Academic Journal
Neoantigen prediction in human breast cancer using RNA sequencing data
| العنوان: | Neoantigen prediction in human breast cancer using RNA sequencing data |
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| المؤلفون: | Hashimoto, Sachie, Noguchi, Emiko, Bando, Hiroko, Miyadera, Hiroko, Morii, Wataru, Nakamura, Takako, Hara, Hisato |
| المساهمون: | Japan Society for the Promotion of Science |
| المصدر: | Cancer Science ; volume 112, issue 1, page 465-475 ; ISSN 1347-9032 1349-7006 |
| بيانات النشر: | Wiley |
| سنة النشر: | 2020 |
| المجموعة: | Wiley Online Library (Open Access Articles via Crossref) |
| الوصف: | Neoantigens have attracted attention as biomarkers or therapeutic targets. However, accurate prediction of neoantigens is still challenging, especially in terms of its accuracy and cost. Variant detection using RNA sequencing (RNA‐seq) data has been reported to be a low‐accuracy but cost‐effective tool, but the feasibility of RNA‐seq data for neoantigen prediction has not been fully examined. In the present study, we used whole‐exome sequencing (WES) and RNA‐seq data of tumor and matched normal samples from six breast cancer patients to evaluate the utility of RNA‐seq data instead of WES data in variant calling to detect neoantigen candidates. Somatic variants were called in three protocols using: (i) tumor and normal WES data (DNA method, Dm); (ii) tumor and normal RNA‐seq data (RNA method, Rm); and (iii) combination of tumor RNA‐seq and normal WES data (Combination method, Cm). We found that the Rm had both high false‐positive and high false‐negative rates because this method depended greatly on the expression status of normal transcripts. When we compared the results of Dm with those of Cm, only 14% of the neoantigen candidates detected in Dm were identified in Cm, but the majority of the missed candidates lacked coverage or variant allele reads in the tumor RNA. In contrast, about 70% of the neoepitope candidates with higher expression and rich mutant transcripts could be detected in Cm. Our results showed that Cm could be an efficient and a cost‐effective approach to predict highly expressed neoantigens in tumor samples. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1111/cas.14720 |
| الاتاحة: | http://dx.doi.org/10.1111/cas.14720 https://onlinelibrary.wiley.com/doi/pdf/10.1111/cas.14720 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/cas.14720 |
| Rights: | http://creativecommons.org/licenses/by-nc/4.0/ |
| رقم الانضمام: | edsbas.2C9A84D2 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1111/cas.14720 |
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