Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer
Abstract Introduction We investigated a commercially available sequencing panel to study the effect of sequencing depth, variant calling strategy, and targeted sequencing region on identifying tumor‐derived variants in cell‐free bronchoalveolar lavage (cfBAL) DNA compared with plasma cfDNA. Methods...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-09-01
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| Series: | Cancer Medicine |
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| Online Access: | https://doi.org/10.1002/cam4.6380 |
| _version_ | 1797672406394863616 |
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| author | Cassandra L. Sather Pamela Yang Chaomei Zhang Matthew P. Fitzgibbon Michelle Fournier Eric Toloza Amit Tandon Matthew Schabath Sean Yoder Viswam S. Nair |
| author_facet | Cassandra L. Sather Pamela Yang Chaomei Zhang Matthew P. Fitzgibbon Michelle Fournier Eric Toloza Amit Tandon Matthew Schabath Sean Yoder Viswam S. Nair |
| author_sort | Cassandra L. Sather |
| collection | DOAJ |
| description | Abstract Introduction We investigated a commercially available sequencing panel to study the effect of sequencing depth, variant calling strategy, and targeted sequencing region on identifying tumor‐derived variants in cell‐free bronchoalveolar lavage (cfBAL) DNA compared with plasma cfDNA. Methods Sequencing was performed at low or high coverage using two filtering algorithms to identify tumor variants on two panels targeting 77 and 197 genes respectively. Results One hundred and four sequencing files from 40 matched DNA samples of cfBAL, plasma, germline leukocytes, and archival tumor specimens in 10 patients with early‐stage lung cancer were analyzed. By low‐coverage sequencing, tumor‐derived cfBAL variants were detected in 5/10 patients (50%) compared with 2/10 (20%) for plasma. High‐coverage sequencing did not affect the number of tumor‐derived variants detected in either biospecimen type. Accounting for germline mutations eliminated false‐positive plasma calls regardless of coverage (0/10 patients with tumor‐derived variants identified) and increased the number of cfBAL calls (5/10 patients with tumor‐derived variants identified). These results were not affected by the number of targeted genes. |
| first_indexed | 2024-03-11T21:29:35Z |
| format | Article |
| id | doaj.art-1b5dbec6d7904d55a7856255aa1f6a45 |
| institution | Directory Open Access Journal |
| issn | 2045-7634 |
| language | English |
| last_indexed | 2024-03-11T21:29:35Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Medicine |
| spelling | doaj.art-1b5dbec6d7904d55a7856255aa1f6a452023-09-27T11:46:08ZengWileyCancer Medicine2045-76342023-09-011217176321763710.1002/cam4.6380Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancerCassandra L. Sather0Pamela Yang1Chaomei Zhang2Matthew P. Fitzgibbon3Michelle Fournier4Eric Toloza5Amit Tandon6Matthew Schabath7Sean Yoder8Viswam S. Nair9Shared Resources Fred Hutchinson Cancer Center Seattle Washington USAShared Resources Fred Hutchinson Cancer Center Seattle Washington USATissue and Molecular Genomics Cores H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USAShared Resources Fred Hutchinson Cancer Center Seattle Washington USATissue and Molecular Genomics Cores H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USADepartment of Thoracic Oncology H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USADepartment of Thoracic Oncology H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USADepartment of Thoracic Oncology H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USATissue and Molecular Genomics Cores H. Lee Moffitt Cancer Center & Research Institute Tampa Florida USADivision of Pulmonary, Critical Care & Sleep Medicine University of Washington Seattle Washington USAAbstract Introduction We investigated a commercially available sequencing panel to study the effect of sequencing depth, variant calling strategy, and targeted sequencing region on identifying tumor‐derived variants in cell‐free bronchoalveolar lavage (cfBAL) DNA compared with plasma cfDNA. Methods Sequencing was performed at low or high coverage using two filtering algorithms to identify tumor variants on two panels targeting 77 and 197 genes respectively. Results One hundred and four sequencing files from 40 matched DNA samples of cfBAL, plasma, germline leukocytes, and archival tumor specimens in 10 patients with early‐stage lung cancer were analyzed. By low‐coverage sequencing, tumor‐derived cfBAL variants were detected in 5/10 patients (50%) compared with 2/10 (20%) for plasma. High‐coverage sequencing did not affect the number of tumor‐derived variants detected in either biospecimen type. Accounting for germline mutations eliminated false‐positive plasma calls regardless of coverage (0/10 patients with tumor‐derived variants identified) and increased the number of cfBAL calls (5/10 patients with tumor‐derived variants identified). These results were not affected by the number of targeted genes.https://doi.org/10.1002/cam4.6380AVENIO®BALCAPP‐Seqgenomicslung cancer |
| spellingShingle | Cassandra L. Sather Pamela Yang Chaomei Zhang Matthew P. Fitzgibbon Michelle Fournier Eric Toloza Amit Tandon Matthew Schabath Sean Yoder Viswam S. Nair Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer Cancer Medicine AVENIO® BAL CAPP‐Seq genomics lung cancer |
| title | Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| title_full | Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| title_fullStr | Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| title_full_unstemmed | Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| title_short | Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| title_sort | protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer |
| topic | AVENIO® BAL CAPP‐Seq genomics lung cancer |
| url | https://doi.org/10.1002/cam4.6380 |
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