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Fig. 4 | Breast Cancer Research

Fig. 4

From: Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models

Fig. 4

Summary of SNVs in breast cancer patient-derived xenograft models: A classifications of SNVs into three categories: overlap with 1000 genome project; overlap with dbSNP but not in 1000 genome project; PDX-specific variants. B Distribution of the SNVs in HCI002 model in respect to location of protein coding genes. C Representative genome browser view of copy number alteration covering PTEN in HCI004 model. Tracks from top to bottom: depth of coverage in HCI004 germline (control) and HCI004 PDX, and the average mapping quality of aligned reads from the sample (MQ, if no reads align MQ = 0), coverage standard deviation from 500 controls (Coverage SD, indicating common CNV), overlapping segmental duplications published by Bailey JA et al. 2002 (SEG-DUP, used as control for germline CNVs), discordant pairs (DP), split reads (SR), variants from the Database of Genomic Variants (DGV), and RefSeq genes (Genes)

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