Increased duplication rates on chromosome 21

Question

[Daniel Gerlach]

Hello,

We are performing paired-end 50bp un-stranded RNA-seq experiments on an Illumina HiSeq 2500 system with around 15 million total fragments per sample. While most previous human cell line RNA-seq experiments had duplication rates of around 20-40% pretty much balanced over all chromosomes, I recently noticed an increase of up to 60% duplication rate. However this feature is limited to chromosome 21. To my knowledge the cell lines do not have particular chromosomal aberrations on chromosome 21.

What could be potential reasons for seeing a increased duplication rate in an RNA-seq experiment limited to just one chromosome?

Daniel