Hi, Sriram. TCGA is a good starting place. About 4000 WGS samples, including both tumor and some matched normal, are available here:
https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22sequencing%20reads%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.experimental_strategy%22%2C%22value%22%3A%5B%22WGS%22%5D%7D%7D%5D%7D dbGaP access is required to actually access the data. FYI, I wouldn’t bother comparing to the reference genome, only to the matched normal. If no matched normal is available, ignore the sample. Sean From: "Sridharan, Sriram (NIH/NCI) [F]" <[email protected]> Reply-To: List BIOINFO-GENERAL-NCI <[email protected]> Date: Monday, December 16, 2019 at 12:09 PM To: List BIOINFO-GENERAL-NCI <[email protected]> Subject: WGS data in human cancer cells and cell-lines Dear All, I am Sriram, a post-doc in NCI. I am writing to ask help regarding whole genome sequencing data for cancer cells and cell-lines that might be publicly available. We are interested in looking at certain repeat sequences and their status in these cancers. Status means- deleted, expanded etc. We want to compare the sizes of the repeats in cancer with the lengths from reference genome. We think Illumina Short Sequencing Reads might not be totally applicable since we cannot map through the repeats. I would really appreciate any help in this regard. Thanks, Sriram
