This repository holds information regarding our assessment of whole-genome sequencing data on WTC-11. We are adding this repository since we have been asked a few times about our copy number variant assessment of the cell line data. Please note the information below is based on mappings to build 38 of the human genome.
The data for this cell line comes from the Allen Institute for Cell Science. The genomics data is available at https://www.allencell.org/genomics.html.
We noticed there was a deletion in AUTS2 when looking at the genome sequence data. Since we have been asked several times about the event, we outline the evidence supporting it here in this GitHub.
The 10x linked read whole-genome sequence data is available at Allen Cell at this link: https://open.quiltdata.com/b/allencell/tree/aics/wtc11_linkedread_wgs/. We downloaded the loupe file in the supporting_files folder and visualized it in the 10x Genomics loupe browser. Below is a png of the deletion event inside the AUTS2 gene:
We used the WTC-11 short-read WGS data for development of our tool called PYRUS (see also https://github.com/TNTurnerLab/PYRUS). The WGS data is available at Allen cell at this link: https://open.quiltdata.com/b/allencell/tree/aics/wtc11_short_read_genome_sequence/. By running QuicK-mer2 on the genome data, we also saw the deletion in AUTS2 and have an image of that in the PYRUS GitHub repository as shown below:
The QuicK-mer2 data we generated on this WGS dataset can be found here: https://github.com/TNTurnerLab/PYRUS/tree/main/Example_Data/WTC-11_Sample