Mapping of cis-regulatory variants by differential allelic expression analysis identifies candidate causal variants and target genes of 41 breast cancer risk loci

Genome-wide association studies (GWAS) have identified hundreds of risk loci for breast cancer, but identifying causal variants and candidate target genes remains challenging. Since most risk loci fall in active gene regulatory regions, we developed a novel approach to identify variants with greater regulatory potential in the disease’s tissue of origin. Using genome-wide differential allelic expression (DAE) analysis on microarray data from 64 normal breast tissue samples, we mapped over 54K variants associated with DAE (daeQTLs). We then intersected these with GWAS data to reveal candidate risk regulatory variants and analyzed their cis-acting regulatory potential. We found 122 daeQTLs in 41 loci in active regulatory regions that are in strong linkage disequilibrium with risk-associated variants (risk-daeQTLs). We also identified 65 new candidate target genes in 29 of these loci for which no previous candidates existed. As validation, we identified and functionally characterized five candidate causal variants at the 5q14.1 risk locus targeting the ATG10 and ATP6AP1L genes, likely acting via modulation of alternative transcription and transcription factor binding. Our study demonstrates the power of DAE analysis and daeQTL mapping to understand breast cancer genetic risk, including in complex genetic regulatory landscapes. It additionally provides a genome-wide resource of variants associated with DAE for future functional studies. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by national Portuguese funding through FCT - Fundação para a Ciência e a Tecnologia and CRESC ALGARVE 2020, institutional support CBMR-UID/BIM/04773/2013, POCI-01-0145-FEDER-022184 "GenomePT", the contract DL 57/2016/CP1361/CT0042 (J.M.X.) and individual postdoctoral fellowship SFRH/BPD/99502/2014 (J.M.X.). The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/under REA grant agreement no. 303745 (A.T.M.), a Maratona da Saúde Award (A.T.M.) and a BCRF project Grant. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Seventy-six samples of normal breast tissue were collected from women submitted to a reduction mastectomy, for reasons unrelated to cancer, at Addenbrooke's Hospital, Cambridge, United Kingdom. Samples were collected with approval from Addenbrooke's Hospital Local Research Ethics Committee (REC reference 06/Q0108/221). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced are available online at .