ASU-RSE Seminar Series

Dr. Susan Massey - TCGA Sex Chromosome Status Pipeline

When: May 06, 2024 at 10:30 AM - 10:30 AM
Location: WXLR A 106 and online on Zoom

Cancers are comprised of cells with diverse mutations, and the goal of precision medicine in the past decade has been to understand and target these mutations to improve patient outcomes. Somatic mutations have been the focus of most cancer genomics research, while sex chromosomes have long been overlooked. As such, there is an outstanding need to assess the status of sex chromosomes in cancer genomics data sets. To help meet that need, this research software engineering project focused on supporting the analysis of publicly available data from samples sequenced for the Cancer Genome Atlas (TCGA; available through the National Cancer Institute Genomic Data Commons) to determine the status of sex chromosomes within individual samples across subjects and various cancer type cohorts. The project was sponsored by the Cross-Institutional Research Engagement Network (CIREN; https://ciren.asu.edu) for ASU primary investigator Melissa Wilson.

We will cover the background and motivation for the effort, as well as the workflow and preliminary results obtained in a cohort of subjects with hepatocellular carcinoma before handing the pipeline over to the primary investigator. This includes the development of a computational workflow to import TCGA data and determine the presence of a Y-chromosome and/or the status of XIST, a marker of X-chromosome inactivation, in each of the samples. The resulting inferred sex chromosome complement was compared to subjects’ clinically recorded sex and was used in analyses of subject outcomes (survival analysis). After completion, this reproducible workflow will be applied to additional cancer types by undergraduate researchers in the primary investigator’s lab.

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