The Experts below are selected from a list of 297 Experts worldwide ranked by ideXlab platform

S. Janssens - One of the best experts on this subject based on the ideXlab platform.

  • How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    Background PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results We introduce the genome coverage parameter to appropriately estimate F_ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

  • how to study runs of homozygosity using plink a guide for analyzing medium density snp data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    BACKGROUND: PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. RESULTS: We introduce the genome coverage parameter to appropriately estimate FROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK's minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. CONCLUSIONS: In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

R. Meyermans - One of the best experts on this subject based on the ideXlab platform.

  • How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    Background PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results We introduce the genome coverage parameter to appropriately estimate F_ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

  • how to study runs of homozygosity using plink a guide for analyzing medium density snp data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    BACKGROUND: PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. RESULTS: We introduce the genome coverage parameter to appropriately estimate FROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK's minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. CONCLUSIONS: In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

W. Gorssen - One of the best experts on this subject based on the ideXlab platform.

  • How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    Background PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results We introduce the genome coverage parameter to appropriately estimate F_ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

  • how to study runs of homozygosity using plink a guide for analyzing medium density snp data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    BACKGROUND: PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. RESULTS: We introduce the genome coverage parameter to appropriately estimate FROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK's minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. CONCLUSIONS: In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

N. Buys - One of the best experts on this subject based on the ideXlab platform.

  • How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    Background PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results We introduce the genome coverage parameter to appropriately estimate F_ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

  • how to study runs of homozygosity using plink a guide for analyzing medium density snp data in livestock and Pet Species
    BMC Genomics, 2020
    Co-Authors: R. Meyermans, W. Gorssen, N. Buys, S. Janssens
    Abstract:

    BACKGROUND: PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and Pet Species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. RESULTS: We introduce the genome coverage parameter to appropriately estimate FROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK's minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. CONCLUSIONS: In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

Michael P Gilmore - One of the best experts on this subject based on the ideXlab platform.

  • The ethnoprimatology of the Maijuna of the Peruvian Amazon and implications for primate conservation
    Journal of Ethnobiology and Ethnomedicine, 2018
    Co-Authors: Carla Mere Roncal, Mark Bowler, Michael P Gilmore
    Abstract:

    Background In Amazonia, primates are not only an important food source but they also hold significant cultural and symbolic value for many indigenous groups. We document the relationship between primates and community members of the Maijuna indigenous community of Sucusari in the Peruvian Amazon and describe how ethnoprimatological studies provide a better understanding of the significance of primates in people’s lives. Additionally, we explore how ethnoprimatological studies can help inform and enhance primate conservation initiatives. Methods Semi-structured interviews were conducted with 50 residents of the community of Sucusari to assess the classification, cultural significance and traditional uses, beliefs, ceremonies and stories of primates within the Sucusari River basin. Results Primates play an important role in the lives of individuals in the Sucusari community. They are distinguished by their arboreal lifestyle, and among the 11 Species reported in the area, seven ( Lagothrix lagotricha , Alouatta seniculus , Pithecia monachus , Callicebus spp., Saimiri sciureus , Leontocebus nigricollis ) are highly recognized and culturally salient. Primates are used as food, medicine, Pets, domestic tools and in the production of handicrafts. They are primarily hunted for local consumption, with larger primates such as  L . lagotricha being preferred. Lagothrix lagotricha was also the most commonly reported Pet Species and the only observed Pet primate in the community during surveys. Maijuna traditional beliefs include ancestral dietary taboos for A . seniculus , which are referred to as sorcerer monkeys, but this taboo is no longer fully adhered to. Maijuna traditional stories associated with primates describe the origin of primates found in Sucusari. Conclusion Primates are embedded in the intricate sociocultural system of the community of Sucusari. Better understanding the relationship between primates and people can help to focus conservation efforts on primate Species of particularly high sociocultural importance as well as ecological value, such as L. lagotricha . We highly recommend the inclusion of ethnoprimatological studies into primate conservation initiatives to accomplish more effective conservation planning, ultimately integrating the goals of biodiversity conservation with the cultural and economic needs of indigenous and local communities.

  • The ethnoprimatology of the Maijuna of the Peruvian Amazon and implications for primate conservation
    Journal of Ethnobiology and Ethnomedicine, 2018
    Co-Authors: Carla Mere Roncal, Mark Bowler, Michael P Gilmore
    Abstract:

    In Amazonia, primates are not only an important food source but they also hold significant cultural and symbolic value for many indigenous groups. We document the relationship between primates and community members of the Maijuna indigenous community of Sucusari in the Peruvian Amazon and describe how ethnoprimatological studies provide a better understanding of the significance of primates in people’s lives. Additionally, we explore how ethnoprimatological studies can help inform and enhance primate conservation initiatives. Semi-structured interviews were conducted with 50 residents of the community of Sucusari to assess the classification, cultural significance and traditional uses, beliefs, ceremonies and stories of primates within the Sucusari River basin. Primates play an important role in the lives of individuals in the Sucusari community. They are distinguished by their arboreal lifestyle, and among the 11 Species reported in the area, seven (Lagothrix lagotricha, Alouatta seniculus, Pithecia monachus, Callicebus spp., Saimiri sciureus, Leontocebus nigricollis) are highly recognized and culturally salient. Primates are used as food, medicine, Pets, domestic tools and in the production of handicrafts. They are primarily hunted for local consumption, with larger primates such as L. lagotricha being preferred. Lagothrix lagotricha was also the most commonly reported Pet Species and the only observed Pet primate in the community during surveys. Maijuna traditional beliefs include ancestral dietary taboos for A. seniculus, which are referred to as sorcerer monkeys, but this taboo is no longer fully adhered to. Maijuna traditional stories associated with primates describe the origin of primates found in Sucusari. Primates are embedded in the intricate sociocultural system of the community of Sucusari. Better understanding the relationship between primates and people can help to focus conservation efforts on primate Species of particularly high sociocultural importance as well as ecological value, such as L. lagotricha. We highly recommend the inclusion of ethnoprimatological studies into primate conservation initiatives to accomplish more effective conservation planning, ultimately integrating the goals of biodiversity conservation with the cultural and economic needs of indigenous and local communities.