Computational protocol: Analysis of functional germline variants in APOBEC3 and driver genes on breast cancer risk in Moroccan study population

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Protocol publication

[…] Regarding driver genes, we focused on genes described to carry BC driver mutations in at least two of the following publications: Stephens et al. 2012; Banerji et al. 2012; Ellis et al. 2012; Shah et al. 2012 [, –]. The well-known and intensively studied genes such as BRCA1 or PTEN were excluded from this study. A total of 36 SNPs across 11 driver genes (ARID1B, ATR, MAP3K1, MLL2, MLL3, NCOR1, RUNX1, SF3B1, SMAD4, TBX3, TTN) and 2 genes of APOBEC3 family (APOBEC3A, APOBEC3B) were selected to the study based on data obtained from Ensembl Genome browser (http://www.ensembl.org/index.html) for the CEU (Utah residents with Northern and Western European ancestry from the CEPH collection). The SNPs selection was based on these criteria: (1) minor allele frequency (MAF) value over 10 %; (2) location within the coding region (non synonymous SNPs), core promoter regions and 5’- and 3’-untranslated regions (UTRs), (3) Haploview was used to select SNPs on the basis of linkage disequilibrium (LD; r2 ≥ 0.80)) to minimize the number of SNPs to be genotyped. RegulomeDB (http://www.regulomedb.org/) was used to explore the potential function of the associated SNPs. [...] To investigate how the SNPs can influence the gene expression and their consequences on protein binding sites, chromatin structure and promoter and enhancer strength, we used HaploReg (http://www.broadinstitute.org/mammals/haploreg/haploreg.php). To identify the possible effects on histone modification we used RegulomeDB (http://regulome.stanford.edu/). These effects were proofed for data in MCF7 (Michigan Cancer Foundation-7 breast cancer cell line), T-47D (epithelial cell line derived from mammary ductal carcinoma), HMEC (human mammary epithelial cells) or MCF10A-ER-SRc (breast epithelial cell line -estrogen receptor –src) cell lines. SIFT and PolyPhen predictions were used to determine the possible effect of amino acid substitutions on protein function and structure (Ensemble release 75, http://www.ensembl.org/index.html). The MicroSNiPer was used to predict the impact of all the significant SNPs of this study located in 3’UTR on micro-RNA binding using microSNiPer (http://epicenter.ie-freiburg.mpg.de/services/microsniper/). […]

Pipeline specifications

Software tools Haploview, HaploReg, PolyPhen, MicroSNiPer
Databases RegulomeDB
Applications sRNA-seq analysis, GWAS, Genome data visualization
Organisms Homo sapiens
Diseases Breast Neoplasms, Neoplasms
Chemicals Estrogens