garfieldfei/bioinfo4b-dmv

Bioinfo4B-DMV

Data Manipulation and Visualization project for the course "Bioinformatics for Beginners"

Project

somatic copy number segmentation data downloaded from TCGA COAD and READ (https://gdac.broadinstitute.org/). There are three major molecular pathways involved in colorectal cancer(CRC), including the chromosomal instability (found in 85% cases), microsatellite instability and CpG island methylator phenotype pathways. Copy number alterations (CNAs) are somatic changes that cause the gain or loss of DNA sections (>1 kb) from a normal genome. In this project, we are going to explore the pattern of copy number alternations across CRC patients and the relationship with MSI status.

Recommended reading

Wang, Huanbin, et al. "Somatic gene copy number alterations in colorectal cancer: new quest for cancer drivers and biomarkers." Oncogene 35.16 (2016): 2011-2019.

Harbers, Luuk, et al. "Somatic copy number alterations in human cancers: An analysis of publicly available data from the cancer genome atlas." Frontiers in oncology 11 (2021): 700568.