Friday, July 24, 2015

Cancer Classification

There is an interesting paper from CSHL on progress on cancer classification. Linnaeus some 300 years ago came up with a classification system for various species. Aristotle was driven by his desire to classify, and ever since we have people trying their best to do that task. Patients always want to know what they have, and that is a form of classification.

We classify cancers based upon organs. We may modify it based on cell types or based on cell markers such as immunological markers. I remember back in the 60s that Leukemias were simple; acute or chronic, you died now or later. Now we have a plethora of substypes and a multiplicity of therapeutics.

But we also now genomic data. Perhaps then we should classify cancers based upon genes, not upon organs, binding proteins, or the like,

As the authors state:

Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we organize knowledge, obtain diagnosis, and assign treatment. Here we discuss the classification of cancer, the process of categorizing cancers based on their observed clinical and biological features. Traditionally, cancer nomenclature is primarily based on organ location, e.g., "lung cancer" designates a tumor originating in lung structures. Within each organ-specific major type, further subgroups can be defined based on patient age, cell type, histological grades, and sometimes molecular markers, e.g., hormonal receptor status in breast cancer, or microsatellite instability in colorectal cancer. In the past 15+ years, high-throughput technologies have generated rich new data for somatic variations in DNA, RNA, protein, or epigenomic features for many cancers. These data, representing increasingly large tumor collections, have provided not only new insights into the biological diversity of human cancers, but also exciting opportunities for discovery of new cancer subtypes.

They continue:

An ever finer classification system has many potential benefits. It is needed to capture the full spectrum of biological diversity—the "endless forms" that Darwin spoke of. It could lead to a better recognition of patient-specific disease mechanisms, and importantly, could suggest treatment options that are more accurately matched to the patient's tumor. Precision medicine, at its very foundation, relies on valid and continuously optimized disease classification that reflect the underlying mechanisms. However, a fine-grained classification system also has many potential drawbacks. The newly proposed splits may not be technically robust. Even when the finer categories are robustly supported by statistical significance and by replication, they may still lack a clear biological meaning, or have little impact on treatment options (#3 below) if it turns out that some subtypes share the same clinical endpoint, or if treatment options are limited.

Indeed, we may find it much more powerful to have a new Linnaeus type look at classification. Classifying genomically, via genes, RNA, and epigenetic factors, may help stratify and focus on therapeutics. This article raises an interesting dialog.