Estimating abundances of retroviral insertion sites from DNA fragment length data.

ABSTRACT:

Motivation

The relative abundance of retroviral insertions in a host genome is important in understanding the persistence and pathogenesis of both natural retroviral infections and retroviral gene therapy vectors. It could be estimated from a sample of cells if only the host genomic sites of retroviral insertions could be directly counted. When host genomic DNA is randomly broken via sonication and then amplified, amplicons of varying lengths are produced. The number of unique lengths of amplicons of an insertion site tends to increase according to its abundance, providing a basis for estimating relative abundance. However, as abundance increases amplicons of the same length arise by chance leading to a non-linear relation between the number of unique lengths and relative abundance

SUBMITTER: Berry CC 

PROVIDER: S-EPMC3307109 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature