Hl60 Copy Number

Question

[Richard]

Hi all,

Does anyone know of a reference for HL60 copy number using high-throughput sequencing? My googling is pointing me toward lots of ACGH and BAC copy number assay results.

Specifically, I want to know if there are large copy number gains of high magnitude that would make getting coverage across the whole genome difficult.

Answer 1

[Sean Davis]

We have done a fair amount of sequencing of cell lines and inference of copy number. I do not think that copy number variation is likely to significantly affect the coverage across the rest of the genome (within the variation in coverage from the application of sequencing technology). That said, the ploidy and subclonal heterogeneity of a cell line is often an unknown and may affect your ability to call variants in certain regions. In the end, sequence with whatever you think should yield the coverage you think you want and then add as necessary to satisfy biological hypothesis testing.