The Experts below are selected from a list of 67173 Experts worldwide ranked by ideXlab platform
Doron M. Behar - One of the best experts on this subject based on the ideXlab platform.
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Performance comparison: exome Sequencing as a single test replacing Sanger Sequencing
Molecular Genetics and Genomics, 2021Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:Next generation Sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome Sequencing as a single test replacing Sanger Sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger Sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger Sequencing and 97–100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger Sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger Sequencing or NGS.
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Performance comparison: exome-Sequencing as a single test replacing Sanger-Sequencing
2020Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:ABSTRACT Systematic performance comparing the results of exome-Sequencing as a single test replacing Sanger-Sequencing of targeted gene(s) is still lacking. In this study we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger-Sequencing was completed for all exons, including flanking ±8bp regions. For the 258 genes, NGS mean coverage was >20x for >98% and >91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger-Sequencing and 97%-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger-Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger-Sequencing and NGS. Both methods demonstrated false positive and false negative calls and similar performances. Consequently, high clinical suspicion for a specific diagnosis should override negative results of either Sanger-Sequencing or NGS.
Ancha V Baranova - One of the best experts on this subject based on the ideXlab platform.
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A comparison of BeadChip and WGS genotyping outputs using partial validation by Sanger Sequencing.
BMC genomics, 2020Co-Authors: Kirill A Danilov, Dimitri A Nikogosov, Sergey V Musienko, Ancha V BaranovaAbstract:Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger Sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques. When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger Sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61. We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.
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A comparison of BeadChip and WGS genotyping outputs using partial validation by Sanger Sequencing
BMC Genomics, 2020Co-Authors: Kirill A Danilov, Dimitri A Nikogosov, Sergey V Musienko, Ancha V BaranovaAbstract:Abstract Background Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger Sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques. Results When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger Sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61. Conclusions We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.
Hila Fridman - One of the best experts on this subject based on the ideXlab platform.
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Performance comparison: exome Sequencing as a single test replacing Sanger Sequencing
Molecular Genetics and Genomics, 2021Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:Next generation Sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome Sequencing as a single test replacing Sanger Sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger Sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger Sequencing and 97–100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger Sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger Sequencing or NGS.
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Performance comparison: exome-Sequencing as a single test replacing Sanger-Sequencing
2020Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:ABSTRACT Systematic performance comparing the results of exome-Sequencing as a single test replacing Sanger-Sequencing of targeted gene(s) is still lacking. In this study we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger-Sequencing was completed for all exons, including flanking ±8bp regions. For the 258 genes, NGS mean coverage was >20x for >98% and >91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger-Sequencing and 97%-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger-Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger-Sequencing and NGS. Both methods demonstrated false positive and false negative calls and similar performances. Consequently, high clinical suspicion for a specific diagnosis should override negative results of either Sanger-Sequencing or NGS.
Kirill A Danilov - One of the best experts on this subject based on the ideXlab platform.
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A comparison of BeadChip and WGS genotyping outputs using partial validation by Sanger Sequencing.
BMC genomics, 2020Co-Authors: Kirill A Danilov, Dimitri A Nikogosov, Sergey V Musienko, Ancha V BaranovaAbstract:Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger Sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques. When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger Sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61. We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.
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A comparison of BeadChip and WGS genotyping outputs using partial validation by Sanger Sequencing
BMC Genomics, 2020Co-Authors: Kirill A Danilov, Dimitri A Nikogosov, Sergey V Musienko, Ancha V BaranovaAbstract:Abstract Background Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger Sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques. Results When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger Sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61. Conclusions We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.
Moshe Einhorn - One of the best experts on this subject based on the ideXlab platform.
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Performance comparison: exome Sequencing as a single test replacing Sanger Sequencing
Molecular Genetics and Genomics, 2021Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:Next generation Sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome Sequencing as a single test replacing Sanger Sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger Sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger Sequencing and 97–100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger Sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger Sequencing or NGS.
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Performance comparison: exome-Sequencing as a single test replacing Sanger-Sequencing
2020Co-Authors: Hila Fridman, Concetta Bormans, Moshe Einhorn, Arjan Bormans, Yuval Porat, Luisa Fernanda Sanchez, Brent Manning, Ephrat Levy-lahad, Doron M. BeharAbstract:ABSTRACT Systematic performance comparing the results of exome-Sequencing as a single test replacing Sanger-Sequencing of targeted gene(s) is still lacking. In this study we compared Sanger-Sequencing results of 258 genes to those obtained from next generation Sequencing (NGS) using two exome-Sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different Sequencing methods and DNA sources). Sanger-Sequencing was completed for all exons, including flanking ±8bp regions. For the 258 genes, NGS mean coverage was >20x for >98% and >91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger-Sequencing and 97%-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger-Sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger-Sequencing and NGS. Both methods demonstrated false positive and false negative calls and similar performances. Consequently, high clinical suspicion for a specific diagnosis should override negative results of either Sanger-Sequencing or NGS.
