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Shahbazi M, Majka J, Kubíková D, Zwierzykowski Z, Glombik M, Wendel JF, Sharbrough J, Hartmann S, Szecówka M, Doležel J, Bartoš J, Kopecký D, Kneřová J. Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1102-1118. [PMID: 38323852 DOI: 10.1111/tpj.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.
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Affiliation(s)
- Mehrdad Shahbazi
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Denisa Kubíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, Iowa, USA
| | - Joel Sharbrough
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, 87801, USA
| | - Stephan Hartmann
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 4, 85354, Freising, Germany
| | - Marek Szecówka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
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Strauss J, Deng L, Gao S, Toseland A, Bachy C, Zhang C, Kirkham A, Hopes A, Utting R, Joest EF, Tagliabue A, Löw C, Worden AZ, Nagel G, Mock T. Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans. Nat Microbiol 2023; 8:2050-2066. [PMID: 37845316 PMCID: PMC10627834 DOI: 10.1038/s41564-023-01498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Microbial rhodopsins are photoreceptor proteins that convert light into biological signals or energy. Proteins of the xanthorhodopsin family are common in eukaryotic photosynthetic plankton including diatoms. However, their biological role in these organisms remains elusive. Here we report on a xanthorhodopsin variant (FcR1) isolated from the polar diatom Fragilariopsis cylindrus. Applying a combination of biophysical, biochemical and reverse genetics approaches, we demonstrate that FcR1 is a plastid-localized proton pump which binds the chromophore retinal and is activated by green light. Enhanced growth of a Thalassiora pseudonana gain-of-function mutant expressing FcR1 under iron limitation shows that the xanthorhodopsin proton pump supports growth when chlorophyll-based photosynthesis is iron-limited. The abundance of xanthorhodopsin transcripts in natural diatom communities of the surface oceans is anticorrelated with the availability of dissolved iron. Thus, we propose that these proton pumps convey a fitness advantage in regions where phytoplankton growth is limited by the availability of dissolved iron.
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Affiliation(s)
- Jan Strauss
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
- German Maritime Centre, Hamburg, Germany.
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, France
| | - Chong Zhang
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Amy Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Utting
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Eike F Joest
- Department of Biology, Biocenter, University of Würzburg, Wuerzburg, Germany
| | | | - Christian Löw
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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3
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Zhao R, Lukacsovich T, Gaut R, Emerson JJ. FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies. G3 (BETHESDA, MD.) 2023; 13:jkad162. [PMID: 37494033 PMCID: PMC10542570 DOI: 10.1093/g3journal/jkad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/26/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.
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Affiliation(s)
- Roy Zhao
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Tamas Lukacsovich
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Rebecca Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - J J Emerson
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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Souza VGP, Forder A, Brockley LJ, Pewarchuk ME, Telkar N, de Araújo RP, Trejo J, Benard K, Seneda AL, Minutentag IW, Erkan M, Stewart GL, Hasimoto EN, Garnis C, Lam WL, Martinez VD, Reis PP. Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis. Int J Mol Sci 2023; 24:ijms24108894. [PMID: 37240238 DOI: 10.3390/ijms24108894] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient's blood, urine, or other body fluids for the detection of biomarkers, including circulating tumor cells or tumor-derived DNA/RNA that have been shed into the bloodstream. Studies have shown that liquid biopsies can detect lung cancer metastases with high accuracy and sensitivity, even before they are visible on imaging scans. Such tests are valuable for early intervention and personalized treatment, aiming to improve patient outcomes. Liquid biopsies are also minimally invasive compared to traditional tissue biopsies, which require the removal of a sample of the tumor for further analysis. This makes liquid biopsies a more convenient and less risky option for patients, particularly those who are not good candidates for invasive procedures due to other medical conditions. While liquid biopsies for lung cancer metastases and relapse are still being developed and validated, they hold great promise for improving the detection and treatment of this deadly disease. Herein, we summarize available and novel approaches to liquid biopsy tests for lung cancer metastases and recurrence detection and describe their applications in clinical practice.
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Affiliation(s)
- Vanessa G P Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Liam J Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rachel Paes de Araújo
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Ana Laura Seneda
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Iael W Minutentag
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Greg L Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Erica N Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Cathie Garnis
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Wan L Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Victor D Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Patricia P Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
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5
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Tachibana A, Fujimura N, Takeuchi M, Watanabe K, Teruuchi Y, Uchiki T. Cationic copolymers that enhance wild-type-specific suppression in BNA-clamp PCR and preferentially increase the Tm of fully matched complementary DNA and BNA strands. BIOLOGY METHODS AND PROTOCOLS 2022; 7:bpac009. [PMID: 35664806 PMCID: PMC9154250 DOI: 10.1093/biomethods/bpac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mutation detection is of major interest in molecular diagnostics, especially in the field of oncology. However, detection can be challenging as mutant alleles often coexists with excess copies of wild-type alleles. Bridged nucleic acid (BNA)-clamp PCR circumvents this challenge by preferentially suppressing the amplification of wild-type alleles and enriching rare mutant alleles. In this study, we screened cationic copolymers containing nonionic and anionic repeat units for their ability to 1) increase the Tm of double-stranded DNA, 2) avoid PCR inhibition, and 3) enhance the suppression of wild-type amplification in BNA-clamp PCR to detect the KRAS G13D mutation. The selected copolymers that met these criteria consisted of four types of amines and anionic and/or nonionic units. In BNA-clamp PCR, these copolymers increased the threshold cycle (Ct) of the wild-type allele only and enabled mutation detection from templates with a 0.01% mutant-to-wild-type ratio. Melting curve analysis with 11-mer DNA-DNA or BNA-DNA complementary strands showed that these copolymers preferentially increased the Tm of perfectly matched strands over strands containing 1-bp mismatches. These results suggested that these copolymers preferentially stabilize perfectly matched DNA and BNA strands and thereby enhance rare mutant detection in BNA-clamp PCR.
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Affiliation(s)
- Ami Tachibana
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
| | | | | | - Koji Watanabe
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Yoko Teruuchi
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Tomoaki Uchiki
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
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6
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Lee DE, Kim HC, Chong ST, Klein TA, Choi KS, Kim YH, Kim JH, Lee SH. Regional and seasonal detection of resistance mutation frequencies in field populations of Anopheles Hyrcanus Group and Culex pipiens complex in Korea. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:33-39. [PMID: 32284134 DOI: 10.1016/j.pestbp.2019.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 06/11/2023]
Abstract
Pyrethroid (PYR) and organophosphate (OP) insecticides have been extensively used for mosquito control for several decades in South Korea, and has resulted in the rapid development of resistance in the field. In this study, quantitative sequencing (QS) protocols were developed for the frequency prediction of insecticide resistance alleles [e.g., the L1014F/C mutation on the voltage sensitive sodium channel as a PYR resistance allele and the G119S mutation on the acetylcholinesterase 1 as OP resistance alleles] in four regional populations of Anopheles Hyrcanus Group and Culex pipiens complex. Both of the L1014F/C and G119S mutations were observed in all examined regional populations of An. Hyrcanus Group, suggesting a wide distribution of both PYR and OP resistance. In contrast, populations of the Cx. pipiens complex were determined to possess almost no G119S mutation, but relatively higher frequencies of the L1014F mutation, showing differential resistance patterns between different mosquito groups. The mutation frequencies were also monitored throughout a mosquito season (May-October) at one collection site to determine the seasonal changes of resistance mutation frequency in mosquito populations. Dramatic decreases of both L1014F/C and G119S mutation frequencies were observed in the An. Hyrcanus Group toward the fall, with no mutations observed in the early spring, suggesting a connection between the fitness costs of overwintering and insecticide resistance. However, no apparent trends were detectable in the Cx. pipiens complex populations due to low or zero mutation frequencies.
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Affiliation(s)
- Do Eun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Sung-Tae Chong
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Terry A Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Kwang Shik Choi
- School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young Ho Kim
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Ju Hyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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7
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Dhas DBB, Ashmi AH, Bhat BV, Parija SC, Banupriya N. Modified low cost SNP genotyping technique using cycle threshold (Ct) & melting temperature (Tm) values in allele specific real-time PCR. Indian J Med Res 2016; 142:555-62. [PMID: 26658590 PMCID: PMC4743342 DOI: 10.4103/0971-5916.171282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background & objectives: Genotyping has now become one of the major diagnostic means for almost all diseases. Among the advanced techniques that are used to study single nucleotide polymorphisms (SNPs), only a few are applicable for routine disease diagnosis. Their applicability mainly depends on three factors: cost, time, and accuracy. The primary objective of this study was to propose allele-specific real-time PCR as a rapid, low cost and simple genotyping method for routine diagnostics. Methods: Two SNPs, rs3014866 and rs2149356 were analysed using allele-specific real-time PCR. The polymerase chain reaction was carried out using RealQ PCR master mix containing SYBR Green DNA I dye followed by melt curve analysis. The results were validated by agarose gel electrophoresis and DNA sequencing. Results: The allelic discrimination and zygosity of the two SNPs were assessed by combined cycle threshold (Ct) and melting temperature (Tm) values. Variations in Ct and Tm values among the two alleles were observed in both rs3014866 (Ct: C allele - 24±1, T allele - 27±1; Tm: C allele - 82.5±0.3, T allele - 86.3±0.2) and rs2149356 (Ct: C allele - 24±1, A allele - 26±1; Tm: C allele - 79.4±0.2, A allele - 80.4±0.3). Based on the variations, homozygous and heterozygous alleles were detected. Agarose gel electrophoresis and DNA sequencing also confirmed the allelic variation and zygosity observed in real-time PCR. Interpretation & conclusions: In diagnostic settings where a large number of samples are analysed daily, allele-specific real-time PCR assay may serve as a simple, low cost and efficient method of genotyping.
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Affiliation(s)
| | | | - B Vishnu Bhat
- Department of Paediatrics, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
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8
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Vaszkó T, Papp J, Krausz C, Casamonti E, Géczi L, Olah E. Discrimination of Deletion and Duplication Subtypes of the Deleted in Azoospermia Gene Family in the Context of Frequent Interloci Gene Conversion. PLoS One 2016; 11:e0163936. [PMID: 27723784 PMCID: PMC5056753 DOI: 10.1371/journal.pone.0163936] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 09/16/2016] [Indexed: 11/18/2022] Open
Abstract
Due to its palindromic setup, AZFc (Azoospermia Factor c) region of chromosome Y is one of the most unstable regions of the human genome. It contains eight gene families expressed mainly in the testes. Several types of rearrangement resulting in changes in the cumulative copy number of the gene families were reported to be associated with diseases such as male infertility and testicular germ cell tumors. The best studied AZFc rearrangement is gr/gr deletion. Its carriers show widespread phenotypic variation from azoospermia to normospermia. This phenomenon was initially attributed to different gr/gr subtypes that would eliminate distinct members of the affected gene families. However, studies conducted to confirm this hypothesis have brought controversial results, perhaps, in part, due to the shortcomings of the utilized subtyping methodology. This proof-of-concept paper is meant to introduce here a novel method aimed at subtyping AZFc rearrangements. It is able to differentiate the partial deletion and partial duplication subtypes of the Deleted in Azoospermia (DAZ) gene family. The keystone of the method is the determination of the copy number of the gene family member-specific variant(s) in a series of sequence family variant (SFV) positions. Most importantly, we present a novel approach for the correct interpretation of the variant copy number data to determine the copy number of the individual DAZ family members in the context of frequent interloci gene conversion.Besides DAZ1/DAZ2 and DAZ3/DAZ4 deletions, not yet described rearrangements such as DAZ2/DAZ4 deletion and three duplication subtypes were also found by the utilization of the novel approach. A striking feature is the extremely high concordance among the individual data pointing to a certain type of rearrangement. In addition to being able to identify DAZ deletion subtypes more reliably than the methods used previously, this approach is the first that can discriminate DAZ duplication subtypes as well.
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Affiliation(s)
- Tibor Vaszkó
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- * E-mail:
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
- Andrology Service, Fundacio´ Puigvert, Instituto de Investigaciones Biome´dicas Sant Pau (IIB-Sant Pau), Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Elena Casamonti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Lajos Géczi
- Department of Chemotherapy, National Institute of Oncology, Budapest, Hungary
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
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9
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Pérez-Ramírez C, Cañadas-Garre M, Robles AI, Molina MÁ, Faus-Dáder MJ, Calleja-Hernández MÁ. Liquid biopsy in early stage lung cancer. Transl Lung Cancer Res 2016; 5:517-524. [PMID: 27826533 DOI: 10.21037/tlcr.2016.10.15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lung cancer is the leading cause of cancer-associated deaths worldwide. Surgery is the standard treatment for early-stage non-small cell lung cancer (NSCLC). However, 30% to 80% of these patients will die within 5 yearS of diagnosis. Circulating cell-free DNA (cfDNA) harbors pathologic characteristics of the original tumor, such as gene mutations or epigenetic alterations. Analysis of cfDNA has revolutionized the clinical care of advanced lung cancer patients undergoing targeted therapies. However, the low concentration of cfDNA in the blood of early-stage NSCLC patients has hampered its use for management of early disease. Continuing development of more specific and sensitive techniques for detection and analysis of cfDNA will soon enable its leverage in early stage and, perhaps, even screening settings. Therefore, cfDNA analysis may become a tool used for routine NSCLC diagnosis and for monitoring tumor burden, as well as for identifying hidden residual disease. In this review, we will focus on the current evidence of cfDNA in patients with early-stage NSCLC, new and upcoming approaches to identify circulating-tumor biomarkers, their clinical applications and future directions.
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Affiliation(s)
- Cristina Pérez-Ramírez
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain;; Department of Biochemistry, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n 18071 Granada, Spain
| | - Marisa Cañadas-Garre
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, 37 Convent Dr, Bethesda, MD 20892, USA
| | - Miguel Ángel Molina
- Pangaea Biotech, S.L., Hospital Universitario Quirón Dexeus, C/ Sabino Arana, 5-19. 08028 Barcelona, Spain
| | - María José Faus-Dáder
- Department of Biochemistry, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n 18071 Granada, Spain
| | - Miguel Ángel Calleja-Hernández
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain;; Department of Pharmacology, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n, 18071 Granada, Spain
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Hung MS, Lung JH, Lin YC, Fang YH, Hsieh MJ, Tsai YH. The content of mutant EGFR DNA correlates with response to EGFR-TKIs in lung adenocarcinoma patients with common EGFR mutations. Medicine (Baltimore) 2016; 95:e3991. [PMID: 27368002 PMCID: PMC4937916 DOI: 10.1097/md.0000000000003991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This study aimed to elucidate the association of the content of mutant epidermal growth factor receptor (EGFR) deoxyribonucleic acid (DNA) with the treatment response to EGFR-tyrosine kinase inhibitor (TKI) and survival in patients with lung cancer.This retrospective cohort study included 77 lung adenocarcinoma patients with common EGFR mutations from December 2012 to February 2015. The content of mutant EGFR DNA in lung cancer tissues was determined using an Amplification Refractory Mutation System. The association of the amount of mutant EGFR DNA with treatment response, the clinical variables, and the progression-free survival (PFS) after EGFR-TKI therapy were evaluated.Using the amount of mutant EGR DNA above 4.77% as the cut-off value, the sensitivity to predict EGFR-TKI responder is 82.0% and the specificity is 75.0% (area under the curve [AUC]: 0.734, P = 0.003). The high content of mutant EGFR DNA is an independent factor associated with the response to EGFR-TKIs (odds ratio: 13.07, 95% confidence interval [CI]: 3.23-52.11, P = 0.0003). A significantly longer PFS was observed in the group with the high content of mutant EGFR DNA (26.3 months, 95% CI: 12.2-26.3) compared with the low content of mutant EGFR DNA groups (12.3 months, 95% CI: 5.7-14.8, P = 0.0155). A better predictive value of the content of mutant EGFR DNA was noted in patients with exon 19 deletions (AUC: 0.892, P < 0.0001) than exon 21 L858R mutations (AUC: 0.675, P = 0.0856).Our results show that the content of mutant EGFR DNA is associated with the clinical response to EGFR-TKIs, especially in patients with exon 19 deletions mutation.
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Affiliation(s)
- Ming-Szu Hung
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi
| | - Jr-Hau Lung
- Department of Medical Research, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
| | - Yu-Ching Lin
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi
| | - Yu-Hung Fang
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
| | - Meng-Jer Hsieh
- Division of Pulmonary Infection and Critical Care, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
- Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Ying-Huang Tsai
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, Puzi City
- Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
- Correspondence: Ying-Huang Tsai, Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi Branch, No. 6, W. Sec., Jiapu Road, Puzi City, Chiayi County 61363, Taiwan (ROC) (e-mail: )
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11
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Sorber L, Zwaenepoel K, Deschoolmeester V, Van Schil PEY, Van Meerbeeck J, Lardon F, Rolfo C, Pauwels P. Circulating cell-free nucleic acids and platelets as a liquid biopsy in the provision of personalized therapy for lung cancer patients. Lung Cancer 2016; 107:100-107. [PMID: 27180141 DOI: 10.1016/j.lungcan.2016.04.026] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022]
Abstract
Lung cancer is the predominant cause of cancer-related mortality in the world. The majority of patients present with locally advanced or metastatic non-small-cell lung cancer (NSCLC). Treatment for NSCLC is evolving from the use of cytotoxic chemotherapy to personalized treatment based on molecular alterations. Unfortunately, the quality of the available tumor biopsy and/or cytology material is not always adequate to perform the necessary molecular testing, which has prompted the search for alternatives. This review examines the use of circulating cell-free nucleic acids (cfNA), consisting of both circulating cell-free (tumoral) DNA (cfDNA-ctDNA) and RNA (cfRNA), as a liquid biopsy in lung cancer. The development of sensitive and accurate techniques such as Next-Generation Sequencing (NGS); Beads, Emulsion, Amplification, and Magnetics (BEAMing); and Digital PCR (dPCR), have made it possible to detect the specific genetic alterations (e.g. EGFR mutations, MET amplifications, and ALK and ROS1 translocations) for which targeted therapies are already available. Moreover, the ability to detect and quantify these tumor mutations has enabled the follow-up of tumor dynamics in real time. Liquid biopsy offers opportunities to detect resistance mechanisms, such as the EGFR T790M mutation in the case of EGFR TKI use, at an early stage. Several studies have already established the predictive and prognostic value of measuring ctNA concentration in the blood. To conclude, using ctNA analysis as a liquid biopsy has many advantages and allows for a variety of clinical and investigational applications.
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Affiliation(s)
- L Sorber
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium.
| | - K Zwaenepoel
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - V Deschoolmeester
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - P E Y Van Schil
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - J Van Meerbeeck
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Thoracic Oncology/MOCA, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - F Lardon
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - C Rolfo
- Oncology & Phase I Unit-Early Clinical Trials, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - P Pauwels
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
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12
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Kwon DH, Kang TJ, Kim YH, Lee SH. Phenotypic- and Genotypic-Resistance Detection for Adaptive Resistance Management in Tetranychus urticae Koch. PLoS One 2015; 10:e0139934. [PMID: 26545209 PMCID: PMC4636269 DOI: 10.1371/journal.pone.0139934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
Rapid resistance detection is necessary for the adaptive management of acaricide-resistant populations of Tetranychus urticae. Detection of phenotypic and genotypic resistance was conducted by employing residual contact vial bioassay (RCV) and quantitative sequencing (QS) methods, respectively. RCV was useful for detecting the acaricide resistance levels of T. urticae, particularly for on-site resistance detection; however, it was only applicable for rapid-acting acaricides (12 out of 19 tested acaricides). QS was effective for determining the frequencies of resistance alleles on a population basis, which corresponded to 12 nonsynonymous point mutations associated with target-site resistance to five types of acaricides [organophosphates (monocrotophos, pirimiphos-methyl, dimethoate and chlorpyrifos), pyrethroids (fenpropathrin and bifenthrin), abamectin, bifenazate and etoxazole]. Most field-collected mites exhibited high levels of multiple resistance, as determined by RCV and QS data, suggesting the seriousness of their current acaricide resistance status in rose cultivation areas in Korea. The correlation analyses revealed moderate to high levels of positive relationships between the resistance allele frequencies and the actual resistance levels in only five of the acaricides evaluated, which limits the general application of allele frequency as a direct indicator for estimating actual resistance levels. Nevertheless, the resistance allele frequency data alone allowed for the evaluation of the genetic resistance potential and background of test mite populations. The combined use of RCV and QS provides basic information on resistance levels, which is essential for choosing appropriate acaricides for the management of resistant T. urticae.
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Affiliation(s)
- Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
- * E-mail: (DHK); (SHL)
| | - Taek-Jun Kang
- Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Jeonju 565–852, Republic of Korea
| | - Young Ho Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
| | - Si Hyeock Lee
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Republic of Korea
- * E-mail: (DHK); (SHL)
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Bordi P, Del Re M, Danesi R, Tiseo M. Circulating DNA in diagnosis and monitoring EGFR gene mutations in advanced non-small cell lung cancer. Transl Lung Cancer Res 2015; 4:584-97. [PMID: 26629427 PMCID: PMC4630520 DOI: 10.3978/j.issn.2218-6751.2015.08.09] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 01/06/2023]
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are current treatments for advanced non-small cell lung cancer (NSCLC) harboring activating EGFR gene mutations. Histological or cytological samples are the standard tumor materials for EGFR mutation analysis. However, the accessibility of tumor samples is not always possible and satisfactory in advanced NSCLC patients. Moreover, totality of EGFR mutated NSCLC patients will develop resistance to EGFR-TKIs. Repeat biopsies to study genetic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumor heterogeneity. Thus, exploring accurate and less invasive techniques to (I) diagnosis EGFR mutation if tissue is not available or not appropriate for molecular analysis and to (II) monitor EGFR-TKI treatment are needed. Circulating DNA fragments carrying tumor specific sequence alterations [circulating cell-free tumor DNA (cftDNA)] are found in the cell-free fraction of blood, representing a variable and generally small fraction of the total circulating DNA. cftDNA has a high degree of specificity to detect EGFR gene mutations in NSCLC. Studies have shown the feasibility of using cftDNA to diagnosis of EGFR activating gene mutations and also to monitor tumor dynamics in NSCLC patients treated with EGFR-TKIs. These evidences suggested that non-invasive techniques based on blood samples had a great potential in EGFR mutated NSCLC patients. In this review, we summarized these non-invasive approaches and relative scientific data now available, considering their possible applications in clinical practice of NSCLC treatment.
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14
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Kwon DH, Clark JM, Lee SH. Toxicodynamic mechanisms and monitoring of acaricide resistance in the two-spotted spider mite. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 121:97-101. [PMID: 26047116 DOI: 10.1016/j.pestbp.2014.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/09/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
The two-spotted spider (Tetranychus urticae) is one of the most serious pests world-wide and has developed resistance to many types of acaricides. Various mutations on acaricide target site genes have been determined to be responsible for toxicodynamic resistance, and the genotyping and frequency prediction of these mutations can be employed as an alternative resistance monitoring strategy. A quantitative sequencing (QS) protocol was reported as a population-based genotyping technique, and applied for the determination of resistance allele frequencies in T. urticae field populations. In addition, a modified glass vial bioassay method (residual contact vial bioassay, RCV) was implemented as a rapid on-site resistance monitoring tool. The QS protocol, together with the RCV, would greatly facilitate monitoring of T. urticae resistance. Recent completion of T. urticae genome analysis should facilitate the identification of additional resistance genetic markers that can be employed for molecular resistance monitoring.
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Affiliation(s)
- Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
| | - J Marshall Clark
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Si Hyeock Lee
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
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16
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Castellanos-Rizaldos E, Milbury CA, Guha M, Makrigiorgos GM. COLD-PCR enriches low-level variant DNA sequences and increases the sensitivity of genetic testing. Methods Mol Biol 2014; 1102:623-39. [PMID: 24259002 DOI: 10.1007/978-1-62703-727-3_33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Detection of low-level mutations is important for cancer biomarker and therapy targets discovery, but reliable detection remains a technical challenge. The newly developed method of CO-amplification at Lower Denaturation temperature PCR (COLD-PCR) helps to circumvent this issue. This PCR-based technology preferentially enriches minor known or unknown variants present in samples with a high background of wild type DNA which often hampers the accurate identification of these minority alleles. This is a simple process that consists of lowering the temperature at the denaturation step during the PCR-cycling protocol (critical denaturation temperature, T c) and inducing DNA heteroduplexing during an intermediate step. COLD-PCR in its simplest forms does not need additional reagents or specific instrumentation and thus, can easily replace conventional PCR and at the same time improve the mutation detection sensitivity limit of downstream technologies. COLD-PCR can be applied in two basic formats: fast-COLD-PCR that can enrich T m-reducing mutations and full-COLD-PCR that can enrich all mutations, though it requires an intermediate cross-hybridization step that lengthens the thermocycling program. An improved version of full-COLD-PCR (improved and complete enrichment, ice-COLD-PCR) has also been described. Finally, most recently, we developed yet another form of COLD-PCR, temperature-tolerant-COLD-PCR, which gradually increases the denaturation temperature during the COLD-PCR reaction, enriching diverse targets using a single cycling program. This report describes practical considerations for application of fast-, full-, ice-, and temperature-tolerant-COLD-PCR for enrichment of mutations prior to downstream screening.
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Affiliation(s)
- Elena Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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17
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García-Mendiola T, Barreiro Martínez T, Pariente F, Molano J, Lorenzo E. Screening of Specific Gene Mutations Associated with Cystic Fibrosis. ELECTROANAL 2014. [DOI: 10.1002/elan.201400042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Del Re M, Vasile E, Falcone A, Danesi R, Petrini I. Molecular analysis of cell-free circulating DNA for the diagnosis of somatic mutations associated with resistance to tyrosine kinase inhibitors in non-small-cell lung cancer. Expert Rev Mol Diagn 2014; 14:453-68. [PMID: 24725257 DOI: 10.1586/14737159.2014.908120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In non-small-cell lung cancer, the molecular diagnosis of somatic mutations is instrumental for the choice of the most appropriate treatment. However, despite an initial response, resistance to tyrosine kinase inhibitors occurs and thereafter tumors progress. For this reason, next generation inhibitors able to overcome acquired resistances are currently in development. Therefore, the identification of the molecular determinants of resistance is needed to adapt treatment accordingly. The analysis of circulating cell-free tumor DNA represents a powerful tool to monitor the somatic changes induced by treatment. This review focuses on the most recent advantages in the diagnosis of acquired resistance in circulating cell-free tumor DNA and underlines the strategies ready to be translated in the clinical practice.
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Affiliation(s)
- Marzia Del Re
- Department of Clinical and Experimental Medicine, Clinical Pharmacology Unit, Pisa University, Pisa, Italy
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19
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Karlep L, Reintamm T, Kelve M. Intragenomic Profiling Using Multicopy Genes: The rDNA Internal Transcribed Spacer Sequences of the Freshwater Sponge Ephydatia fluviatilis. PLoS One 2013; 8:e66601. [PMID: 23825547 PMCID: PMC3688955 DOI: 10.1371/journal.pone.0066601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multicopy genes, like ribosomal RNA genes (rDNA), are widely used to describe and distinguish individuals. Despite concerted evolution that homogenizes a large number of rDNA gene copies, the presence of different gene variants within a genome has been reported. Characterization of an organism by defining every single variant of tens to thousands of rDNA repeat units present in a eukaryotic genome would be quite unreasonable. Here we provide an alternative approach for the characterization of a set of internal transcribed spacer sequences found within every rDNA repeat unit by implementing direct sequencing methodology. The prominent allelic variants and their relative amounts characterizing an individual can be described by a single sequencing electropherogram of the mixed amplicon containing the variants present within the genome. We propose a method for rational analysis of heterogeneity of multicopy genes by compiling a profile based on quantification of different sequence variants of the internal transcribed spacers of the freshwater sponge Ephydatia fluviatilis as an example. In addition to using conventional substitution analysis, we have developed a mathematical method, the proportion model method, to quantify the relative amounts of allelic variants of different length using data from direct sequencing of the heterogeneous amplicon. This method is based on determining the expected signal intensity values (corresponding to peak heights from the sequencing electropherogram) by sequencing clones from the same or highly similar amplicon and comparing hypothesized combinations against the values obtained by direct sequencing of the heterogeneous amplicon. This method allowed to differentiate between all specimens analysed.
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Affiliation(s)
- Liisi Karlep
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Tõnu Reintamm
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Merike Kelve
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
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20
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An electronic sensor array for label-free detection of single-nucleotide polymorphisms. Biosens Bioelectron 2013; 43:165-72. [DOI: 10.1016/j.bios.2012.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 11/22/2022]
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21
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FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations. PLoS One 2012; 7:e47959. [PMID: 23118913 PMCID: PMC3485326 DOI: 10.1371/journal.pone.0047959] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/17/2012] [Indexed: 01/07/2023] Open
Abstract
Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >105 reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.
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22
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Shen W, Deng H, Teo AKL, Gao Z. Colorimetric detection of single-nucleotide polymorphisms with a real-time PCR-like sensitivity. Chem Commun (Camb) 2012; 48:10225-7. [DOI: 10.1039/c2cc35070j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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23
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The role of evolutionary intermediates in the host adaptation of canine parvovirus. J Virol 2011; 86:1514-21. [PMID: 22114336 DOI: 10.1128/jvi.06222-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The adaptation of viruses to new hosts is a poorly understood process likely involving a variety of viral structures and functions that allow efficient replication and spread. Canine parvovirus (CPV) emerged in the late 1970s as a host-range variant of a virus related to feline panleukopenia virus (FPV). Within a few years of its emergence in dogs, there was a worldwide replacement of the initial virus strain (CPV type 2) by a variant (CPV type 2a) characterized by four amino acid differences in the capsid protein. However, the evolutionary processes that underlie the acquisition of these four mutations, as well as their effects on viral fitness, both singly and in combination, are still uncertain. Using a comprehensive experimental analysis of multiple intermediate mutational combinations, we show that these four capsid mutations act in concert to alter antigenicity, cell receptor binding, and relative in vitro growth in feline cells. Hence, host adaptation involved complex interactions among both surface-exposed and buried capsid mutations that together altered cell infection and immune escape properties of the viruses. Notably, most intermediate viral genotypes containing different combinations of the four key amino acids possessed markedly lower fitness than the wild-type viruses.
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Milbury CA, Li J, Liu P, Makrigiorgos GM. COLD-PCR: improving the sensitivity of molecular diagnostics assays. Expert Rev Mol Diagn 2011; 11:159-69. [PMID: 21405967 DOI: 10.1586/erm.10.115] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The detection of low-abundance DNA variants or mutations is of particular interest to medical diagnostics, individualized patient treatment and cancer prognosis; however, detection sensitivity for low-abundance variants is a pronounced limitation of most currently available molecular assays. We have recently developed coamplification at lower denaturation temperature-PCR (COLD-PCR) to resolve this limitation. This novel form of PCR selectively amplifies low-abundance DNA variants from mixtures of wild-type and mutant-containing (or variant-containing) sequences, irrespective of the mutation type or position on the amplicon, by using a critical denaturation temperature. The use of a lower denaturation temperature in COLD-PCR results in selective denaturation of amplicons with mutation-containing molecules within wild-type mutant heteroduplexes or with a lower melting temperature. COLD-PCR can be used in lieu of conventional PCR in several molecular applications, thus enriching the mutant fraction and improving the sensitivity of downstream mutation detection by up to 100-fold.
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Affiliation(s)
- Coren A Milbury
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
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25
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Zu Y, Ting AL, Gao Z. Visualizing low-level point mutations: enzyme-like selectivity offered by nanoparticle probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:306-310. [PMID: 21294256 DOI: 10.1002/smll.201001774] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Yanbing Zu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore 138669.
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26
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BUSSIÈRE LF, DEMONT M, PEMBERTON AJ, HALL MD, WARD PI. The assessment of insemination success in yellow dung flies using competitive PCR. Mol Ecol Resour 2010; 10:292-303. [DOI: 10.1111/j.1755-0998.2009.02754.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. F. BUSSIÈRE
- Zoology Museum, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - M. DEMONT
- Zoology Museum, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - A. J. PEMBERTON
- Zoology Museum, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - M. D. HALL
- Evolution & Ecology Research Centre and School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - P. I. WARD
- Zoology Museum, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
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27
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Li J, Wang L, Jänne PA, Makrigiorgos GM. Coamplification at lower denaturation temperature-PCR increases mutation-detection selectivity of TaqMan-based real-time PCR. Clin Chem 2009; 55:748-56. [PMID: 19233916 DOI: 10.1373/clinchem.2008.113381] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND DNA genotyping with mutation-specific TaqMan(R) probes (Applied Biosystems) is broadly used in detection of single-nucleotide polymorphisms but is less so for somatic mutations because of its limited selectivity for low-level mutations. We recently described coamplification at lower denaturation temperature-PCR (COLD-PCR), a method that amplifies minority alleles selectively from mixtures of wild-type and mutation-containing sequences during the PCR. We demonstrate that combining COLD-PCR with TaqMan technology provides TaqMan genotyping with the selectivity needed to detect low-level somatic mutations. METHODS Minor-groove binder-based or common TaqMan probes were designed to contain a nucleotide that matches the desired mutation approximately in the middle of the probe. The critical denaturation temperature (T(c)) of each amplicon was then experimentally determined. COLD-PCR/TaqMan genotyping was performed in 2 steps: denaturation at the T(c), followed by annealing and extension at a single temperature (fast COLD-PCR). The threshold cycle was used to identify mutations on the basis of serial dilutions of mutant DNA into wild-type DNA and to identify TP53 (tumor protein p53) and EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] mutations in tumors. RESULTS COLD-PCR/TaqMan genotyping identified G>A mutations within TP53 exon 8 (codon 273 mutation hot spot) and C>T mutations within the EGFR gene (drug-resistance mutation T790M) with a selectivity improvement of 15- to 30-fold over regular PCR/TaqMan genotyping. A second round of COLD-PCR/TaqMan genotyping improved the selectivity by another 15- to 30-fold and enabled detection of 1 mutant in 2000 wild-type alleles. Use of COLD-PCR/TaqMan genotyping allowed quantitative identification of low-level TP53 and T790 mutations in colon tumor samples and in non-small-cell lung cancer cell lines treated with kinase inhibitors. CONCLUSIONS The major improvement in selectivity provided by COLD-PCR enables the popular TaqMan genotyping method to become a powerful tool for detecting low-level mutations in clinical samples.
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Affiliation(s)
- Jin Li
- Department of Radiation Oncology, Divisions of Genomic Stability and DNA Repair, and Medical Physics, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Schneider M, von Känel T, Sanz J, Gallati S. Ligation dependent allele specific quantification (LASQ) of CFTR cDNA on the LightCycler using MLPA hybridization probes. Clin Chim Acta 2009; 402:47-53. [PMID: 19146842 DOI: 10.1016/j.cca.2008.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 11/16/2008] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
Abstract
BACKGROUND As for Cystic Fibrosis (CF) and many other hereditary diseases there is still a lack in understanding the relationship between genetic (e.g. allelic) and phenotypic diversity. Therefore methods which allow fine quantification of allelic proportions of mRNA transcripts are of high importance. METHODS We used either genomic DNA (gDNA) or total RNA extracted from nasal cells as starting nucleic acid template for our assay. The subjects included in this study were 9 CF patients compound heterozygous for the F508del mutation and each one F508del homozygous and one wild type homozygous respectively. We established a novel ligation based quantification method which allows fine quantification of the allelic proportions of ss and ds CFTR cDNA. To verify reliability and accuracy of this novel assay we compared it with semiquantitative fluorescent PCR (SQF-PCR). RESULTS We established a novel assay for allele specific quantification of gene expression which combines the benefits of the specificity of the ligation reaction and the accuracy of quantitative real-time PCR. The comparison with SQF-PCR clearly demonstrates that LASQ allows fine quantification of allelic proportions. CONCLUSION This assay represents an alternative to other fine quantitative methods such as ARMS PCR and Pyrosequencing.
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Affiliation(s)
- Mircea Schneider
- Division of Human Genetics, Department of Paediatrics Inselspital, University of Bern, Bern, Switzerland
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Monsion B, Duborjal H, Blanc S. Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples. BMC Genomics 2008; 9:85. [PMID: 18291029 PMCID: PMC2276495 DOI: 10.1186/1471-2164-9-85] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 02/21/2008] [Indexed: 11/17/2022] Open
Abstract
Background Pathogens such as fungi, bacteria and especially viruses, are highly variable even within an individual host, intensifying the difficulty of distinguishing and accurately quantifying numerous allelic variants co-existing in a single nucleic acid sample. The majority of currently available techniques are based on real-time PCR or primer extension and often require multiplexing adjustments that impose a practical limitation of the number of alleles that can be monitored simultaneously at a single locus. Results Here, we describe a novel method that allows the simultaneous quantification of numerous allelic variants in a single reaction tube and without multiplexing. Quantitative Single-letter Sequencing (QSS) begins with a single PCR amplification step using a pair of primers flanking the polymorphic region of interest. Next, PCR products are submitted to single-letter sequencing with a fluorescently-labelled primer located upstream of the polymorphic region. The resulting monochromatic electropherogram shows numerous specific diagnostic peaks, attributable to specific variants, signifying their presence/absence in the DNA sample. Moreover, peak fluorescence can be quantified and used to estimate the frequency of the corresponding variant in the DNA population. Using engineered allelic markers in the genome of Cauliflower mosaic virus, we reliably monitored six different viral genotypes in DNA extracted from infected plants. Evaluation of the intrinsic variance of this method, as applied to both artificial plasmid DNA mixes and viral genome populations, demonstrates that QSS is a robust and reliable method of detection and quantification for variants with a relative frequency of between 0.05 and 1. Conclusion This simple method is easily transferable to many other biological systems and questions, including those involving high throughput analysis, and can be performed in any laboratory since it does not require specialized equipment.
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Affiliation(s)
- Baptiste Monsion
- Biologie et Génétique des Interactions Plante-Parasite (BGPI), INRA-CIRAD-SupagroM, TA A-54/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
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Hall GS, Little DP. Relative quantitation of virus population size in mixed genotype infections using sequencing chromatograms. J Virol Methods 2007; 146:22-8. [PMID: 17640742 PMCID: PMC2246048 DOI: 10.1016/j.jviromet.2007.05.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 05/22/2007] [Accepted: 05/31/2007] [Indexed: 11/17/2022]
Abstract
In order to quantitatively distinguish between highly similar RNA sequences, specific primers or probes must be designed. Unfortunately, consistent and reliable results are not always obtained with conventional techniques. This study uses reverse transcription-PCR coupled with direct terminator sequencing to economically and efficiently distinguish between sequence types in pooled samples while providing accurate relative quantification. As an example, the method is applied to measure template concentration of two Barley yellow dwarf virus (BYDV; family Luteoviridae) species in doubly infected wheat plants. A PERL script (polySNP) was developed that uses PHRED to automatically extract relative peak areas and heights from sequencing chromatograms at polymorphic sites. Peak measurements from experimental samples were compared to a standard curve generated by mixing in vitro transcribed RNA from BYDV-PAV and PAS templates in several ratios (ranging from 1:9 to 9:1 PAV:PAS) prior to RT-PCR amplification and sequencing. The relative amount of RNA template added to a sample was regressed onto the proportion of the chromatogram peak height or area corresponding to one virus species. The function of the best fit line was used to calculate template frequency in the experimental samples.
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Affiliation(s)
- Gerod S. Hall
- New York State Department of Health/Arbovirus Laboratory, 5668 State Farm Rd., Slingerland, NY 12159, Office phone 518-869-4592, Fax 518-869-4530,
| | - Damon P. Little
- The New York Botanical Garden, Bronx, New York 10458, Office phone 718-817-8130, Fax 718-817-8101,
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Short nucleotide polymorphic insertions in the MCL-1 promoter affect gene expression. Cancer Lett 2007; 251:114-31. [PMID: 17198743 DOI: 10.1016/j.canlet.2006.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 11/03/2006] [Accepted: 11/07/2006] [Indexed: 10/23/2022]
Abstract
We have recently reported novel short nucleotide (six and eighteen) polymorphic insertions, in the MCL-1 promoter and their association with higher mRNA and protein levels. The aim of the present study was to test the hypothesis that these insertions directly affect MCL-1 gene expression. Haematopoietic and epithelial human cell lines were transfected with +0, +6, or +18 MCL-1 promoter fragments positioned upstream of the Firefly luciferase reporter gene. The cells were stimulated with phorbol 12-myristate 13-acetate (PMA) and granulocyte macrophage colony-stimulating factor (GM-CSF). Compared to +0, both polymorphic insertions (+6 and +18) were associated with increased promoter activity. Although chromatin immunoprecipitation assay showed that there are Sp1/Sp3 binding sites in the MCL-1 promoter, electrophoretic mobility shift assay showed that it is unlikely that these sites are in the region harboring these insertions. These results provide further evidence for the biological effect of MCL-1 promoter polymorphisms on gene expression.
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Minarik M, Benesova L, Fantova L, Horacek J, Heracek J, Loukola A. Parallel optimization and genotyping of multiple single-nucleotide polymorphism markers by sample pooling approach using cycling-gradient CE with multiple injections. Electrophoresis 2006; 27:3856-63. [PMID: 16972303 DOI: 10.1002/elps.200600289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Increasing importance of single-nucleotide polymorphisms (SNPs) in determination of disease susceptibility or in prediction of therapy response brings attention of many molecular diagnostic laboratories to simple and low-cost SNP genotyping methodologies. We have recently introduced a mutation detection technique based on analysis of homo- and heteroduplex PCR fragments resolved in cycling temperature gradient conditions on a conventional multicapillary-array DNA sequencer. The main advantage of this technique is in its simplicity with no requirement for sample cleanup prior to the analysis. In this report we present a practical application of the technology for genotyping of SNP markers in two separate clinical projects resulting in a combined set of 44 markers screened in over 500 patients. Initially, a design of PCR primers and conditions was performed for each SNP marker. Then, optimization of CE running conditions (limited just to the proper selection of temperature cycling) was performed on pools of 20 DNA samples to increase the probability of having each of the two allele types represented in the sample. After selecting the optimum conditions, screening of markers in patients was performed using a multiple-injection approach for further acceleration of the sample throughput. The rate of successful optimization of experimental conditions without any pre-selection based on the SNP sequence or melting characteristics was 80% from the initial SNP marker candidates. By studying the failed markers, we attempt to identify critical factors enabling successful typing. The presented technique is very useful for low to medium sized SNP genotyping projects mostly applied in pharmacogenomic research as well as in clinical diagnostics. The main advantages include low cost, simple setup and validation of SNP markers.
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Affiliation(s)
- Marek Minarik
- Genomac International, Laboratory for Molecular Genetics, Prague, Czech Republic.
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Wilkening S, Hemminki K, Rudnai P, Gurzau E, Koppova K, Kumar R, Försti A. Case-control study in basal cell carcinoma of the skin: single nucleotide polymorphisms in three interleukin promoters pre-analysed in pooled DNA. Br J Dermatol 2006; 155:1139-44. [PMID: 17107380 DOI: 10.1111/j.1365-2133.2006.07440.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Basal cell carcinoma (BCC) is one of the most common neoplasms in the world. Development of BCC is associated with environmental factors (especially sun exposure) as well as heritable factors. OBJECTIVES To analyse three single nucleotide polymorphisms (SNPs) in the promoter regions of interleukin (IL) genes in genomic DNA from 527 cases of BCC and 530 matched controls and to examine if DNA pooling is a useful method on which to base decisions regarding further SNP analysis. METHODS The SNPs analysed were IL6-597, IL10-1082 and IL1B-511. The SNPs were first analysed from pooled DNA and afterwards from individual samples. The DNA pools resulted from a division of the samples into cases and controls, female and male, and three age groups. In these pools the allele frequencies were estimated by two methods, real-time polymerase chain reaction with allele-specific primers, and quantitative sequencing. RESULTS No significant association was found when the allele frequencies in cases and controls were compared. However, by analysis of the individual genotypes we found SNP IL6-597 G/A to be significantly associated with BCC risk (P =0.007). Hereby the heterozygous genotype 'GA' had a protective effect (odds ratio 0.64, 95% confidence interval 0.49-0.84). No significant association was found for IL10-1082 and IL1B-511. CONCLUSIONS The association of SNP IL6-597 with BCC could be found only by individual genotyping, but would have been missed if only data from the pooling analysis had been known.
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Affiliation(s)
- S Wilkening
- Department of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
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Chowdari KV, Northup A, Pless L, Wood J, Joo YH, Mirnics K, Lewis DA, Levitt PR, Bacanu SA, Nimgaonkar VL. DNA pooling: a comprehensive, multi-stage association analysis of ACSL6 and SIRT5 polymorphisms in schizophrenia. GENES BRAIN AND BEHAVIOR 2006; 6:229-39. [PMID: 16827919 DOI: 10.1111/j.1601-183x.2006.00251.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many candidate gene association studies have evaluated incomplete, unrepresentative sets of single nucleotide polymorphisms (SNPs), producing non-significant results that are difficult to interpret. Using a rapid, efficient strategy designed to investigate all common SNPs, we tested associations between schizophrenia and two positional candidate genes: ACSL6 (Acyl-Coenzyme A synthetase long-chain family member 6) and SIRT5 (silent mating type information regulation 2 homologue 5). We initially evaluated the utility of DNA sequencing traces to estimate SNP allele frequencies in pooled DNA samples. The mean variances for the DNA sequencing estimates were acceptable and were comparable to other published methods (mean variance: 0.0008, range 0-0.0119). Using pooled DNA samples from cases with schizophrenia/schizoaffective disorder (Diagnostic and Statistical Manual of Mental Disorders edition IV criteria) and controls (n=200, each group), we next sequenced all exons, introns and flanking upstream/downstream sequences for ACSL6 and SIRT5. Among 69 identified SNPs, case-control allele frequency comparisons revealed nine suggestive associations (P<0.2). Each of these SNPs was next genotyped in the individual samples composing the pools. A suggestive association with rs 11743803 at ACSL6 remained (allele-wise P=0.02), with diminished evidence in an extended sample (448 cases, 554 controls, P=0.062). In conclusion, we propose a multi-stage method for comprehensive, rapid, efficient and economical genetic association analysis that enables simultaneous SNP detection and allele frequency estimation in large samples. This strategy may be particularly useful for research groups lacking access to high throughput genotyping facilities. Our analyses did not yield convincing evidence for associations of schizophrenia with ACSL6 or SIRT5.
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Affiliation(s)
- K V Chowdari
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
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