Statistical Methods for Tissue Array Images - Algorithmic Scoring and Co-training

Big Data to Knowledge: Application of Machine Learning to Predictive Modeling of Therapeutic Response in Cancer

Background

In recent years, the availability of high throughput technologies, establishment of large molecular patient data repositories, and advancement in computing power and storage have allowed elucidation of complex mechanisms implicated in therapeutic response in cancer patients. The breadth and depth of such data, alongside experimental noise and missing values, requires a sophisticated human-machine interaction that would allow effective learning from complex data and accurate forecasting of future outcomes, ideally embedded in the core of machine learning design.

Objective

In this review, we will discuss machine learning techniques utilized for modeling of treatment response in cancer, including Random Forests, support vector machines, neural networks, and linear and logistic regression. We will overview their mathematical foundations and discuss their limitations and alternative approaches in light of their application to therapeutic response modeling in cancer.

Conclusion

We hypothesize that the increase in the number of patient profiles and potential temporal monitoring of patient data will define even more complex techniques, such as deep learning and causal analysis, as central players in therapeutic response modeling.

Incorporating Deep Features in the Analysis of Tissue Microarray Images

Tissue microarray (TMA) images have been used increasingly often in cancer studies and the validation of biomarkers. TACOMA-a cutting-edge automatic scoring algorithm for TMA images-is comparable to pathologists in terms of accuracy and repeatability. Here we consider how this algorithm may be further improved. Inspired by the recent success of deep learning, we propose to incorporate representations learnable through computation. We explore representations of a group nature through unsupervised learning, e.g., hierarchical clustering and recursive space partition. Information carried by clustering or spatial partitioning may be more concrete than the labels when the data are heterogeneous, or could help when the labels are noisy. The use of such information could be viewed as regularization in model fitting. It is motivated by major challenges in TMA image scoring-heterogeneity and label noise, and the cluster assumption in semi-supervised learning. Using this information on TMA images of breast cancer, we have reduced the error rate of TACOMA by about 6%. Further simulations on synthetic data provide insights on when such representations would likely help. Although we focus on TMAs, learnable representations of this type are expected to be applicable in other settings.

Gene Expression Detection Assay for Cancer Clinical Use

Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.

Opportunities and challenges of disease biomarkers: a new section in the Journal of Translational Medicine

Disease biomarkers are defined to diagnose various phases of diseases, monitor severities of diseases and responses to therapies, or predict prognosis of patients. Disease-specific biomarkers should benefit drug discovery and development, integrate multidisciplinary sciences, be validated by molecular imaging. The opportunities and challenges in biomarker development are emphasized and considered. The Journal of Translational Medicine opens a new Section of Disease Biomarkers to bridge identification and validation of gene or protein-based biomarkers, network biomarkers, dynamic network biomarkers in human diseases, patient phenotypes, and clinical applications. Disease biomarkers are also important for determining drug effects, target specificities and binding, dynamic metabolism and pharmacological kinetics, or toxicity profiles.