aneuploidy detection from sequencing data

Question

[kanwarjag]

I have tissue samples that have been DNA sequenced. I aligned to human genome and want to detect aneuploidy genome-wide. Is there a tool / software that can be useful in this case. Different papers suggest use of CGH array mostly and few others have used custom tools. Thanks for pointers.

Answer 1

[Wayne]

See here and here and here That last one concerns Brent Pedersen's and colleagues' Indexcov, see here. There is also an article The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions by Fijarczyk et al that goes into determining ploidy per chromosome in Figure 1 and has the accompanying code for making the figures here, in particular there is R code for plotting coverage across the genome that produces a plot reminiscent of my script plot_expression_across_chromosomes.py discussed below.

I tried to make a tool that would do this for ngs data. See here. It should work with humans if you have a genome annotation file.

Even though my script was developed with RNA-Seq data, if you can point plot_expression_across_chromosomes.py at the components of a baseline vs. coverage for your other genomes as columns in a spreadsheet, it should work with DNA coverage data, I think. Actually, you may need to use coverage among different chromosomes as the columns, i.e., baseline vs. experimental, depending on how you have your data.

Answer 2

[Wayne]

People looking into this might be interested in this discussion and related pre-print.