Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples.

ABSTRACT:

Background

Next-generation sequencing (NGS) of tumour samples is a critical component of personalised cancer treatment, but it requires high-quality DNA samples. Routine neutral-buffered formalin (NBF) fixation has detrimental effects on nucleic acids, causing low yields, as well as fragmentation and DNA base changes, leading to significant artefacts.

Patients and methods

We have carried out a detailed comparison of DNA quality from matched samples isolated from high-grade serous ovarian cancers from 16 patients fixed in methanol and NBF. These experiments use tumour fragments and mock biopsies to simulate routine practice, ensuring that results are applicable to standard clinical biopsies.

Results

Using matched snap-frozen tissue as gold standard comparator, we show

SUBMITTER: Piskorz AM 

PROVIDER: S-EPMC4769995 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature