Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing.
DNA methylation
Epigenetics
Formalin-fixed paraffin-embedded tissue
Fresh frozen tissue
Targeted-bisulfite sequencing
Journal
Pathology international
ISSN: 1440-1827
Titre abrégé: Pathol Int
Pays: Australia
ID NLM: 9431380
Informations de publication
Date de publication:
Feb 2021
Feb 2021
Historique:
received:
29
07
2020
revised:
28
10
2020
accepted:
16
11
2020
pubmed:
18
12
2020
medline:
26
10
2021
entrez:
17
12
2020
Statut:
ppublish
Résumé
Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.
Identifiants
pubmed: 33333623
doi: 10.1111/pin.13054
pmc: PMC7898333
doi:
Substances chimiques
Fixatives
0
Sulfites
0
Formaldehyde
1HG84L3525
DNA
9007-49-2
hydrogen sulfite
OJ9787WBLU
Types de publication
Comparative Study
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
135-140Subventions
Organisme : Japan Agency for Medical Research and Development
ID : JP17km0105004
Informations de copyright
© 2020 The Authors. Pathology International published by Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.
Références
JCO Precis Oncol. 2018;2018:
pubmed: 29862382
BMC Med Genomics. 2011 Sep 29;4:68
pubmed: 21958464
Pathol Int. 2018 Nov;68(11):633-635
pubmed: 30239063
Clin Epigenetics. 2017 Apr 4;9:33
pubmed: 28392843
Histol Histopathol. 2011 Jun;26(6):797-810
pubmed: 21472693
NPJ Genom Med. 2017 Apr 13;2:11
pubmed: 29263827
Pathol Int. 2018 Feb;68(2):63-90
pubmed: 29431262
Pract Lab Med. 2020 Feb 03;19:e00153
pubmed: 32123717
PLoS One. 2019 Apr 11;14(4):e0211400
pubmed: 30973937
Hum Genome Var. 2018 Mar 29;5:18008
pubmed: 29619235
Circ Genom Precis Med. 2020 Feb;13(1):e002649
pubmed: 31928219
BMC Genomics. 2015 Nov 03;16:892
pubmed: 26531060
Oncotarget. 2015 Sep 22;6(28):25943-61
pubmed: 26305677
Cell Oncol. 2004;26(5-6):329-34
pubmed: 15623943
BMC Med Genomics. 2017 Aug 31;10(1):54
pubmed: 28859641
Brief Funct Genomics. 2016 Nov;15(6):399-407
pubmed: 27107288
PLoS One. 2015 Dec 07;10(12):e0144162
pubmed: 26641479