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Correlation of DNA methylation levels in blood and saliva DNA in young girls of the LEGACY Girls study.

Author(s): Wu HC, Wang Q, Chung WK, Andrulis IL, Daly MB, John EM, Keegan TH, Knight J, Bradbury AR, Kappil MA, Gurvich I, Santella RM, Terry MB

Publication: Epigenetics, 2014, Vol. 9, Page 929-33

PubMed ID: 24756002 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared DNA methylation of three repetitive elements (Sat2, Alu, and LINE-1) and four CpG sites (cg23576855, cg05575921, cg05951221, and cg11924019) among saliva specimens to white blood cells. Blood and saliva were collected on the same day from 57 girls (6-15 years old) participating in the LEGACY Girls Study (Lessons in Epidemiology and Genetics of Adult Cancer from Youth). Saliva was collected using Oragene kits. No details were provided for blood collection or processing for white cell isolation. DNA was extracted from white cells and saliva by a salting out procedure. Briefly, cells were lysed with SDS in a nuclei lysis buffer and treated with RNase, DNA was co-precipitated with proteins using NaCl and centrifugation, and then genomic DNA was precipitated from the supernatant with ethanol. DNA was bisulfite-treated with the EZ DNA methylation kit and stored at -20 °C until analysis. All DNA methylation markers were measured by bisulfite-pyrosequencing except Sat2 and Alu which were measured by the MethyLight assay.

   Summary of Findings:

   DNA methylation levels were lower in saliva specimens than in white blood cells for all elements (for Sat2, 126.8 ± 64.0% versus 130.2 ± 76.0%, P=0.02; for Alu, 67.1 ± 24.4% versus 69.0 ± 25.9%, P=0.09; for LINE-1, 75.2 ± 3.4 versus 79.0 ± 2.6, P<0.0001; for cg05575921, 65.9 ± 6.1 versus 80.0 ± 3.4, P=0.01; for cg05951221, 46.6 ± 6.7 versus 52.4 ± 7.1, P=0.001; and for cg11924019, 21.8 ± 4.4 versus 27.3 ± 5.6, P<0.0001); however, results were correlated between the specimen types ranging from weak (Sat2, r=0.32; Alu, r=0.24; cg05575921, r=0.33; cg05951221, r=0.42) to strong (LINE-1, r=0.73;  cg11924019, r=0.79). Results for cg23576855 were excluded because the methylation levels in both white blood cells and saliva DNA were over 90%.

   Biospecimens

   • Bodily Fluid - Blood
   • Cell - White Cells
   • Bodily Fluid - Saliva

   Preservative Types

   • None (Fresh)

   Diagnoses:

   • Normal

   Platform:

   Analyte	Technology Platform
   DNA	Bisulfite conversion assay

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Bisulfite conversion assay Specific	Targeted nucleic acid	Sat2 Alu LINE-1 cg23576855 cg05575921 cg05951221 cg11924019
   Biospecimen Acquisition	Biospecimen location	White cells Saliva

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