NDLI: Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Kalmár, Alexandra Péterfia, Bálint Hollósi, Péter Wichmann, Barnabás Bodor, András Patai, Árpád V. Schöller, Andrea Krenács, Tibor Tulassay, Zsolt Molnár, Béla
Description	Author Affiliation: Kalmár A ( 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi utca 46, 1088, Budapest, Hungary, alexandra.kalmar@gmail.com.)
Abstract	We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from 'recent', collected within 6 months, and 'archived', collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 µg DNA; Q: 3.00 ± 4.04 µg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 µg DNA; Q: 11.51 ± 7.50 µg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.
File Format	HTM / HTML
ISSN	12194956
Issue Number	4
Volume Number	21
e-ISSN	15322807
Journal	Pathology & Oncology Research
Language	English
Publisher	Springer
Publisher Date	2015-09-01
Publisher Place	Netherlands
Access Restriction	Subscribed
Subject Keyword	Discipline Oncology Colorectal Neoplasms Genetics Dna Methylation Dna Formaldehyde Chemistry Paraffin Sulfites Humans Paraffin Embedding Methods Reproducibility Of Results Sequence Analysis, Dna Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Cancer Research Pathology and Forensic Medicine Oncology

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