COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics

TL;DR

COSINE is a web server that integrates 12 popular subclonal reconstruction methods, enabling researchers to infer clonal and subclonal structures in cancer genomics data through a user-friendly online platform, facilitating cancer evolution studies.

Contribution

This work introduces the first web-based platform that consolidates multiple subclonal reconstruction methods for cancer genomics, simplifying analysis and comparison.

Findings

Provides online access to 12 subclonal reconstruction methods.

Includes detailed workflows for each method.

Facilitates cancer evolution research through user-friendly interface.

Abstract

Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact on cancer evolution studies. Clonal state and mutational order can provide detailed insight into tumor origin and its future development. In the past decade, a variety of methods have been developed for subclonal reconstruction using bulk tumor sequencing data. As these methods have been developed in different programming languages and using different input data formats, their use and comparison can be problematic. Therefore, we established a web server for clonal and subclonal structure inference and evolution of cancer genomic data (COSINE), which included 12 popular subclonal reconstruction methods. We decomposed each method via a detailed workflow of single processing steps with a user-friendly interface. To the best of our knowledge, this is the first web server providing online subclonal inference, including the most popular subclonal reconstruction methods. COSINE is freely accessible at www.clab-cosine.net or http://bio.rj.run:48996/cun-web.