دورية أكاديمية
Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series
| العنوان: | Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series |
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| المؤلفون: | Picornell, A. C., Echevarria, I., Álvarez, E., López-Tarruella, S., Jerez, Y., Hoadley, K., Parker, J. S., Monte-Millán, M. del, Ramos-Medina, R., Gayarre, Javier, Ocaña, I., Cebollero, M., Massarrah, T., Moreno, Fernando, García‐Sáenz, José Ángel, Gómez Moreno, H., Ballesteros, A., Ruiz-Borrego, Manuel, Perou, C. M., Martín, M. |
| المساهمون: | Ministerio de Economía y Competitividad (España), European Commission, Instituto de Salud Carlos III |
| بيانات النشر: | BioMed Central |
| سنة النشر: | 2019 |
| المجموعة: | Digital.CSIC (Consejo Superior de Investigaciones Científicas / Spanish National Research Council) |
| مصطلحات موضوعية: | PAM50, Breast cancer, Triple negative breast cancer, RNA-Seq, Multiplexed gene expression |
| الوصف: | [Background]: Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular. ; [Results]: The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80. ; [Conclusions]: In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method. ; M.M was supported by two research grants from Ministry of Economy and ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 1471-2164 |
| العلاقة: | Publisher's version; https://doi.org/10.1186/s12864-019-5849-0Test; Sí; BMC Genomics 20: 452 (2019); http://hdl.handle.net/10261/212408Test; http://dx.doi.org/10.13039/501100000780Test; http://dx.doi.org/10.13039/501100004587Test; http://dx.doi.org/10.13039/501100003329Test |
| DOI: | 10.1186/s12864-019-5849-0 |
| DOI: | 10.13039/501100000780 |
| DOI: | 10.13039/501100004587 |
| DOI: | 10.13039/501100003329 |
| الإتاحة: | https://doi.org/10.1186/s12864-019-5849-0Test https://doi.org/10.13039/501100000780Test https://doi.org/10.13039/501100004587Test https://doi.org/10.13039/501100003329Test http://hdl.handle.net/10261/212408Test |
| حقوق: | open |
| رقم الانضمام: | edsbas.BDC00 |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 14712164 |
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| DOI: | 10.1186/s12864-019-5849-0 |