المؤلفون: A. C. Picornell, I. Echavarria, E. Alvarez, S. López-Tarruella, Y. Jerez, K. Hoadley, J. S. Parker, M. del Monte-Millán, R. Ramos-Medina, J. Gayarre, I. Ocaña, M. Cebollero, T. Massarrah, F. Moreno, J. A. García Saenz, H. Gómez Moreno, A. Ballesteros, M. Ruiz Borrego, C. M. Perou, M. Martin

المصدر: BMC Genomics, Vol 20, Iss 1, Pp 1-11 (2019)

مصطلحات موضوعية: PAM50, Breast cancer, Triple negative breast cancer, RNA-Seq, Multiplexed gene expression, Biotechnology, TP248.13-248.65, Genetics, QH426-470

الوصف: Abstract 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.

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s12864-019-5849-0Test; https://doaj.org/toc/1471-2164Test

الوصول الحر: https://doaj.org/article/a4c86a212a354eefa324dd3785aa8597Test

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

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 ...

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

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

المؤلفون: Picornell, A.C., Echavarria, I., Alvarez, E., López-Tarruella, S., Jerez, Y., Hoadley, K., Parker, J.S., Del Monte-Millán, M., Ramos-Medina, R., Gayarre, J., Ocaña, I., Cebollero, M., Massarrah, T., Moreno, F., García Saenz, J.A., Gómez Moreno, H., Ballesteros, A., Ruiz Borrego, M., Perou, C.M., Martin, M.

المصدر: BMC Genomics, 20(1)

مصطلحات موضوعية: Breast cancer, RNA-Seq, PAM50, Multiplexed gene expression, Triple negative breast cancer

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.

العلاقة: https://doi.org/10.17615/473k-rz18Test; https://cdr.lib.unc.edu/downloads/w3763g266?file=thumbnailTest; https://cdr.lib.unc.edu/downloads/w3763g266Test

الإتاحة: https://doi.org/10.17615/473k-rz18Test
https://cdr.lib.unc.edu/downloads/w3763g266?file=thumbnailTest
https://cdr.lib.unc.edu/downloads/w3763g266Test

المؤلفون: Isabel Echavarria, Ana Isabel Ballesteros, J. A. Garcia Saenz, Katherine A. Hoadley, Rocío Ramos-Medina, Yolanda Jerez, Antoni Picornell, Javier Gayarre, M. del Monte-Millán, Enrique Alvarez, M. Ruiz Borrego, M. Martin, Joel S. Parker, Sara López-Tarruella, Inmaculada Ocaña, Tatiana Massarrah, Fernando Salvador Moreno, Charles M. Perou, Maria Cebollero, H. Gomez Moreno

المساهمون: Ministerio de Economía y Competitividad (España), European Commission, Instituto de Salud Carlos III, Instituto de Investigación Sanitaria Gregorio Marañón

المصدر: BMC Genomics, Vol 20, Iss 1, Pp 1-11 (2019)
Digital.CSIC. Repositorio Institucional del CSIC
instname
BMC Genomics
Repositorio Institucional de la Consejería de Sanidad de la Comunidad de Madrid
Consejería de Sanidad de la Comunidad de Madrid

مصطلحات موضوعية: 0106 biological sciences, Oncology, Male, medicine.medical_specialty, lcsh:QH426-470, Multiplexed gene expression, Concordance, lcsh:Biotechnology, RNA-Seq, Triple Negative Breast Neoplasms, Biomarkers, Tumor / genetics, Biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, Breast cancer, Internal medicine, lcsh:TP248.13-248.65, NanoString, Genetics, medicine, Biomarkers, Tumor, Humans, Triple negative breast cancer, PAM50, Prospective Studies, Gene, Triple-negative breast cancer, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, medicine.disease, Prognosis, 3. Good health, Gene Expression Regulation, Neoplastic, lcsh:Genetics, Gene Expression Profiling / methods, High-Throughput Nucleotide Sequencing / methods, Female, RNA extraction, DNA microarray, Neoplasm Recurrence, Local, 010606 plant biology & botany, Biotechnology, Research Article, Follow-Up Studies

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 Competitiveness ISCIII-FIS grants (PI 12/02684): “Predictores genómicos de respuesta a la quimioterapia neoadyuvante con docetaxel-carboplatino en pacientes con cáncer de mama triple negativo”/“Genomic predictors of response to neoadjuvant chemotherapy with docetaxel-carboplatin in patients with triple negative breast cancer”; and (PI 15/00117): “Cáncer de mama triple negative: Predicción de respuesta a docetaxel-carboplatino neoadyuvante mediante caracterización de TILs y firmas inmunes basadas en secuenciación masiva de RNA”/” Triple negative breast cancer: Prediction of response to neoadjuvant docetaxel-carboplatin by characterization of TILs and immune signatures based on massive RNA sequencing”. C.M.P was supported by funds from the NCI Breast SPORE program (P50-CA58223).

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::15af69da654ee268964110134d380685Test
https://hdl.handle.net/10668/14068Test

المؤلفون: Ippolito,Danielle L, AbdulHameed,Mohamed D, Tawa,Gregory J, Baer,Christine E, Permenter,Matthew G, McDyre,Bonna C, Dennis,William E, Boyle,Molly H, Hobbs,Cheryl A, Streicker,Michael A, Snowden,Bobbi S, Lewis,John A, Wallqvist,Anders, Stallings,Jonathan D

المساهمون: Army Center for Environmental Health Research Fort Detrick United States

مصطلحات موضوعية: gene expression, LIVER DISEASES, fibrosis, Histopathology, TOXIC AGENTS, computation science, rats, MASS SPECTROMETRY, data mining, BIOMEDICAL INFORMATION SYSTEMS, DrugMatrix, gene microarray data, multiplexed-gene expression assays, toxic liver injury, transcriptomics, biomarkers

الوصف: Toxic industrial chemicals induce liver injury, which is difficult to diagnose without invasive procedures. Identifying indicators of end organ injury can complement exposure-based assays and improve predictive power. A multiplexed approach was used to experimentally evaluate a panel of 67 genes predicted to be associated with the fibrosis pathology by computationally mining Drug Matrix, a publicly available repository of gene microarray data. Five-day oral gavage studies in male Sprague Dawley rats dosed with varying concentrations of 3 fibrogenic compounds (allyl alcohol, carbon tetrachloride, and 4,40-methylenedianiline) and 2 nonfibrogenic compounds (bromobenzene and dexamethasone) were conducted. Fibrosis was definitively diagnosed by histopathology. The 67-plex gene panel accurately diagnosed fibrosis in both microarray and multiplexed-gene expression assays. Necrosis and inflammatory infiltration were comorbid with fibrosis. ANOVA with contrasts identified that 51 of the 67 predicted genes were significantly associated with the fibrosis phenotype,with 24 of these specific to fibrosis alone. The protein product of the gene most strongly correlated with the fibrosis phenotype PCOLCE (Procollagen C-Endopeptidase Enhancer) was dose-dependently elevated in plasma from animals administered fibrogenic chemicals (P.05). Semiquantitative global mass spectrometry analysis of the plasma identified an additional 5 protein products of the gene panel which increased after fibrogenic toxicant administration: fibronectin, ceruloplasmin, vitronectin, insulin-like growth factor binding protein, and a2-macroglobulin. These results support the data mining approach for identifying gene and/or protein panels for assessing liver injury and may suggest bridging biomarkers for molecular mediators linked to histopathology. ; Toxicological Sciences , 149, 1, 01 Jan 0001, 01 Jan 0001

وصف الملف: text/html

العلاقة: http://www.dtic.mil/docs/citations/AD1003890Test

الإتاحة: http://www.dtic.mil/docs/citations/AD1003890Test
http://oai.dtic.mil/oai/oai?&verb=getRecord&metadataPrefix=html&identifier=AD1003890Test

مستخلص: [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.

مصطلحات الفهرس: PAM50, Breast cancer, Triple negative breast cancer, RNA-Seq, Multiplexed gene expression, artículo

URL: http://hdl.handle.net/10261/212408Test
https://doi.org/10.1186/s12864-019-5849-0Test
Publisher's version
https://doi.org/10.1186/s12864-019-5849-0Test
Sí