Sample sources for epigenetic studies
Caroline Relton
Institute of Genetic Medicine
Newcastle University, UK
Contents
• Tissue specificity
• Sample sources for epidemiological investigations
• Variables to consider and record
• Cellularity of peripheral blood
• Options for complementing population-based studies
• Strategies to account for cellularity
Epigenetic patterns are tissue specific
High-throughput
DNA methylation
analysis of 11
different tissues
from six individuals
Venn diagram showing the number of T-DMR
and/or I-DMR loci
i.e. Inter-individual differences are generally in
different places in the genome to tissue specific
differences in methylation patterns
Byun H et al. Hum. Mol. Genet. 2009;18:4808-17
Sample sources
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Peripheral blood leucocytes
Saliva (mixed buccal cells and leucocytes)
Buccal scrapes
Cell lines (lymphoblastoid cell lines, iPSC)
Opportunistic samples
– Surgical resection
– Placenta
– Umbilical cord
• Tissue biopsies
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Tumour tissue
Adjacent ‘normal tissue’
Post-mortem
Fresh / snap frozen
Variables to consider and record
• Peripheral blood
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Time of blood draw (fasting/non-fasting)
Anti-coagulant (LithHep, EDTA, Paxgene, RNAeasy, other)
Time to DNA/RNA extraction
Extraction method (buffy coat or whole blood)
• Cell lines
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Passage
Culture media
Level of confluence
Method of harvesting
Time to DNA/RNA extraction
• Biopsies
– Storage and handling post-sampling
– Time to DNA/RNA extraction
Cellularity and methylation of peripheral blood
• Factors that influence global methylation in peripheral blood DNA
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Age, sex, ethnicity
Environmental toxicants
Smoking, alcohol
Disease / inflammation / infection
Pregnancy / haemodilution
Obesity
Physical activity
Dietary folate
Factors that
influence
differential
blood count
Strategies to account for cellularity
• Differential blood cell count
– White cells (multiple types), red cells, platelets
• Fluorescence activated cell sorting (FACS)
• Post hoc correction