Global DNA methylation profiling of Fanconi anemia cases using Illumina EPIC array
Babu Rao Vundinti, ICMR National Institute of Immunohaematology
Project Accession:
IADA-PRne3xjtnb
Project Description:
Fanconi anemia (FA) is a rare inherited bone marrow failure syndrome characterized by genomic instability and a high predisposition to malignancies. While the genetic basis of FA is well established, the contribution of epigenetic alterations to disease heterogeneity and cancer susceptibility remains poorly understood. In this project, we performed genome-wide DNA methylation profiling of peripheral blood samples from molecularly confirmed FA patients and matched controls using the Illumina Infinium MethylationEPIC (850K) BeadChip. Differential methylation analysis identified methylated CpG sites across FA complementation groups, revealing a predominant hypermethylation pattern affecting genes involved in DNA repair, immune regulation, cell-cycle control, and developmental pathways. This dataset provides a valuable resource for studying epigenetic dysregulation in Fanconi anemia and may support future investigations into disease mechanisms, biomarker discovery, and cancer predisposition in FA.
Project Mode:
Individual
Access Mode:
Open Access
Grant No.:
Intramural grant
Funding Agency:
ICMR- National Institute of Immunohaematology
Release Date:
May 28, 2026
Organism Category:
Human
Number of Study:
1
Study(s):
Study Date:
Feb. 9, 2026
Study Type:
Epigenetics Study (EFO:0002692)
Study Abstract:
Fanconi Anemia (FA) is a rare autosomal recessive disorder; characterized by bone marrow failure, congenital malformation, and a markedly increased risk of cancers. Despite well characterized genetic defects in the FA/BRCA pathway, the mechanisms underlining variable disease severity and cancer susceptibility remains unknown. In this study, we performed epigenome-wide DNA methylation profiling of peripheral blood samples from molecularly confirmed FA patients and matched controls using the Illumina Infinium MethylationEPIC (850K) BeadChip. The analysis revealed a predominant global hypermethylation pattern, with recurrent alterations affecting genes involved in DNA damage response, immune regulation, cell-cycle control, and developmental pathways.
This dataset provides a high-resolution epigenomic resource for investigating the role of DNA methylation in FA pathophysiology and cancer predisposition and is made available through controlled access to support reproducible and ethical secondary research.
Organism:
Homo sapiens (Taxon ID: 9606)
Authors:
- Merin Mariya George, ICMR-National Institute of Immunohaematology, meringeorge_94@yahoo.com
Publications:
-
Keywords:
Fanconi anemia, DNA methylation, epigenetics, Illumina EPIC array, bone marrow failure, cancer predisposition, genome-wide methylation
Samples:
24 Download
Experiment(s):
Experiment Description:
Genome-wide DNA methylation profiling was performed on peripheral blood DNA from Fanconi anemia patients and matched controls using the Illumina Infinium MethylationEPIC BeadChip. Raw IDAT files were processed using the minfi pipeline with quality control, quantile normalization, and differential methylation analysis using limma
Experiment Date:
March 25, 2021 - April 21, 2024
Experiment Technology:
DNA Microarray (OBI:0000630)
Experiment Type:
Methylation profiling by array
Molecule Name:
DNA
Instrument Model:
Illumina Infinium MethylationEPIC version 2 (GPL33022)
Experiment Label:
biotin
Experiment Protocols:
- Array Scanning and Feature Extraction Protocol - After post-hybridization washing and staining, methylation signal intensities were detected using the Illumina NextSeq 550 platform according to the manufacturer’s instructions. Raw image data were processed to generate IDAT files for downstream bioinformatic analysis.
- Nucleic Acid Extraction Protocol - Genomic DNA was extracted from 200 µL of peripheral blood using the QIAamp DNA Blood Mini Kit (Qiagen, Cat. No. 51104) according to the manufacturer’s instructions. DNA quantity and purity were assessed using spectrophotometry and agarose gel electrophoresis. A total of 1000 ng high-quality genomic DNA was used for downstream bisulfite conversion.
- Nucleic Acid Hybridization to Array Protocol - The bisulfite-converted and amplified DNA was hybridized to the Illumina Infinium MethylationEPIC BeadChip according to the manufacturer’s Infinium HD assay methylation protocol. Hybridization was performed overnight, followed by single-base extension and staining steps as per Illumina standard procedures
- Nucleic Acid Labeling Protocol - Genomic DNA (1000 ng) was subjected to sodium bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s protocol. Bisulfite-converted DNA was subsequently whole-genome amplified, enzymatically fragmented, and prepared for array hybridization according to the Illumina Infinium HD Methylation protocol.
- Sample Collection Protocol - Peripheral blood samples were collected from clinically and molecularly confirmed Fanconi anemia patients and matched controls after obtaining informed consent. Approximately 2–3 mL of whole blood was collected in EDTA vacutainers and stored at 4 °C until genomic DNA extraction. All procedures were conducted in accordance with institutional ethical guidelines
Experiment Design:
Case Control Design
Datafiles:
Raw Files: 24
| # | Filename | Size |
|---|---|---|
| 1 | 203824910045_R01C01_Grn.idat | 13676242 |
| 2 | 203824910045_R01C01_Red.idat | 13676242 |
| 3 | 203824910045_R02C01_Grn.idat | 13676241 |
| 4 | 203824910045_R02C01_Red.idat | 13676241 |
| 5 | 203824910045_R03C01_Grn.idat | 13676241 |
| 6 | 203824910045_R03C01_Red.idat | 13676241 |
| 7 | 203824910045_R04C01_Grn.idat | 13676241 |
| 8 | 203824910045_R04C01_Red.idat | 13676241 |
| 9 | 203824910045_R05C01_Grn.idat | 13676241 |
| 10 | 203824910045_R05C01_Red.idat | 13676241 |
| 11 | 203824910045_R06C01_Grn.idat | 13676241 |
| 12 | 203824910045_R06C01_Red.idat | 13676241 |
| 13 | 203824910045_R07C01_Grn.idat | 13676241 |
| 14 | 203824910045_R07C01_Red.idat | 13676241 |
| 15 | 203824910045_R08C01_Grn.idat | 13676241 |
| 16 | 203824910045_R08C01_Red.idat | 13676241 |
| 17 | 205676800021_R05C01_Grn.idat | 13677980 |
| 18 | 205676800021_R05C01_Red.idat | 13677980 |
| 19 | 205676800021_R06C01_Grn.idat | 13677980 |
| 20 | 205676800021_R06C01_Red.idat | 13677980 |
| 21 | 205676800021_R07C01_Grn.idat | 13677980 |
| 22 | 205676800021_R07C01_Red.idat | 13677980 |
| 23 | 205676800021_R08C01_Grn.idat | 13677980 |
| 24 | 205676800021_R08C01_Red.idat | 13677980 |