what is the difference between cell lines and tissue when doing sequencing analysis

Question

[charlie]

Hi,

As title, what is the difference between cell lines and tissue when doing sequencing analysis like DNA sequencing, finding SNV or structural variation? Is it because cell lines may become less similar to the original tissue after several generation of cell culture, and the genomic variation may change?

Thanks

Answer 1

[GenoMax]

In current form the question does not have a concrete answer.

There is no difference in methods for doing sequencing or analysis between cell lines or tissues. As you have indicated they will have differences induced by way samples have been handled in lab. e.g. tissue is more likely to have come from a fresh sample (unless you have a paraffin embedded example). In order to establish a cell line one may need to transform it with a virus and that can certainly lead to genomic changes. Passage in culture over time definitely changes genomes of the cell lines. There are papers on this topic that question the identity of particular cell lines after a large number of passages.

Some links to show why cell line authentication is important since we have not touched upon contamination yet. (LINK1) and (LINK2).