The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

David B Mcdonald - One of the best experts on this subject based on the ideXlab platform.

  • technical advances effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Resources, 2008
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and 'comparative method') in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7-32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.

  • effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Notes, 2007
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and ‘comparative method’) in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7–32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.

Shuanglin Zhang - One of the best experts on this subject based on the ideXlab platform.

  • haplotype sharing transmission disequilibrium tests that allow for Genotyping Errors
    Genetic Epidemiology, 2005
    Co-Authors: Qiuying Sha, Jianping Dong, Renfang Jiang, Huannsheng Chen, Shuanglin Zhang
    Abstract:

    The present study introduces new Haplotype Sharing Transmission/Disequilibrium Tests (HS-TDTs) that allow for random Genotyping Errors. We evaluate the type I error rate and power of the new proposed tests under a variety of scenarios and perform a power comparison among the proposed tests, the HS-TDT and the single-marker TDT. The results indicate that the HS-TDT shows a significant increase in type I error when applied to data in which either Mendelian inconsistent trios are removed or Mendelian inconsistent markers are treated as missing genotypes, and the magnitude of the type I error increases both with an increase in sample size and with an increase in Genotyping error rate. The results also show that a simple strategy, that is, merging each rare haplotype to a most similar common haplotype, can control the type I error inflation for a wide range of Genotyping error rates, and after merging rare haplotypes, the power of the test is very similar to that without merging the rare haplotypes. Therefore, we conclude that a simple strategy may make the HS-TDT robust to Genotyping Errors. Our simulation results also show that this strategy may also be applicable to other haplotype-based TDTs.

Heidi Hansen - One of the best experts on this subject based on the ideXlab platform.

  • technical advances effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Resources, 2008
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and 'comparative method') in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7-32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.

  • effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Notes, 2007
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and ‘comparative method’) in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7–32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.

Peter Shipley - One of the best experts on this subject based on the ideXlab platform.

  • micro checker software for identifying and correcting Genotyping Errors in microsatellite data
    Molecular Ecology Notes, 2004
    Co-Authors: Cock Van Oosterhout, William F. Hutchinson, Derek P. M. Wills, Peter Shipley
    Abstract:

    DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the Genotyping of microsatellites from diploid populations. The program aids identification of Genotyping Errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic Errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.

  • micro checker software for identifying and correcting Genotyping Errors in microsatellite data
    Molecular Ecology Notes, 2004
    Co-Authors: Cock Van Oosterhout, William F. Hutchinson, Derek P. M. Wills, Peter Shipley
    Abstract:

    DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the Genotyping of microsatellites from diploid populations. The program aids identification of Genotyping Errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic Errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.

Merav Bendavid - One of the best experts on this subject based on the ideXlab platform.

  • technical advances effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Resources, 2008
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and 'comparative method') in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7-32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.

  • effects of Genotyping protocols on success and Errors in identifying individual river otters lontra canadensis from their faeces
    Molecular Ecology Notes, 2007
    Co-Authors: Heidi Hansen, Merav Bendavid, David B Mcdonald
    Abstract:

    In noninvasive genetic sampling, when Genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating Genotyping Errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two Genotyping protocols (multiple-tubes and ‘comparative method’) in respect to Genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative Genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because Genotyping Errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7–32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.