Breast cancer PAM50 signature: Correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

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

Pathological response in a triple-negative breast cancer cohort treated with neoadjuvant carboplatin and docetaxel according to Lehmann's refined classification

Purpose: Triple-negative breast cancer (TNBC) requires the identification of reliable predictors of response to neoadjuvant chemotherapy (NACT). For this purpose, we aimed to evaluate the performance of the TNBCtype-4 classifier in a cohort of patients with TNBC treated with neoadjuvant carboplatin and docetaxel (TCb). Methods: Patients with TNBC were accrued in a nonrandomized trial of neoadjuvant carboplatin AUC 6 and docetaxel 75 mg/m2 for six cycles. Response was evaluated in terms of pathologic complete response (pCR, ypT0/is ypN0) and residual cancer burden by Symmans and colleagues. Lehmann's subtyping was performed using the TNBCtype online tool from RNAseq data, and germline sequencing of a panel of seven DNA damage repair genes was conducted. Results: Ninety-four out of the 121 patients enrolled in the trial had RNAseq available. The overall pCR rate was 44.7%. Lehmann subtype distribution was 34.0% BL1, 20.2% BL2, 23.4% M, 14.9% LAR, and 7.4% were classified as ERþ. Response to NACT with TCb was significantly associated with Lehmann subtype (P ¼ 0.027), even in multivariate analysis including tumor size and nodal involvement, with BL1 patients achieving the highest pCR rate (65.6%), followed by BL2 (47.4%), M (36.4%), and LAR (21.4%). BL1 was associated with a significant younger age at diagnosis and higher ki67 values. Among our 10 germline mutation carriers, 30% were BL1, 40% were BL2, and 30% were M. Conclusions: TNBCtype-4 is associated with significantly different pCR rates for the different subtypes, with BL1 and LAR displaying the best and worse responses to NACT, respectively

Thermochronometer record of central Andean Plateau growth, Bolivia (19.5°S)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94850/1/tect1973.pd

Impact evaluation of the technological implementation at goat´s farming systems.

Después de realizar un diagnóstico estático, se definieron los factores limitantes y tecnologías con las cuales intervenir 12 fincas agropecuarias para incrementar su productividad. Por reducir costos, no se establecieron fincas control, por lo que se efectuó una evaluación intermedia del impacto, comparando indices biológicos y sociales entre dos sub-poblaciones. La información se recavó a través de una encuesta realizada en 44 fincas de trece comunidades de Zacatecas, México. Con un muestreo piloto, se estimó la varianza y el tamaño de muestra. Se identificó la distribución de cada variable. Como respuesta a la intervención de tecnología en el subsistema pecuario, se logró una reducción significativa del indice de aborto ( 9. 4%) y una tendencia a reducir el de mortalidad ( 3. 8%) , respecto a productores externos. En la etapa actual del proyecto no se observan indicadores sociales que indiquen impacto sobre el bienestar familiar. La evaluación intermedia substituye al seguimiento en fincas control

Seroprevalence of human Trypanosoma cruzi infection in diferent geografic zones of Chiapas, Mexico Soroprevalência da infecção humana pelo Trypanosoma cruzi em diferentes regiões de Chiapas, México

A serologic survey was carried out in four different geographic zones of Chiapas, Mexico. A total of 1,333 samples were collected from residents of thirteen communities located on the Coast, Central Mountain, Lacandon Forest and a zone called Mesochiapas. One hundred and fifty one seropositive individuals (11.3%) were identified. Human Trypanosoma cruzi infection was influenced by geography. In the Lacandon Forest and Central Mountains there was a higher seroprevalence 32.1 and 13.8% respectively, than on the coast (1.2%). In Mesochiapas there were no seropositive individuals among the 137 persons tested. An active transmission is probably continuing because seropositive cases (13.8%) were detected in children under 10 years of age. The vector recognized on the Coast was Triatoma dimidiata while in the Lacandon Forest it was Rhodnius prolixus.<br>Foi feito um estudo sorológico em quatro zonas geográficas do estado de Chiapas México. Foram colhidas 1333 amostras dos habitantes das 13 comunidades situadas na costa, na região central montanhosa, na floresta lacandona e na região chamada mesochiapas. Cento cinqüenta e uma pessoas (11,3%) foram identificadas como soropositivas. A infecção pelo Trypanosoma cruzi teve a influência da geografia local. Na floresta lacandona nas montanhas centrais, foi encontrada uma prevalência de 32,1 e 13,8% respectivamente, mais que na costa 1,2%. Na zona de mesochiapas não foi encontrada nenhuma pessoa com sorologia positiva entre 137 estudadas. Como encontramos sorologia positiva em crianças menores de 10 anos, pensamos que exista uma transmissão ativa contínua. Na costa foi reconhecido o vetor Triatoma dimidiata e na floresta Lacandona o Rhodnius prolixus

mantisGRID: a grid platform for DICOM medical images management in Colombia and Latin America.

This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records