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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Dumenil, Troy D. Wockner, Leesa F. Bettington, Mark McKeone, Diane M. Klein, Kerenaftali Bowdler, Lisa M. Montgomery, Grant W. Leggett, Barbara A. Whitehall, Vicki L. J. |
| Description | Country affiliation: Australia Author Affiliation: Dumenil TD ( Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital, Clinical Research Centre and QIMR Berghofer Medical Research Institute, Brisbane, Australia.) |
| Abstract | Formalin fixation and embedding of clinical tissue samples in paraffin is a common method for archiving biological material. These samples are often well annotated and provide an invaluable resource for research. However, this process of fixation and storage of tissue leads to DNA damage and fragmentation. The use of DNA from formalin fixed, paraffin-embedded (FFPE) tissue to interrogate methylation levels on a genome-wide scale can pose challenges. We compared fresh and matched FFPE tissue DNA samples using the Illumina Infinium HD Human Methylation 450K BeadChip platform with a companion application for repair and 'restoration' of DNA from FFPE tissue. Our results showed good correlation between fresh and FFPE sample data. FFPE DNA captured 99% of the CpG sites on the array on average. Significant cancer subgroups based on the CpG island methylator phenotype (CIMP) were clearly distinguished for both fresh and FFPE sample sets with cluster and scaling analysis. The DNA methylation status for the five standard CIMP panel genes which was evaluated for all samples by the MethyLight assay was correctly assigned in both fresh and FFPE samples by the array data. We conclude that the 'restoration' method followed by assay on the Infinium HD Human Methylation 450K microarray can produce good quality data for DNA from FFPE samples. |
| File Format | HTM / HTML |
| ISSN | 10452257 |
| Issue Number | 7 |
| Volume Number | 53 |
| e-ISSN | 10982264 |
| Journal | Genes, Chromosomes and Cancer |
| Language | English |
| Publisher | Wiley-Liss |
| Publisher Date | 2014-07-01 |
| Publisher Place | United States |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Discipline Molecular Biology Discipline Oncology Colorectal Neoplasms Metabolism Dna Methylation Fixatives Formaldehyde Genome, Human Genetics Pathology Cpg Islands Dna Damage Humans Paraffin Embedding Tissue Fixation Methods Journal Article Research Support, Non-u.s. Gov't |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics Cancer Research |
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