Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures
Capture-based library preparation for next generation sequencing (NGS) offers a balance between sequencing depth and bioinformatics cost of analysis. Liquid handling automation enhances the reliability of the library preparation process by reducing sample-to-sample variation and substantially enhanc...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-06-01
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| Series: | SLAS Technology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2472630321000169 |
| _version_ | 1828516448574636032 |
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| author | Eric Zimmerman Zuckerman Joseph A. Thompson Amber R. Schneider Michael B. Campion Jennifer J Johns Theodore J. Stier Lisa M. Peterson Amanda M. Ward Joseph H. Blommel Rohan D. Gnanaolivu Kimberly P. Lauer Gopinath Sivasankaran Jagadheshwar Balan Surendra Dasari Yuta Sakai Cherisse A. Marcou Gang Zheng Kevin C. Halling Wei Shen David S. Viswanatha Zhiyv Niu |
| author_facet | Eric Zimmerman Zuckerman Joseph A. Thompson Amber R. Schneider Michael B. Campion Jennifer J Johns Theodore J. Stier Lisa M. Peterson Amanda M. Ward Joseph H. Blommel Rohan D. Gnanaolivu Kimberly P. Lauer Gopinath Sivasankaran Jagadheshwar Balan Surendra Dasari Yuta Sakai Cherisse A. Marcou Gang Zheng Kevin C. Halling Wei Shen David S. Viswanatha Zhiyv Niu |
| author_sort | Eric Zimmerman Zuckerman |
| collection | DOAJ |
| description | Capture-based library preparation for next generation sequencing (NGS) offers a balance between sequencing depth and bioinformatics cost of analysis. Liquid handling automation enhances the reliability of the library preparation process by reducing sample-to-sample variation and substantially enhances throughput, particularly when it can be employed in a 'walk-away' fashion with limited hands-on interaction. This requires complex series of mixing and heating steps like those utilized in capture chemistries to happen on the liquid handler. While developing liquid handling automation for Integrated DNA Technologies (IDT) xGen Exome, Illumina TruSight Oncology 500, and Personal Genome Diagnostics (PGDx) elio Plasma Resolve chemistries on the PerkinElmer Sciclone liquid handler, we found that applying the capture temperatures recommended for manual library preparation results in low yield on automation. To restore the final library yield, we reduced bead binding and/or heated wash temperatures of the Peltier heaters on the liquid handlers by about 10°C. Since this applied across three unique capture-based chemistries, we consider this a generalizable principle of automating capture on the Sciclone. We hypothesize that this is driven by the very different thermodynamic environments represented by a sealed plate on a thermal cycler and a plate with a lid on a Peltier heater. This phenomenon should be considered when automating NGS library preparation on PerkinElmer Sciclone instruments. |
| first_indexed | 2024-12-11T18:26:53Z |
| format | Article |
| id | doaj.art-9e0d66a0738b4e5fb671ba7d2e797b41 |
| institution | Directory Open Access Journal |
| issn | 2472-6303 |
| language | English |
| last_indexed | 2024-12-11T18:26:53Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SLAS Technology |
| spelling | doaj.art-9e0d66a0738b4e5fb671ba7d2e797b412022-12-22T00:55:02ZengElsevierSLAS Technology2472-63032022-06-01273214218Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperaturesEric Zimmerman Zuckerman0Joseph A. Thompson1Amber R. Schneider2Michael B. Campion3Jennifer J Johns4Theodore J. Stier5Lisa M. Peterson6Amanda M. Ward7Joseph H. Blommel8Rohan D. Gnanaolivu9Kimberly P. Lauer10Gopinath Sivasankaran11Jagadheshwar Balan12Surendra Dasari13Yuta Sakai14Cherisse A. Marcou15Gang Zheng16Kevin C. Halling17Wei Shen18David S. Viswanatha19Zhiyv Niu20Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States; Corresponding author at: 210 2nd Street SW, Rochester, MN 55905, United States; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United StatesCapture-based library preparation for next generation sequencing (NGS) offers a balance between sequencing depth and bioinformatics cost of analysis. Liquid handling automation enhances the reliability of the library preparation process by reducing sample-to-sample variation and substantially enhances throughput, particularly when it can be employed in a 'walk-away' fashion with limited hands-on interaction. This requires complex series of mixing and heating steps like those utilized in capture chemistries to happen on the liquid handler. While developing liquid handling automation for Integrated DNA Technologies (IDT) xGen Exome, Illumina TruSight Oncology 500, and Personal Genome Diagnostics (PGDx) elio Plasma Resolve chemistries on the PerkinElmer Sciclone liquid handler, we found that applying the capture temperatures recommended for manual library preparation results in low yield on automation. To restore the final library yield, we reduced bead binding and/or heated wash temperatures of the Peltier heaters on the liquid handlers by about 10°C. Since this applied across three unique capture-based chemistries, we consider this a generalizable principle of automating capture on the Sciclone. We hypothesize that this is driven by the very different thermodynamic environments represented by a sealed plate on a thermal cycler and a plate with a lid on a Peltier heater. This phenomenon should be considered when automating NGS library preparation on PerkinElmer Sciclone instruments.http://www.sciencedirect.com/science/article/pii/S2472630321000169 |
| spellingShingle | Eric Zimmerman Zuckerman Joseph A. Thompson Amber R. Schneider Michael B. Campion Jennifer J Johns Theodore J. Stier Lisa M. Peterson Amanda M. Ward Joseph H. Blommel Rohan D. Gnanaolivu Kimberly P. Lauer Gopinath Sivasankaran Jagadheshwar Balan Surendra Dasari Yuta Sakai Cherisse A. Marcou Gang Zheng Kevin C. Halling Wei Shen David S. Viswanatha Zhiyv Niu Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures SLAS Technology |
| title | Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures |
| title_full | Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures |
| title_fullStr | Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures |
| title_full_unstemmed | Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures |
| title_short | Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures |
| title_sort | automation of hybridization and capture based next generation sequencing library preparation requires reduction of on deck bead binding and heated wash temperatures |
| url | http://www.sciencedirect.com/science/article/pii/S2472630321000169 |
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