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Fig. 3 | Breast Cancer Research

Fig. 3

From: A knowledge-based framework for the discovery of cancer-predisposing variants using large-scale sequencing breast cancer data

Fig. 3

Analysis of rare variants. This flowchart represents the step-wise procedure in the central arm of Fig. 1 and is performed by filtering 73,544 non-synonymous coding variants down to 16,014 rare variants (MAF <1%), with a deleteriousness score over 0.5 and where the MAF in the cases is higher than in the controls. Rare variants are prioritized into two branches: on the left, variants falling in GWAS breast cancer linkage disequilibrium blocks (LD blocks); on the right, variants overlapping with cancer somatic mutations from COSMIC or cBioPortal (see Additional file 3: Table S6 and S7). For both datasets, overlaps are shown both at the initial level and after filtering for variants belonging to our list of 758 target genes (known cancer-predisposing genes, known somatic driver genes, and DNA repair genes). Six common (i.e., both overlapping with somatic mutations and falling into a GWAS LD block) variants on our target gene list, are reported at the bottom of this figure

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