Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research
Analysis of the T-cell receptor (TCR) repertoire is essential to characterize the extensive collections of T-cell populations with recognizing antigens in cancer research, and whole transcriptome sequencing (WTS) and immune repertoire sequencing (IR-seq) are commonly used for this measure. To date,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-12-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/12/12/3693 |
| _version_ | 1797545270332882944 |
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| author | Sungyoung Lee Seulki Song Sung-Soo Yoon Youngil Koh Hongseok Yun |
| author_facet | Sungyoung Lee Seulki Song Sung-Soo Yoon Youngil Koh Hongseok Yun |
| author_sort | Sungyoung Lee |
| collection | DOAJ |
| description | Analysis of the T-cell receptor (TCR) repertoire is essential to characterize the extensive collections of T-cell populations with recognizing antigens in cancer research, and whole transcriptome sequencing (WTS) and immune repertoire sequencing (IR-seq) are commonly used for this measure. To date, no standard read filtering method for IR measurement has been presented. We assessed the diversity of the TCR repertoire results from the paired WTS and IR-seq data of 31 multiple myeloma (MM) patients. To invent an adequate read filtering strategy for IR analysis, we conducted comparisons with WTS results. First, our analyses for determining an optimal threshold for selecting clonotypes showed that the clonotypes supported by a single read largely affected the shared clonotypes and manifested distinct patterns of mapping qualities, unlike clonotypes with multiple reads. Second, although IR-seq could reflect a wider TCR region with a higher capture rate than WTS, an adequate comparison with the removal of unwanted bias from potential sequencing errors was possible only after applying our read filtering strategy. As a result, we suggest that TCR repertoire analysis be carried out through IR-seq to produce reliable and accurate results, along with the removal of single-read clonotypes, to conduct immune research in cancer using high-throughput sequencing. |
| first_indexed | 2024-03-10T14:13:03Z |
| format | Article |
| id | doaj.art-c3d0509b76b54fc188883b3c37e96b8b |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T14:13:03Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-c3d0509b76b54fc188883b3c37e96b8b2023-11-21T00:01:50ZengMDPI AGCancers2072-66942020-12-011212369310.3390/cancers12123693Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu ResearchSungyoung Lee0Seulki Song1Sung-Soo Yoon2Youngil Koh3Hongseok Yun4Center for Precision Medicine, Seoul National University Hospital, Seoul 03082, KoreaCancer Research Institute, Seoul National University College of Medicine, Seoul 03080, KoreaCancer Research Institute, Seoul National University College of Medicine, Seoul 03080, KoreaCancer Research Institute, Seoul National University College of Medicine, Seoul 03080, KoreaCenter for Precision Medicine, Seoul National University Hospital, Seoul 03082, KoreaAnalysis of the T-cell receptor (TCR) repertoire is essential to characterize the extensive collections of T-cell populations with recognizing antigens in cancer research, and whole transcriptome sequencing (WTS) and immune repertoire sequencing (IR-seq) are commonly used for this measure. To date, no standard read filtering method for IR measurement has been presented. We assessed the diversity of the TCR repertoire results from the paired WTS and IR-seq data of 31 multiple myeloma (MM) patients. To invent an adequate read filtering strategy for IR analysis, we conducted comparisons with WTS results. First, our analyses for determining an optimal threshold for selecting clonotypes showed that the clonotypes supported by a single read largely affected the shared clonotypes and manifested distinct patterns of mapping qualities, unlike clonotypes with multiple reads. Second, although IR-seq could reflect a wider TCR region with a higher capture rate than WTS, an adequate comparison with the removal of unwanted bias from potential sequencing errors was possible only after applying our read filtering strategy. As a result, we suggest that TCR repertoire analysis be carried out through IR-seq to produce reliable and accurate results, along with the removal of single-read clonotypes, to conduct immune research in cancer using high-throughput sequencing.https://www.mdpi.com/2072-6694/12/12/3693T-cell receptorimmune repertoireimmune repertoire sequencingwhole transcriptome sequencingclonotype |
| spellingShingle | Sungyoung Lee Seulki Song Sung-Soo Yoon Youngil Koh Hongseok Yun Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research Cancers T-cell receptor immune repertoire immune repertoire sequencing whole transcriptome sequencing clonotype |
| title | Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research |
| title_full | Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research |
| title_fullStr | Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research |
| title_full_unstemmed | Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research |
| title_short | Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research |
| title_sort | proper read filtering method to adequately analyze whole transcriptome sequencing and rna based immune repertoire sequencing data for tumor milieu research |
| topic | T-cell receptor immune repertoire immune repertoire sequencing whole transcriptome sequencing clonotype |
| url | https://www.mdpi.com/2072-6694/12/12/3693 |
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