Extended Data Fig. 3: Local read depth normalization of recurrent repeat expansion (rRE) candidates. | Nature

Extended Data Fig. 3: Local read depth normalization of recurrent repeat expansion (rRE) candidates.

From: Recurrent repeat expansions in human cancer genomes

Extended Data Fig. 3

a, Examples of read depth before and after local normalization. b, Examples of anchored in-repeat read (IRRs) before and after local normalization. The read depth for the locus on the left is derived from TCGA data, and the read depth for the locus on the right is derived from PCAWG data. Q-values were calculated from two-tailed Student’s t-test with FDR correction by Benjamini-Hochberg. FDR q-value=4.83e-05 and 0.54 for Kidney-RCC and Breast-AdenoCA, respectively (n = 74 Kidney-RCC genomes and n = 193 Breast-AdenoCA genomes analyzed). c, Workflow to identify rREs. d, Detection rate in an independent cohort of samples.

Back to article page