Validate the Prevalence of ATR Mutations in Melanoma

To validate the prevalence of ATR mutations in melanoma, whole exome DNA sequencing will be performed on frozen tumor blocks of de-identified metastatic melanoma brain tumors and matched normal tissues at the Markey Cancer Center under an IRB-exempted status (please see letter). DNA will be isolated for each specimen using the DNeasy Blood and Tissue Kit (Qiagen) and library preparation and exome enrichment will be accomplished with the Nextera Rapid Capture Exome kit (Illumina). Samples will be sequenced on the Illumina HiSeq platform using 2x100 bp sequencing reads. Sequencing data for the NCI dbGaP samples as well as Markey melanoma samples will be processed and analyzed by utilizing a variety of genome-scale bioinformatics software. Specifically, data quality will be evaluated by using FastQC. Paired-end reads will be aligned to the reference genome (hg19) by using BWA. Somatic variants will be detected by using Mutect and Indelocator and annotated by using Oncotator. ATR mutation frequency will be reported. The MutSig software will be used to assess whether the mutation frequency is significantly higher than expected by chance given background mutation processes. Result summarization, visualization, and customized downstream statistical analysis will be performed by using R/Bioconductor.

Students

Collaborators

John D’Orazio
Chi Wang
Dave Fardo
Sally Ellingson

Software

FastOC
Mutect
Indelocator
Oncotator
MutSig
R/Bioconductor

ALU repeats in Age-Related Macular Degeneration (AMD

Collaboration with Jinze Liu about ALU repeats in Age-Related Macular Degeneration (AMD). We briefly discussed the project but I’m not sure what tools and software we are going to use.

Students

Collaborators

Jinze Liu

Softare

Publications

Grants