axis to flowering date and possibly to adaptation to different climates. Our results provide arguments highlighting the effect of the maintenance process on the within population genetic variability as well as on the impact of breeding for major agronomic traits on the between population variability of the collection. Propositions are made to improve sunflower population maintenance procedures to keep maximum genetic variability for future breeding.
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Affiliation(s)
- Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Felicity Vear
- GDEC, INRA, Université Clermont II Blaise Pascal, Clermont-Ferrand, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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Obliosca JM, Cheng SY, Chen YA, Llanos MF, Liu YL, Imphean DM, Bell DR, Petty JT, Ren P, Yeh HC. LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature. J Am Chem Soc 2017; 139:7110-7116. [PMID: 28463488 DOI: 10.1021/jacs.7b03395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-resolution melting (HRM) analysis of DNA is a closed-tube single-nucleotide polymorphism (SNP) detection method that has shown many advantages in point-of-care diagnostics and personalized medicine. While recently developed melting probes have demonstrated significantly improved discrimination of mismatched (mutant) alleles from matched (wild-type) alleles, no effort has been made to design a simple melting probe that can reliably distinguish all four SNP alleles in a single experiment. Such a new probe could facilitate the discovery of rare genetic mutations at lower cost. Here we demonstrate that a melting probe embedded with a single locked thymidine monomer (tL) can reliably differentiate the four SNP alleles by four distinct melting temperatures (termed the "4Tm probe"). This enhanced discriminatory power comes from the decreased melting temperature of the tL·C mismatched hybrid as compared to that of the t·C mismatched hybrid, while the melting temperatures of the tL-A, tL·G and tL·T hybrids are increased or remain unchanged as compared to those of their canonical counterparts. This phenomenon is observed not only in the HRM experiments but also in the molecular dynamics simulations.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Sara Y Cheng
- Department of Physics, College of Natural Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mariana F Llanos
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Darren M Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - David R Bell
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jeffrey T Petty
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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Park JH, Jang H, Jung YK, Jung YL, Shin I, Cho DY, Park HG. A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosens Bioelectron 2017; 91:122-127. [DOI: 10.1016/j.bios.2016.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/21/2023]
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30
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Zaid IU, Tang W, Liu E, Khan SU, Wang H, Mawuli EW, Hong D. Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica. FRONTIERS IN PLANT SCIENCE 2017; 8:143. [PMID: 28228768 PMCID: PMC5297617 DOI: 10.3389/fpls.2017.00143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/24/2017] [Indexed: 05/26/2023]
Abstract
Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 106 short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits. From our results, we suggest that heterosis in japonica rice would be improved by pyramiding the favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes.
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Affiliation(s)
- Imdad U. Zaid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Weijie Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Sana U. Khan
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Edzesi W. Mawuli
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
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Bergallo M, Montanari P, Mareschi K, Rassu M, Galliano I, Ravanini P. A novel TaqMAMA assay for allelic discrimination of TLR9 rs352140 polymorphism. J Virol Methods 2017; 243:25-30. [PMID: 28143777 DOI: 10.1016/j.jviromet.2017.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
TaqMAMA is an allele-specific PCR-based (ASPCR) method that may be suitable for broad and cost-effective genotyping applications in all types of laboratories. There is evidence that interactions between some toll like receptors (TLRs) with viruses influence both the immune response and outcome of HCMV infection. We developed a TaqMAMA genotyping assay for the detection of rs352140 TLR9 polymorphism in transplant recipients with and without HCMV infections. Performance parameters to ensure a solid pre-validation protocol have been here argued. We analysed a population of 74 kidney transplants recipients subdivided in 58 HCMV PCR positive and 16 HCMV PCR negative in the post-transplant routine control. All 74 samples were tested with 31/74 (41.9%) homozygotes (11 CC and 20 TT) and 43/74 (58.1%) heterozygotes (CT). Our preliminary data suggest that there is no correlation between TLR9 rs352140 polymorphism and frequency of HCMV infection.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy.
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Katia Mareschi
- Pediatric Oncohematology, Stem Cell Transplantation and Cell Therapy Division, A.O.U. Città della Salute e della Scienza-Regina Margherita Children Hospital, Turin, Italy
| | - Marco Rassu
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Paolo Ravanini
- Laboratory of Molecular Virology, Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
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Puggioni V, Chiesa O, Panini M, Mazzoni E. Qualitative Sybr Green real-time detection of single nucleotide polymorphisms responsible for target-site resistance in insect pests: the example of Myzus persicae and Musca domestica. BULLETIN OF ENTOMOLOGICAL RESEARCH 2017; 107:96-105. [PMID: 27444359 DOI: 10.1017/s0007485316000675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical insecticides have been widely used to control insect pests, leading to the selection of resistant populations. To date, several single nucleotide polymorphisms (SNPs) have already been associated with insecticide resistance, causing reduced sensitivity to many classes of products. Monitoring and detection of target-site resistance is currently one of the most important factors for insect pest management strategies. Several methods are available for this purpose: automated and high-throughput techniques (i.e. TaqMan or pyrosequencing) are very costly; cheaper alternatives (i.e. RFLP or PASA-PCRs) are time-consuming and limited by the necessity of a final visualization step. This work presents a new approach (QSGG, Qualitative Sybr Green Genotyping) which combines the specificity of PASA-PCR with the rapidity of real-time PCR analysis. The specific real-time detection of Cq values of wild-type or mutant alleles (amplified used allele-specific primers) allows the calculation of ΔCqW-M values and the consequent identification of the genotypes of unknown samples, on the basis of ranges previously defined with reference clones. The methodology is applied here to characterize mutations described in Myzus persicae and Musca domestica and we demonstrate it represents a valid, rapid and cost-effective technique that can be adopted for monitoring target-site resistance in field populations of these and other insect species.
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Affiliation(s)
- V Puggioni
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - O Chiesa
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - M Panini
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - E Mazzoni
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
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Heo HY, Chung S, Kim YT, Kim DH, Seo TS. A valveless rotary microfluidic device for multiplex point mutation identification based on ligation-rolling circle amplification. Biosens Bioelectron 2016; 78:140-146. [DOI: 10.1016/j.bios.2015.11.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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35
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Wampande EM, Hatzios SK, Achan B, Mupere E, Nsereko M, Mayanja HK, Eisenach K, Boom WH, Gagneux S, Joloba ML. A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala. BMC Infect Dis 2015; 15:396. [PMID: 26423522 PMCID: PMC4590274 DOI: 10.1186/s12879-015-1121-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 09/11/2015] [Indexed: 01/25/2023] Open
Abstract
Background Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB). In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients. Method Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. The MTBC lineages present in 300 smear-positive sputum samples were then determined by the validated LRPS method without prior culturing. Results The LSP-PCR and LRPS assays produced consistent genotyping data for all 70 MTBC strains; however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. Of the 300 sputum samples analyzed, 58 % contained MTBC from the MTBC-Uganda family, 27 % from the MTBC lineage 4 (excluding MTBC Uganda family), 13 % from the MTBC lineage 3, and the remaining 2 % were of indeterminate lineage. Conclusion The LRPS assay is a sensitive, high-throughput technique with potential application to routine genotyping of MTBC in sputum samples from TB patients. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1121-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Department of Bio-molecular Resources and Biolab Sciences, College of Veterinary Medicine, Animal Resources and Bio Security, Makerere University, Kampala, Uganda.
| | - Stavroula K Hatzios
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
| | - Beatrice Achan
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda.
| | - Ezekiel Mupere
- Department of Pediatrics and Child Health College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Mary Nsereko
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | - Harriet K Mayanja
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - W Henry Boom
- Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA.
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
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Miyanoshita M, Nakashima T, Kakuta Y, Kimura M. Archaeal ribonuclease P proteins have potential for biotechnological applications where precise hybridization of nucleic acids is needed. Biosci Biotechnol Biochem 2015; 79:2014-7. [PMID: 26114935 DOI: 10.1080/09168451.2015.1058699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescence resonance energy transfer-based assay showed that archaeal ribonuclease P (RNase P) proteins significantly promoted DNA annealing and strand displacement. Moreover, we found that archaeal RNase P proteins could discriminate nucleotide exchanges in DNA chains via their activity accelerating DNA strand displacement, suggesting that they have potential for biotechnological application to genetic diagnosis.
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Affiliation(s)
- Mitsuru Miyanoshita
- a Laboratory of Structural Biology , Graduate School of Systems Life Sciences , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan
| | - Takashi Nakashima
- a Laboratory of Structural Biology , Graduate School of Systems Life Sciences , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan.,b Laboratory of Biochemistry, Faculty of Agriculture, Department of Bioscience and Biotechnology, Graduate School , Kyushu University , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan
| | - Yoshimitsu Kakuta
- a Laboratory of Structural Biology , Graduate School of Systems Life Sciences , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan.,b Laboratory of Biochemistry, Faculty of Agriculture, Department of Bioscience and Biotechnology, Graduate School , Kyushu University , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan
| | - Makoto Kimura
- a Laboratory of Structural Biology , Graduate School of Systems Life Sciences , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan.,b Laboratory of Biochemistry, Faculty of Agriculture, Department of Bioscience and Biotechnology, Graduate School , Kyushu University , Hakozaki 6-10-1, Fukuoka 812-8581 , Japan
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37
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Cheli S, Pietrantonio F, Clementi E, Falvella FS. LightSNiP assay is a good strategy for pharmacogenetics test. Front Pharmacol 2015; 6:114. [PMID: 26082719 PMCID: PMC4451335 DOI: 10.3389/fphar.2015.00114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/12/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- Stefania Cheli
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano Milan, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori Milan, Italy
| | - Emilio Clementi
- Scientific Institute IRCCS Eugenio Medea Lecco, Italy ; Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, CNR Institute of Neuroscience, "Luigi Sacco" University Hospital, Università di Milano Milan, Italy
| | - Felicia S Falvella
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano Milan, Italy
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38
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Castiblanco Rodriguez AL. Approaches and perspectives to toxicogenetics and toxicogenomics. REVISTA DE LA FACULTAD DE MEDICINA 2015. [DOI: 10.15446/revfacmed.v62n4.45218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Toxicology is one of the scientific disciplines that has most<br />evolved in recent years due to scientific and technological<br />advances that have created a deeper understanding of the<br />genetic and molecular basis for appreciative variability in<br />toxic response from one person to another. The application<br />of this knowledge in toxicology is known as toxicogenetics<br />and toxicogenomics. The latter is the discipline that studies<br />the genomic response of organisms exposed to chemical<br />agents, including drugs, environmental pollutants, food<br />additives, and other commonly used chemical products.<br />The use of emerging omic technologies, such as genomics,<br />transcriptomics, proteomics, metabolomics and bioinformatics<br />techniques, permits the analysis of many variants of genes<br />simultaneously in an organism exposed to toxic agents in order<br />to search for genes susceptible to damage, to detect patterns<br />and mechanisms of toxicity, and determine specific profiles<br />of gene expression that give origin to biomarkers of exposure<br />and risk. This constitutes predictive toxicology.
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Cho YI, Ahn YK, Tripathi S, Kim JH, Lee HE, Kim DS. Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea. PLoS One 2015; 10:e0120163. [PMID: 25790283 PMCID: PMC4366180 DOI: 10.1371/journal.pone.0120163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.
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Affiliation(s)
- Young-Il Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Yul-Kyun Ahn
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
- * E-mail:
| | - Swati Tripathi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jeong-Ho Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
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Medrano RFV, de Oliveira CA. Guidelines for the tetra-primer ARMS-PCR technique development. Mol Biotechnol 2015; 56:599-608. [PMID: 24519268 DOI: 10.1007/s12033-014-9734-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR) reaction is a simple and economical method to genotype single-nucleotide polymorphisms (SNPs). It uses four primers in a single PCR and is followed just by gel electrophoresis. However, the optimization step can be very hardworking and time-consuming. Hence, we propose to demonstrate and discuss critical steps for its development, in a way to provide useful information. Two SNPs that provided different amplification conditions were selected. DNA extraction methods, annealing temperatures, PCR cycles protocols, reagents, and primers concentration were also analyzed. The use of tetra-primer ARMS-PCR could be impaired for SNPs in DNA regions rich in cytosine and guanine and for samples with DNA not purified. The melting temperature was considered the factor of greater interference. However, small changes in the reagents concentration significantly affect the PCR, especially MgCl2. Balancing the inner primers band is also a key step. So, in order to balance the inner primers band, intensity is important to observe which one has the weakest band and promote its band by increasing its concentration. The use of tetra-primer ARMS-PCR attends the expectations of modern genomic research and allows the study of SNPs in a fast, reliable, and low-cost way.
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41
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Trindade F, Ferreira R, Amado F, Vitorino R. Biofluid proteases profiling in diabetes mellitus. Adv Clin Chem 2015; 69:161-207. [PMID: 25934362 DOI: 10.1016/bs.acc.2014.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The investigation of protease relevance in biologic systems beyond catabolism of proteins and peptides to amino acids has stimulated interest as to their role in the pathogenesis of several disorders including diabetes mellitus (DM). Evaluation of proteases and the assessment of their activity in biofluids are fundamental to elucidate these proteolytic systems in DM and its related complications. In contrast to traditional immunoassay or substrate based approaches that targeted specific proteases and their inhibitors, the field of degradomics has provided a comprehensive approach to study these enzymes. Although the degradome contains over 500 proteases, very few have been associated with DM and its micro- and macrovascular complications. In this paper, we review these proteases and their respective inhibitors with emphasis on DM. It is likely that future research will expand these initial studies and look to develop high throughput automated technologies to identify and characterize biofluid proteases of diagnostic and prognostic value in other pathologies.
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Affiliation(s)
- Fábio Trindade
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; School of Health Sciences, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; Institute for Research in Biomedicine, iBiMED, Health Sciences Program, University of Aveiro, Aveiro, Portugal.
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42
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Mesrian Tanha H, Mojtabavi Naeini M, Rahgozar S, Rasa SMM, Vallian S. Modified tetra-primer ARMS PCR as a single-nucleotide polymorphism genotyping tool. Genet Test Mol Biomarkers 2015; 19:156-61. [PMID: 25658900 DOI: 10.1089/gtmb.2014.0289] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Genotyping of single-nucleotide polymorphisms (SNPs) has been applied in various genetic contexts. Tetra-primer amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) is reported as a prominent assay for SNP genotyping. However, there were published data that may question the reliability of this method on some occasions, in addition to a laborious and time-consuming procedure of the optimization step. In the current study, a new SNP genotyping method named modified tetra-primer ARMS (MTPA) PCR was developed based on tetra-primer ARMS PCR. DESIGN AND METHODS The modified method has two improvements in its instruction, including equalization of outer primer and inner primer strength by additional mismatch in outer primers, and consideration of equal annealing temperature of specific fragments more than melting temperature of primers. Advantageously, a new computer software was provided for designing primers based on novel concepts. RESULTS The usual tetra-primer ARMS PCR has a laborious process for optimization. In nonoptimal PCR programs, identification of the accurate genotype was found to be very difficult. However, in MTPA PCR, equalization of the amplicons and primer strength leads to increasing specificity and convenience of genotyping, which was validated by sequencing. CONCLUSIONS In the MTPA PCR technique, a new mismatch at -2 positions of outer primers and equal annealing temperature improve the genotyping procedure. Together, the introduced method could be suggested as a powerful tool for genotyping single-nucleotide mutations and polymorphisms.
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Affiliation(s)
- Hamzeh Mesrian Tanha
- Division of Cell and Molecular Biology, Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
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43
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Wang Y, Wee EJH, Trau M. Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced Raman scattering via ligase chain reaction. Chem Commun (Camb) 2015; 51:10953-6. [DOI: 10.1039/c5cc03921e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly sensitive DNA methylation analysis at CpG resolution is demonstrated by employing SERS nanotags via ligase chain reaction (LCR) and validated with sequencing.
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Affiliation(s)
- Yuling Wang
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
| | - Eugene J. H. Wee
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
| | - Matt Trau
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
- School of Chemistry and Molecular Biosciences
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Detection of single-nucleotide polymorphisms in Plasmodium falciparum by PCR primer extension and lateral flow immunoassay. Antimicrob Agents Chemother 2014; 59:365-71. [PMID: 25367901 DOI: 10.1128/aac.03395-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The resistance of Plasmodium falciparum to some antimalarial drugs is linked to single-nucleotide polymorphisms (SNPs). Currently, there are no methods for the identification of resistant parasites that are sufficiently simple, cheap, and fast enough to be performed at point-of-care, i.e., in local hospitals where drugs are prescribed. Primer extension methods (PEXT) were developed to identify 4 SNPs in P. falciparum positioned at amino acids 86, 184, and 1246 of the P. falciparum multidrug resistance 1 gene (pfmdr1) and amino acid 76 of the chloroquine resistance transporter gene (pfcrt). The PEXT products were visualized by a nucleic acid lateral flow immunoassay (NALFIA) with carbon nanoparticles as the detection labels. PCR-PEXT-NALFIAs showed good correlation to the reference methods, quantitative PCR (qPCR) or direct amplicon sequence analysis, in an initial open-label evaluation with 17 field samples. The tests were further evaluated in a blind study design in a set of 150 patient isolates. High specificities of 98 to 100% were found for all 4 PCR-PEXT genotyping assays. The sensitivities ranged from 75% to 100% when all PEXT-positive tests were considered. A number of samples with a low parasite density were successfully characterized by the reference methods but failed to generate a result in the PCR-PEXT-NALFIA, particularly those samples with microscopy-negative subpatent infections. This proof-of principle study validates the use of PCR-PEXT-NALFIA for the detection of resistance-associated mutations in P. falciparum, particularly for microscopy-positive infections. Although it requires a standard thermal cycler, the procedure is cheap and rapid and thus a potentially valuable tool for point-of-care detection in developing countries.
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Park JH, Park KS, Lee K, Jang H, Park HG. Universal probe amplification: multiplex screening technologies for genetic variations. Biotechnol J 2014; 10:45-55. [PMID: 25350275 DOI: 10.1002/biot.201400219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/04/2014] [Accepted: 09/25/2014] [Indexed: 11/06/2022]
Abstract
In order to achieve multiplex screening of genetic variations, multiplex amplification of target genomic DNA is necessary. Universal amplification technology meets this requirement by simultaneously amplifying a number of different regions within the target genomic DNA using a single pair of universal primers and thus eliminating the limitations associated with the use of multiple pairs of primers. We comprehensively review universal probe amplification and its use with multiplex technologies for the identification of the most representative genetic variation, i. e. single nucleotide polymorphisms. The progress and key issues relating to universal probe amplification are discussed and the representative technologies are summarized with an emphasis on their application for the identification of susceptibility to human diseases.
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Affiliation(s)
- Jung Hun Park
- Department of Chemical and Biomolecular Engineering, KAIST, Yuseong-gu, Daejeon, Republic of Korea
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46
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Bag SS, Pradhan MK, Das SK, Jana S, Bag R. Wavelength shifting oligonucleotide probe for the detection of adenosine of a target DNA with enhanced fluorescence signal. Bioorg Med Chem Lett 2014; 24:4678-4681. [DOI: 10.1016/j.bmcl.2014.08.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/23/2014] [Accepted: 08/12/2014] [Indexed: 12/23/2022]
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Fu GH, Wan ZY, Xia JH, Liu F, Liu XJ, Yue GH. The MCP-8 gene and its possible association with resistance to Streptococcus agalactiae in tilapia. FISH & SHELLFISH IMMUNOLOGY 2014; 40:331-336. [PMID: 25042289 DOI: 10.1016/j.fsi.2014.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Mast cell proteases play an important role in the regulation of the immune response. We identified the cDNA of the mast cell protease 8 (MCP-8) gene and analyzed its genomic structure in tilapia. The ORF of the MCP-8 was 768 bp, encoding 255 amino acids. Quantitative real-time PCR revealed that the MCP-8 gene was expressed predominantly in spleen, moderately in liver, blood, brain, gill, intestine, skin, and weakly expressed in kidney, muscle and eye. After a challenge with Streptococcus agalactiae, the gene was induced significantly (p < 0.05) in intestine, kidney, spleen and liver. Furthermore, we identified five single nucleotide polymorphisms (SNPs) in the MCP-8 gene and found that three SNPs were significantly associated (p < 0.05) with resistance against S. agalactiae. However, we found no association between four SNPs and growth traits (p > 0.05). These results suggest that the MCP-8 gene play an important role in the resistance to S. agalactiae in tilapia. The SNP markers in the MCP-8 gene associated with the resistance to the bacterial pathogen may facilitate selection of tilapia resistant to the bacterial disease.
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Affiliation(s)
- Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Xiao Jun Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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48
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Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, Warkentin TD, Tar'an B. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 2014; 15:708. [PMID: 25150411 PMCID: PMC4158123 DOI: 10.1186/1471-2164-15-708] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. RESULTS Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. CONCLUSIONS A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.
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Affiliation(s)
| | | | | | | | | | | | | | - Bunyamin Tar'an
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
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Gentilini F, Turba ME. Optimization of the Divergent method for genotyping single nucleotide variations using SYBR Green-based single-tube real-time PCR. Mutat Res 2014; 766-767:14-18. [PMID: 25847266 DOI: 10.1016/j.mrfmmm.2014.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/10/2014] [Accepted: 05/21/2014] [Indexed: 06/04/2023]
Abstract
A novel technique, called Divergent, for single-tube real-time PCR genotyping of point mutations without the use of fluorescently labeled probes has recently been reported. This novel PCR technique utilizes a set of four primers and a particular denaturation temperature for simultaneously amplifying two different amplicons which extend in opposite directions from the point mutation. The two amplicons can readily be detected using the melt curve analysis downstream to a closed-tube real-time PCR. In the present study, some critical aspects of the original method were specifically addressed to further implement the technique for genotyping the DNM1 c.G767T mutation responsible for exercise-induced collapse in Labrador retriever dogs. The improved Divergent assay was easily set up using a standard two-step real-time PCR protocol. The melting temperature difference between the mutated and the wild-type amplicons was approximately 5°C which could be promptly detected by all the thermal cyclers. The upgraded assay yielded accurate results with 157pg of genomic DNA per reaction. This optimized technique represents a flexible and inexpensive alternative to the minor grove binder fluorescently labeled method and to high resolution melt analysis for high-throughput, robust and cheap genotyping of single nucleotide variations.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia, Bologna, Italy.
| | - Maria E Turba
- Genefast srl, Via Castelfranco 17/d, 40053 Bazzano, Bologna, Italy.
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50
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Okumura S, Kuroda R, Inouye K. Single Nucleotide Polymorphism Typing with a Surface Plasmon Resonance-Based Sensor Using Hybridization Enhancement Blockers. Appl Biochem Biotechnol 2014; 174:494-505. [DOI: 10.1007/s12010-014-1072-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
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