Our pre-print on using allelic imbalance to identify regulatory elements that are involved in germline-somatic interactions is out:
Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma. A Gusev[+], S Spisak[+], AP Fay, H Carol, KC Vavra, S Signoretti, V Tisza, M Pomerantz, F Abbasi, J Seo, TK Choueiri, K Lawrenson, ML Freedman. 2019
We develop a method to precisely identify regulatory QTLs that operate in a context-specific manner. We apply our method to chromatin and expression data from kidney cancer tumor/normal samples and identify wide-spread context-specific QTLs that appear to be driven by germline-somatic interactions. We connect these QTLs to GWAS loci and kidney cancer risk heritability, and we validate one locus using CRISPRi. We believe this is a powerful tool to identify important regulatory variants in many contexts.
stratAS and the analysis pipeline are available in the stratAS repository.