Type

Journal Article

Authors

Darran P O'Connor
William M Gallagher
Annette T Byrne
Diether Lambrechts
Bauke Ylstra
Verena Murphy
Bryan Hennessy
Elaine Kay
Orna Bacon
Jochen HM Prehn
and 9 others

Subjects

Biochemistry

Topics
fresh sequencing next generation sequencing cancer cell lines tumor dna methylation embedded colorectal cancer

Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. (2016)

Abstract DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a 'bowing' pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads. We have found no evidence that this affected methylation calling, nor concordance of results. We also found no significant increase in deamination, measured by C>T transitions, previously considered a result of crosslinking DNA by formalin fixation and a barrier to the use of FFPE in methylation studies. The methods used in this study have shown sensitivity of between 60-70% based on positions also methylated in colorectal cancer cell lines. We demonstrate that FFPE material is a useful source of tumor material for methylation studies using targeted sequencing.
Collections Ireland -> Royal College of Surgeons in Ireland -> PubMed

Full list of authors on original publication

Darran P O'Connor, William M Gallagher, Annette T Byrne, Diether Lambrechts, Bauke Ylstra, Verena Murphy, Bryan Hennessy, Elaine Kay, Orna Bacon, Jochen HM Prehn and 9 others

Experts in our system

1
Darran P O'Connor
Royal College of Surgeons in Ireland
Total Publications: 43
 
2
William M Gallagher
University College Dublin
Total Publications: 148
 
3
Annette T Byrne
Royal College of Surgeons in Ireland
Total Publications: 41
 
4
Bryan T Hennessy
Royal College of Surgeons in Ireland
Total Publications: 33
 
5
Elaine W Kay
Royal College of Surgeons in Ireland
Total Publications: 157
 
6
Orna Bacon
Royal College of Surgeons in Ireland
Total Publications: 13
 
7
Jochen H M Prehn
Royal College of Surgeons in Ireland
Total Publications: 206