Quantitative Whole Slide Assessment of Tumor-Infiltrating CD8-Positive Lymphocytes in ER-Positive Breast Cancer in Relation to Clinical Outcome.

There is a need for a reliable and reproducible quantification of the immune infiltrate within the heterogeneous microenvironment of tumors in order to support therapy selection in oncology. Here we present an automated, modular method for whole-slide image analysis of the spatial distribution of tumor-infiltrating CD8-positive lymphocytes. The method uses a deep learning tissue-type classification algorithm on the hematoxylin eosin (HE) stained tissue section to identify the central tumor (CT) and invasive margin (IM) of the tumor.

Improving DNA capture on microarrays by integrated repeated denaturing.

Hybridization of nucleic acids to microarrays is a crucial step for several biological and biomedical applications. However, the poor efficiency and resulting long incubation times are major drawbacks. In addition to diffusion limitation, back hybridization to complementary strands in solution is shown to be an important cause of the low efficiency.

Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR.

Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that allows quantitative amplification detection at higher multiplexing by the integration of amplification in solution and monitoring via hybridization to a microarray in real-time.

Three-dimensional flow-through protein platform.

We have developed a new protein microarray (ImmunoFlow Protein Platform, IFPP) that utilizes a porous nitrocellulose (NC) membrane with printed spots of capture probes. The sample is pumped actively through the NC membrane, to enhance binding efficiency and introduce stringency. Compared to protein microarrays assayed with the conventional incubation-shaking method the rate of binding is enhanced on the IFPP by at least a factor of 10, so that the total assay time can be reduced drastically without compromising sensitivity.