Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton
Library preparation for whole-exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missin...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00856/full |
| _version_ | 1818901192402534400 |
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| author | Piyush Gampawar Yasaman Saba Ulrike Werner Reinhold Schmidt Bertram Müller-Myhsok Bertram Müller-Myhsok Bertram Müller-Myhsok Helena Schmidt |
| author_facet | Piyush Gampawar Yasaman Saba Ulrike Werner Reinhold Schmidt Bertram Müller-Myhsok Bertram Müller-Myhsok Bertram Müller-Myhsok Helena Schmidt |
| author_sort | Piyush Gampawar |
| collection | DOAJ |
| description | Library preparation for whole-exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Here, we systematically evaluate the performance of AmpliSeq and SureSelect and present an improved variant calling pipeline. We used 12 in-house DNA samples with genome-wide and exome microarray data and a commercially available reference DNA (NA12878) for evaluation. Both methods had a high concordance (>97%) with microarray genotypes and, when validating against NA12878, a sensitivity and positive predictive values of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in positive predictive value of 97%. This improvement is highly relevant in research as well as clinical setting. |
| first_indexed | 2024-12-19T20:15:51Z |
| format | Article |
| id | doaj.art-8f30f84611344f23beef0b9dea364f7c |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T20:15:51Z |
| publishDate | 2019-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-8f30f84611344f23beef0b9dea364f7c2022-12-21T20:07:10ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-09-011010.3389/fgene.2019.00856477863Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion ProtonPiyush Gampawar0Yasaman Saba1Ulrike Werner2Reinhold Schmidt3Bertram Müller-Myhsok4Bertram Müller-Myhsok5Bertram Müller-Myhsok6Helena Schmidt7Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, AustriaResearch Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, AustriaResearch Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, AustriaDepartment of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz, AustriaMax Planck Institute of Psychiatry, Munich, GermanyMunich Cluster for Systems Neurology (SyNergy), Munich, GermanyInstitute of Translational Medicine, University of Liverpool, Liverpool, United KingdomResearch Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, AustriaLibrary preparation for whole-exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Here, we systematically evaluate the performance of AmpliSeq and SureSelect and present an improved variant calling pipeline. We used 12 in-house DNA samples with genome-wide and exome microarray data and a commercially available reference DNA (NA12878) for evaluation. Both methods had a high concordance (>97%) with microarray genotypes and, when validating against NA12878, a sensitivity and positive predictive values of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in positive predictive value of 97%. This improvement is highly relevant in research as well as clinical setting.https://www.frontiersin.org/article/10.3389/fgene.2019.00856/fullexome sequencingion proton sequencerAmpliSeqSureSelectlibrary preparationvalidation |
| spellingShingle | Piyush Gampawar Yasaman Saba Ulrike Werner Reinhold Schmidt Bertram Müller-Myhsok Bertram Müller-Myhsok Bertram Müller-Myhsok Helena Schmidt Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton Frontiers in Genetics exome sequencing ion proton sequencer AmpliSeq SureSelect library preparation validation |
| title | Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton |
| title_full | Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton |
| title_fullStr | Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton |
| title_full_unstemmed | Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton |
| title_short | Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton |
| title_sort | evaluation of the performance of ampliseq and sureselect exome sequencing libraries for ion proton |
| topic | exome sequencing ion proton sequencer AmpliSeq SureSelect library preparation validation |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00856/full |
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