SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R)

SynthEx is a comprehensive suite of tools for CNA detection and tumor heterogeneity profiling. It is tailored to cater for the multiple characteristics of different next generation sequencing technologies.

SynthEx is the first method aware of the sample-specific bias in targeted regions due to fold enrichment differences in tumor and normal samples. Fundamentally different from current methods, it applies different analytical strategies for single subject and large-scale cancer genomics studies. For large-scale cancer genomics studies, it corrects the technical bias due to capture efficiency by using a "synthetic normal" strategy. The "synthetic normal" samples were generated by stratifying existing normal samples (including samples outside the current study) based on capture protocols. Therefore, instead of requiring a matched pair normal sample from each tumor subject, a "synthetic normal" is used that mimics the targeted sequencing profile with the same capture efficiency level as the tumor sample. This strategy can potentially reduce both the experiment and analysis burden within a sequencing facility.