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Liu T, Ho CL, Chen YJ, Chen PJ, Chen WL, Lee CT, Chow NH, Huang W, Chen YL. A pilot study on the detection of microsatellite instability using long mononucleotide repeats in solid tumors. Oncol Lett 2024; 28:445. [PMID: 39099584 PMCID: PMC11294907 DOI: 10.3892/ol.2024.14578] [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: 02/07/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024] Open
Abstract
Microsatellite instability (MSI) status is a prognostic biomarker for immunotherapy in certain types of cancers, such as colorectal cancers (CRCs) and endometrial cancers (ECs). Tumors that are categorized as having high MSI (MSI-H) express high levels of neoantigens for immune recognition. The typical MSI test measures the length of short mononucleotide repeats (SMR) poly(A) 21-27; however, a limitation of this test is the difficulty in determining the shift size, particularly in endometrial cancer. To investigate an MSI detection assay with improved performance, the present study analyzed the use of poly(A) 40-44 mononucleotide repeats to detect the MSI status of 100 patients with either CRC (n=50) or EC (n=50). Capillary electrophoresis was used to evaluate five long mononucleotide repeat (LMR) markers, including poly(A) 40-A, 40-B, 40-C, 40-D and 44. The concordance rate of the LMR-MSI assay compared with an immunohistochemistry MSI detection assay was 96.0 and 95.1% for CRCs and ECs respectively, with the detection limit of the LMR-MSI assay demonstrated to be 2.5% MSI-H in HCT116 colorectal carcinoma cell lines. The LMR-MSI assay yielded a 95.1% concordance rate in ECs compared with that in the SMR-MSI test (87.8%). The LMR-MSI test identified a significantly higher mean shift size (13 bp) in MSI-H tumors compared with the SMR-MSI test (10 bp), in both EC and CRC tissue samples. Together, the present study suggested that the LMR-MSI test could potentially be a sensitive and practical technology for molecular laboratory testing, particularly in the use of immunotherapy for patients with CRCs and ECs.
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Affiliation(s)
- Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Chung-Liang Ho
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Department of Laboratory Medicine, Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Yan-Jhen Chen
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Pin-Jun Chen
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Wan-Li Chen
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Chung-Ta Lee
- Department of Laboratory Medicine, Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Nan-Haw Chow
- Department of Laboratory Medicine, Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Wenya Huang
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Yi-Lin Chen
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
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Nowicki M, Hadziabdic D, Trigiano RN, Runge F, Thines M, Boggess SL, Ristaino J, Spring O. Microsatellite Markers from Peronospora tabacina, the Cause of Blue Mold of Tobacco, Reveal Species Origin, Population Structure, and High Gene Flow. PHYTOPATHOLOGY 2022; 112:422-434. [PMID: 34058860 DOI: 10.1094/phyto-03-21-0092-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
- Department of Life Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, D-60323 Frankfurt am Main, Germany
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Jean Ristaino
- Department of Entomology and Plant Pathology, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh 27650, U.S.A
| | - Otmar Spring
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
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Garmendia A, Merle H, Sanía M, López C, Ferriol M. Morphologic, genetic, and biogeographic continua among subspecies hinder the conservation of threatened taxa: the case of Centaurea aspera ssp. scorpiurifolia (Asteraceae). Sci Rep 2022; 12:932. [PMID: 35042932 PMCID: PMC8766572 DOI: 10.1038/s41598-022-04934-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 12/03/2022] Open
Abstract
Subspecies are widely included as conservation units because of their potential to become new species. However, their practical recognition includes variable criteria, such as morphological, genetic, geographic and other differences. Centaurea aspera ssp. scorpiurifolia is a threatened taxon endemic to Andalusia (Spain), which coexists in most of its distribution area with similar taxa. Because of the difficulty to identify it using morphology alone, we aimed to sample all the populations cited as ssp. scorpiurifolia as exhaustively as possible, morphologically characterise them, and analyse their genetic structuring using microsatellites, to better understand difficulties when conserving subspecies. Three different Centaurea species were found which were easily identified. Within C. aspera, two genetic populations and some admixed individuals were observed, one including ssp. scorpiurifolia individuals and the other including individuals identified as subspecies aspera, stenophylla, and scorpiurifolia. A morphological continuum between these two genetic populations and a wide overlapping of their biogeographic distribution were also found. This continuum can affect the conservation of ssp. scorpiurifolia because of potential misidentifications and harmful effects of subspecific hybridization. Misidentifications could be partly overcome by using as many different traits as possible, and conservation priority should be given to populations representative of the ends of this continuum.
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Affiliation(s)
- Alfonso Garmendia
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Hugo Merle
- Departamento de Ecosistemas Agroforestales, Universitat Politècnica de València, Valencia, Spain
| | - Marta Sanía
- Departamento de Ecosistemas Agroforestales, Universitat Politècnica de València, Valencia, Spain
| | - Carmelo López
- Centro Para La Conservación Y Mejora de La Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
| | - María Ferriol
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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Propagation Methods for the Conservation and Preservation of the Endangered Whorled Sunflower ( Helianthus verticillatus). PLANTS 2021; 10:plants10081565. [PMID: 34451610 PMCID: PMC8399636 DOI: 10.3390/plants10081565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022]
Abstract
Helianthus verticillatus Small, the whorled sunflower, is a perennial species only found at a few sites in the southeastern United States and was declared federally (USA) endangered in 2014. The species spreads locally via rhizomes and can produce copious seeds when sexually compatible genotypes are present. Vegetative propagation of the species via cuttings and the optimum conditions for seed germination have not been determined. To investigate asexual propagation via cuttings, stem sections were harvested in late May, June, and July in Knoxville, Tennessee (USA) and trimmed to a minimum of two nodes. The base of the cuttings was treated with either auxin or water, and grown in a Promix BX potting medium with intermittent mist and 50% shade for one month. Seeds were harvested from a population of multiple genotypes in Maryville, Tennessee and used to determine viability and the range of temperatures suitable for germination. A clonal population was developed and used for three years to assess sexual compatibility at three locations in Knoxville, Tennessee. Ninety-five percent of the cuttings from May rooted in two-to-three weeks and formed more than 20 adventitious roots per cutting with auxin and 18 with water treatments. The ability of cuttings to root decreased in June to about 20%, and none rooted in July with either water or auxin pretreatments. Pre-germination tetrazolium tests indicated that about 91% of seeds (achenes) were viable. Subsequent germination tests revealed high germination at varying temperatures (96 to 99% of seeds (achenes) germinated at 22/11, 27/15, and 29/19 °C), whereas germination was significantly inhibited by 33/24 °C. Fifty percent of the seeds germinated at 22/11 °C in 7.5 days, whereas only 2.0 to 2.5 days were required for 50% germination at 27/15, 29/19, and 33/24 °C. Seeds were not produced at any of the clonal planting locations during the three years. Vegetative propagation via rooted cuttings was successful in the mid-spring, seed germination was possible over a wide range of temperatures, and self-incompatibility was evident in this species. The results of this study will permit fast and efficient propagation of multiple and selected genotypes for conservation, commerce, and breeding of elite cultivars with disease resistance or other desirable attributes.
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Tsai SK, Chen CC, Lin HJ, Lin HY, Chen TT, Wang LC. Combination of multiplex reverse transcription recombinase polymerase amplification assay and capillary electrophoresis provides high sensitive and high-throughput simultaneous detection of avian influenza virus subtypes. J Vet Sci 2020; 21:e24. [PMID: 32233132 PMCID: PMC7113572 DOI: 10.4142/jvs.2020.21.e24] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 12/30/2019] [Indexed: 11/20/2022] Open
Abstract
The pandemic of avian influenza viruses (AIVs) in Asia has caused enormous economic loss in poultry industry and human health threat, especially clade 2.3.4.4 H5 and H7 subtypes in recent years. The endemic chicken H6 virus in Taiwan has also brought about human and dog infections. Since wild waterfowls is the major AIV reservoir, it is important to monitor the diversified subtypes in wildfowl flocks in early stage to prevent viral reassortment and transmission. To develop a more efficient and sensitive approach is a key issue in epidemic control. In this study, we integrate multiplex reverse transcription recombinase polymerase amplification (RT-RPA) and capillary electrophoresis (CE) for high-throughput detection and differentiation of AIVs in wild waterfowls in Taiwan. Four viral genes were detected simultaneously, including nucleoprotein (NP) gene of all AIVs, hemagglutinin (HA) gene of clade 2.3.4.4 H5, H6 and H7 subtypes. The detection limit of the developed detection system could achieve as low as one copy number for each of the four viral gene targets. Sixty wild waterfowl field samples were tested and all of the four gene signals were unambiguously identified within 6 h, including the initial sample processing and the final CE data analysis. The results indicated that multiplex RT-RPA combined with CE was an excellent alternative for instant simultaneous AIV detection and subtype differentiation. The high efficiency and sensitivity of the proposed method could greatly assist in wild bird monitoring and epidemic control of poultry.
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Affiliation(s)
- Shou Kuan Tsai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chen Chih Chen
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.,Animal Biologics Pilot Production Center, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Han Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Han You Lin
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Ting Tzu Chen
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Lih Chiann Wang
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan.
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Edwards TP, Trigiano RN, Ownley BH, Windham AS, Wyman CR, Wadl PA, Hadziabdic D. Genetic Diversity and Conservation Status of Helianthus verticillatus, an Endangered Sunflower of the Southern United States. Front Genet 2020; 11:410. [PMID: 32499812 PMCID: PMC7243268 DOI: 10.3389/fgene.2020.00410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in Helianthus verticillatus (whorled sunflower). This endangered, wild relative of the common sunflower, Helianthus annuus, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for H. verticillatus, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of H. verticillatus individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between H. verticillatus collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of H. verticillatus populations in Georgia. Our results can underpin an original recovery plan for H. verticillatus that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.
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Affiliation(s)
- Tyler P Edwards
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Bonnie H Ownley
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Alan S Windham
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Christopher R Wyman
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Phillip A Wadl
- United States Department of Agriculture, Agriculture Research Service, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Haerinasab M, Ali-Farsangi F, Bordbar F, Eslami Farouji A. Genetic Diversity and Infraspecific Relationships of Trifolium fragiferum L. in Iran. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2020. [DOI: 10.1007/s40995-020-00834-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mans BJ, Pienaar R, Christo Troskie P, Combrink MP. Investigation into limiting dilution and tick transmissibility phenotypes associated with attenuation of the S24 vaccine strain. Parasit Vectors 2019; 12:419. [PMID: 31455385 PMCID: PMC6712794 DOI: 10.1186/s13071-019-3678-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2019] [Indexed: 12/27/2022] Open
Abstract
Background Babesia bovis is the causal agent of Asiatic redwater, transmitted by the pandemic tick Rhipicephalus (Boophilus) microplus. Disease control may target the tick vector using acaricides or anti-tick vaccines, or the parasite using chemoprophylaxis or anti-parasite vaccines. Current anti-parasite vaccines comprise live blood vaccines using attenuated B. bovis strains. Attenuation is attained by rapid passage that may result in different phenotypes such as reduced virulence, non-transmissibility by the tick vector, inability to sequester in the host (lack of limiting dilution) and limited genetic diversity. Attenuation and phenotypes may be linked to selection of subpopulations during rapid passage. The South African B. bovis S24 vaccine strain comprise a subpopulation that present low virulence, non-transmissibility, lack of limiting dilution phenotype and the presence of a single A558 Bv80 allele. The S24 strain could be co-transmitted with a field strain (05-100) suggesting sexual recombination. The present study investigated the change in phenotype for the S24 vaccine strain during rapid passage and co-transmission. Methods Vaccine phenotype change during passage as well as co-transmissibility was monitored using Bv80 allele specific PCR, limiting dilution and Illumina-based genome sequencing. Results The S24 population could not be rescued from the S16 passage as previously attained suggesting that selection of the S24 vaccine strain was a serendipitous and stochastic event. Passage from S16 to S24 also resulted in loss of the limiting dilution phenotype. Genome sequencing indicated sexual recombination during co-transmission with the 05-100 field strain. Analysis of the recombinant strain indicate that VESA1, smORF and SBP2 family members are present and may be responsible for the limiting dilution phenotypes, while various regions may also be responsible for the tick transmission phenotype. Conclusions The molecular basis for tick transmission and limiting dilution phenotypes may be defined in future using selection based on these traits in combination with sexual recombination.![]()
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Affiliation(s)
- Ben J Mans
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, 0110, South Africa. .,Department of Life and Consumer Sciences, University of South Africa, Florida, South Africa.
| | - Ronel Pienaar
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, 0110, South Africa
| | - P Christo Troskie
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, 0110, South Africa
| | - Michael P Combrink
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, 0110, South Africa
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Förster I, Brockmann M, Schildgen O, Schildgen V. Microsatellite instability testing in colorectal cancer using the QiaXcel advanced platform. BMC Cancer 2018; 18:484. [PMID: 29703179 PMCID: PMC5923018 DOI: 10.1186/s12885-018-4400-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background Microsatellite instability (MSI) is a major predictive and diagnostic marker in several cancers including colorectal carcinomas. Diagnostic testing for microsatellites is generally performed using capillary sequencers, which requires expensive high-end equipment including expensive chemistry using fluorescent dyes labelling the PCR products of interest. In this study we have modified such a diagnostic protocol and established the microsatellite testing on the QiaXcel Advanced platform. Methods MSI testing was based on a previously established protocol describing a multiplex PCR followed by fluorescent detection of PCR products in a capillary sequencing device. Ten microsatellites were included in the new protocol: BAT25, BAT26, BAT40, D2s123, D10s197, D13s153, D17s250, D18s58, D5s346, and MycI. In this protocol the PCR was demultiplexed and established on the QiaXcel Advanced system (Qiagen, Hilden, Germany). Results Making use of a series of FFPE control samples with known MSI status including those with and without MSI a protocol for MSI testing was successfully established on the QiaXcel Advanced platform. Conclusions MSI testing for human colorectal cancers using the QiaXcel Advanced system could serve as an economic acceptable tool for rapid diagnostics in laboratories that do not have access to a capillary sequencing unit.
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Affiliation(s)
- Isabel Förster
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Köln, Cologne, Germany
| | - Michael Brockmann
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Köln, Cologne, Germany
| | - Oliver Schildgen
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Köln, Cologne, Germany.
| | - Verena Schildgen
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, D-51109 Köln, Cologne, Germany.
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A Novel Capillary Electrophoresis-Based High-Throughput Multiplex Polymerase Chain Reaction System for the Simultaneous Detection of Nine Pathogens in Swine. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7243909. [PMID: 28691030 PMCID: PMC5485272 DOI: 10.1155/2017/7243909] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/14/2017] [Indexed: 11/18/2022]
Abstract
Here we aimed to develop a capillary electrophoresis-based high-throughput multiplex polymerase chain reaction (PCR) system for the simultaneous detection of nine pathogens in swine. Nine pairs of specific primers and a set of universal primers were designed; the multiplex PCR was established. The specificity and cross-reactivity of this assay were examined, and the detection limit was determined using serial 10-fold dilutions of plasmids containing the target sequences. The assay was further tested using 144 clinical samples. We found that the nine specific amplification peaks were observed, and the assay had a high degree of specificity, without nonspecific amplification. The simultaneous detection limit for the nine viruses reached 10000 copies μL-1 when all of the premixed viral targets were present. Seventy-seven of the clinical samples tested positive for at least one of the viruses; the principal viral infections in the clinical samples were porcine circovirus type 2 and porcine reproductive and respiratory syndrome virus. This approach has much potential for further development of high-throughput detection tools for the diagnosis of diseases in animals.
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Pecorino B, Rubino C, Guardalà VF, Galia A, Scollo P. Genetic screening in young women diagnosed with endometrial cancer. J Gynecol Oncol 2017; 28:e4. [PMID: 27670258 PMCID: PMC5165072 DOI: 10.3802/jgo.2017.28.e4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To evaluate the importance of Lynch syndrome associated risk screening in the patients aged less than 50 years affected from endometrial cancer. METHODS From 2007 to 2014, 41 patients affected from endometrial cancer and aged less than 50 years underwent surgery at the Complex Operative Unit of Gynecology and Obstetrics, Cannizzaro Hospital of Catania, Italy. They were selected to undergo mismatch repair gene mutation analysis using immunohistochemistry (IHC; four markers: MLH1, MSH2, MSH6, PMS2) and microsatellite instability (MSI) test. For samples that resulted negative to IHC (abnormal finding), MSI test was performed to further study the suspected mutation. Samples were classified as MSI-high (MSI-H) if more than one marker was identified as unstable; MSI-low (MSI-L) if only one marker was identified as unstable; or MSI-stable (MSI-S) if no marker was identified as unstable. Samples were subdivided into two groups: MSI-H/L and MSI-S. Statistical analysis was performed to assess differences regarding survival, tumor staging, grading, and invasion of lymphovascular space between these two groups. RESULTS IHC analysis showed that in 46% (19/41) of samples there was negative outcome. Forty-two percent (8/19) of these negative samples were unstable (either low or high). Of eight patients showing MSI, 75% were MSI-L, while 25% were MSI-H. Differences in survival, stage, grade, lymphovascular space invasion and Amsterdam criteria adherence were not statistically significant due to the small size of the cohort. CONCLUSION IHC and MSI test results of our cohort lead us to assess the relevance of performing Lynch syndrome genetic screening in endometrial cancer patients aged less than 50 years at the time of diagnosis.
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Affiliation(s)
- Basilio Pecorino
- Division of Gynecology and Obstetrics, Maternal and Child Department, Cannizzaro Hospital, Catania, Italy.
| | - Cinzia Rubino
- Division of Gynecology and Obstetrics, Magati Hospital, Scandiano AUSL Reggio Emilia, Scandiano, Italy
| | - Vito Fabio Guardalà
- Division of Gynecology and Obstetrics, Maternal and Child Department, Cannizzaro Hospital, Catania, Italy
| | - Antonio Galia
- Department of Pathology, Cannizzaro Hospital, Catania, Italy
| | - Paolo Scollo
- Division of Gynecology and Obstetrics, Maternal and Child Department, Cannizzaro Hospital, Catania, Italy
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Pajuelo MJ, Eguiluz M, Dahlstrom E, Requena D, Guzmán F, Ramirez M, Sheen P, Frace M, Sammons S, Cama V, Anzick S, Bruno D, Mahanty S, Wilkins P, Nash T, Gonzalez A, García HH, Gilman RH, Porcella S, Zimic M. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium. PLoS Negl Trop Dis 2015; 9:e0004316. [PMID: 26697878 PMCID: PMC4689449 DOI: 10.1371/journal.pntd.0004316] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies. Taenia solium, the pork tapeworm, is an important pathogen as it is a major cause of acquired epilepsy in developing countries. The parasite was eliminated from most developed countries decades ago due to improvement in sanitary conditions but it remains a common infection across Asia, Africa and Latin America. Identification of genetic variants within T. solium will enable to study the genetic epidemiology, distribution and movement of this parasite within endemic communities, which will ultimately facilitate the design of control strategies to reduce the health and economic burden of disease. Microsatellites have been used in other parasites to identify genetic variants. In this study, we partially sequenced the genome of T. solium and identified microsatellites widely distributed in the genome using bioinformatics tools. We evaluated the distribution of these microsatellites collected from 20 tapeworms from the north and 20 tapeworms from the south of Peru. We identified seven polymorphic microsatellites, and evaluated their capacity to differentiate genetic variants of T. solium. Interestingly, tapeworms from the North and South of Peru showed different genotypes, suggesting its use as a potential marker to differentiate geographic origin.
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Affiliation(s)
- Mónica J. Pajuelo
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - María Eguiluz
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - David Requena
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Frank Guzmán
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Manuel Ramirez
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Michael Frace
- Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott Sammons
- Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sarah Anzick
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Dan Bruno
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Siddhartha Mahanty
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Patricia Wilkins
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Theodore Nash
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Armando Gonzalez
- Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Héctor H. García
- Departamento de Microbiología, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima Peru
- Instituto Nacional de Ciencias Neurológicas. Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Steve Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America
| | - Mirko Zimic
- Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail:
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Manrique P, Hoshi M, Fasabi M, Nolasco O, Yori P, Calderón M, Gilman RH, Kosek MN, Vinetz JM, Gamboa D. Assessment of an automated capillary system for Plasmodium vivax microsatellite genotyping. Malar J 2015; 14:326. [PMID: 26293655 PMCID: PMC4546211 DOI: 10.1186/s12936-015-0842-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several platforms have been used to generate the primary data for microsatellite analysis of malaria parasite genotypes. Each has relative advantages but share a limitation of being time- and cost-intensive. A commercially available automated capillary gel cartridge system was assessed in the microsatellite analysis of Plasmodium vivax diversity in the Peruvian Amazon. METHODS The reproducibility and accuracy of a commercially-available automated capillary system, QIAxcel, was assessed using a sequenced PCR product of 227 base pairs. This product was measured 42 times, then 27 P. vivax samples from Peruvian Amazon subjects were analyzed with this instrument using five informative microsatellites. Results from the QIAxcel system were compared with a Sanger-type sequencing machine, the ABI PRISM(®) 3100 Genetic Analyzer. RESULTS Significant differences were seen between the sequenced amplicons and the results from the QIAxcel instrument. Different runs, plates and cartridges yielded significantly different results. Additionally, allele size decreased with each run by 0.045, or 1 bp, every three plates. QIAxcel and ABI PRISM systems differed in giving different values than those obtained by ABI PRISM, and too many (i.e. inaccurate) alleles per locus were also seen with the automated instrument. CONCLUSIONS While P. vivax diversity could generally be estimated using an automated capillary gel cartridge system, the data demonstrate that this system is not sufficiently precise for reliably identifying parasite strains via microsatellite analysis. This conclusion reached after systematic analysis was due both to inadequate precision and poor reproducibility in measuring PCR product size.
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Affiliation(s)
- Paulo Manrique
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Mari Hoshi
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | | | - Oscar Nolasco
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Pablo Yori
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Martiza Calderón
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Robert H Gilman
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Margaret N Kosek
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Joseph M Vinetz
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Dionicia Gamboa
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru.
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Combrink M, Troskie P, Pienaar R, Latif A, Mans B. Genotypic diversity in Babesia bovis field isolates and vaccine strains from South Africa. Vet Parasitol 2014; 199:144-52. [DOI: 10.1016/j.vetpar.2013.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/02/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
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