Analytical protocol to identify local ancestry-associated molecular features in cancer

People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the localancestry composition at each genetic locus across ancestry-admixed populations can suggest causal associations. We present a protocol to identify local ancestry and detect the associated molecular changes, using data from the Cancer Genome Atlas. This workflow can be applied to cancer cohorts with matched tumor and normal data from admixed patients to examine germline contributions to cancer. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).

Automated summary

This protocol presents a method to identify local ancestry and detect associated molecular changes in admixed populations, utilizing data from the Cancer Genome Atlas. It can be applied to examine germline contributions to cancer in patients with mixed ancestries. For more detailed information, refer to Carrot-Zhang et al. (2020).