The Experts below are selected from a list of 41520 Experts worldwide ranked by ideXlab platform
Michael J Hurley - One of the best experts on this subject based on the ideXlab platform.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3′ position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3′ LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3′ LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3′ LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3′ LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications. Hum Mutat 22:79–85, 2003.© 2003 Wiley-Liss, Inc.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3' position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3' LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3' LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3' LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3' LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications.
David Latorra - One of the best experts on this subject based on the ideXlab platform.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3′ position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3′ LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3′ LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3′ LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3′ LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications. Hum Mutat 22:79–85, 2003.© 2003 Wiley-Liss, Inc.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3' position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3' LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3' LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3' LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3' LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications.
James E Bron - One of the best experts on this subject based on the ideXlab platform.
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development and validation of a high density SNP Genotyping array for atlantic salmon salmo salar
BMC Genomics, 2014Co-Authors: Ross D Houston, John B Taggart, Timothe Cezard, Michael Bekaert, Natalie R Lowe, Alison Downing, Richard Talbot, Stephen Bishop, Alan Archibald, James E BronAbstract:Background: Dense single nucleotide polymorphism (SNP) Genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP Genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results: SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genomewide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions: This manuscript describes the first high-density SNP Genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
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development and validation of a high density SNP Genotyping array for atlantic salmon salmo salar
BMC Genomics, 2014Co-Authors: Ross D Houston, John B Taggart, Timothe Cezard, Michael Bekaert, Natalie R Lowe, Alison Downing, Richard Talbot, Stephen Bishop, Alan Archibald, James E BronAbstract:Dense single nucleotide polymorphism (SNP) Genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP Genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP Genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
Göran Spong - One of the best experts on this subject based on the ideXlab platform.
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Moving far, staying close: red fox dispersal patterns revealed by SNP Genotyping
Conservation Genetics, 2021Co-Authors: Zea Walton, Mari Hagenlund, Kjartan Østbye, Gustaf Samelius, Morten Odden, Anita Norman, Tomas Willebrand, Göran SpongAbstract:The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP Genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.
Andreas Wolter - One of the best experts on this subject based on the ideXlab platform.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3′ position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3′ LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3′ LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3′ LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3′ LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications. Hum Mutat 22:79–85, 2003.© 2003 Wiley-Liss, Inc.
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enhanced allele specific pcr discrimination in SNP Genotyping using 3 locked nucleic acid lna primers
Human Mutation, 2003Co-Authors: David Latorra, Krista Campbell, Andreas Wolter, Michael J HurleyAbstract:The specificity and reliability of locked nucleic acid (LNA) substitution at the 3' position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3' LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3' LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3' LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3' LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP Genotyping applications.
