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Materials and methods To study the effects of mutations in the ATR region on melanoma, we downloaded the Melanoma Genome Sequencing Project dataset (dbGaP Study Accession: phs000452.v1.p1) from the dbGaP repository [2]. The dataset contained full exome sequencing data of paired normal and tumor samples of 122 phenotyped subjects in the format of trimmed and aligned BAM files. The dataset also included basic demographic information, such as gender and age; as well as disease specific variables, such as the localization of the melanoma and stage. The total size of the dataset was over 4TB, so we only downloaded the region of interest (ATR gene region) with 50Kbp padding before and after the ATR gene region. We used an available pipeline (Figure 1) for analysis that was previously developed for a lung cancer project by the Biostatistics and Bioinformatics Shared Resource Facility of the University of Kentucky Markey Cancer Center. The details of the data analysis pipeline will be published elsewhere. We used Python to automate data submission to the pipeline in combination with a configuration file that allowed us to easily swap different versions of the tools used in the pipeline and to match normal and tumor samples for the same patient (Figures 2, 3). Our experiments were executed on the Lipscomb High Performance Computing Cluster at the University of Kentucky.

Using large public data repositories to discover novel genetic mutations with prospective links to melanoma