Search results for " microarrays"
showing 6 items of 16 documents
The Role of Immunohistochemistry in Rhabdomyosarcoma Diagnosis Using Tissue Microarray Technology and a Xenograft Model
2015
Rhabdomyosarcomas (RMS) may resemble other non-myogenic sarcomas and malignant rhabdoid tumor (MRT). Alveolar rhabdomyosarcoma (ARMS) often harbors a typical translocation, but embryonal rhabdomyosarcoma (ERMS) lacks any specific rearrangement. Histopathology is not always sufficient for an unequivocal diagnosis, necessitating ancillary studies, including immunohistochemistry (IHC). Sixteen genetically tested RMS and two MRT were xenografted and followed in successive passages. Tissue microarrays were constructed including samples from original and xenograft tumors. Desmin, myogenin, CK, EMA, INI1, LSD1, AP2 beta, fibrillin-2, HMGA2, nestin, and SIRT1 were tested using immunohistochemical s…
Imbibition of Femtoliter-Scale DNA-Rich Aqueous Droplets into Porous Nylon Substrates by Molecular Printing
2019
This work presents the first reported imbibition mechanism of femtoliter (fL)-scale droplets produced by microchannel cantilever spotting (μCS) of DNA molecular inks into porous substrates (hydrophilic nylon). Differently from macroscopic or picoliter droplets, the downscaling to the fL-size leads to an imbibition process controlled by the subtle interplay of evaporation, spreading, viscosity, and capillarity, with gravitational forces being quasi-negligible. In particular, the minimization of droplet evaporation, surface tension, and viscosity allows for a reproducible droplet imbibition process. The dwell time on the nylon surface permits further tuning of the droplet lateral size, in acc…
Abstract P2-05-04: Gene expression associated with poor prognosis of young TNBC patients
2015
Abstract Background: Among TNBC patients those of very young age (<40 years) display a significantly worse prognosis (Liedtke et al. 2013 Breast Cancer Res Treat). We verified this result in 1161 TNBC samples with full Affymetrix gene expression data of which 845 patients had both detailed age and follow up information. Materials and Methods: We split the full sample set into a finding cohort of 394 TNBC and a validation cohort of 767 TNBC encompassing 309 and 536 samples, respectively, with both age and follow up data. We then used significance analysis of microarrays (SAM) in the finding cohort to look for genes whose expression is associated with young age (<40 years). Iden…
Models of Biobanking and Tissue Preservation: RNA Quality in Archival Samples in Pathology Laboratories and “In Vivo Biobanking” by Tumor Xenografts …
2011
Tissue banks represent essential resources and platforms for biomedical research serving basic, translational, and clinical research projects. In this article, we describe 2 models of biobanking and tissue preservation with different approaches and aims. Archive tissue biobanking is described here as a resource of residual pathology tissues for translational research, which represents the huge clinical heterogeneity. In this context, managing of tissues and RNA quality in archive tissue are discussed. The other model of tissue biobanking is referred to as xenograft tissue banking, which represents an alternative method for obtaining large amounts of tissue, over an indefinite period, in so …
Control of dataset bias in combined Affymetrix cohorts of triple negative breast cancer
2014
AbstractHeterogenous subtypes of breast cancer need to be analyzed separately. Pooling of datasets can provide reasonable sample sizes but dataset bias is an important concern. We assembled a combined dataset of 579 Affymetrix microarrays from triple negative breast cancer (TNBC) in Gene Expression Omnibus (GEO) series GSE31519. We developed a method for selecting comparable datasets and to control for the amount of dataset bias of individual probesets.
Gene Expression Profile of Chronic Myeloid Leukemia Innately Resistant to Imatinib
2007
Background. Most chronic myeloid leukemia patients who receive imatinib as first line-terapy will obtain, after 12 months treatment, complete cytogenetic and molecular response . However several cases will not achieve molecular response, but their innate mechanism(s) of resistance remain poorly understood. We tried to explore the molecular events involved in innate resistance in CML. Study design. Five patients who were molecular “non responder” and seven “major” responder were investigated by using the expression profile of a set of 380 genes. Multiple testing procedure (MTP), Significance Analysis of Microarrays (SAM), Empirical Bayes Analysis of Microarrays (EBAM), False Discovery Rate (…