Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) for quantitative measurement of DNA methylation

2007 ◽  
Vol 2 (8) ◽  
pp. 1931-1936 ◽  
Author(s):  
Mark L Gonzalgo ◽  
Gangning Liang
Keyword(s):  
Dna Methylation ◽  
Quantitative Measurement ◽  
Primer Extension ◽  
Single Nucleotide ◽  
Single Nucleotide Primer Extension

scholarly journals Seven-CpG DNA Methylation Age determined by Single Nucleotide Primer Extension and Illumina's Infinium MethylationEPIC array provide highly comparable results

2021 ◽  
Author(s):  
Valentin Max Vetter ◽  
Christian Humberto Kalies ◽  
Yasmine Sommerer ◽  
Lars Bertram ◽  
Ilja Demuth
Keyword(s):  
Dna Methylation ◽  
Methylation Status ◽  
Cost Effective ◽  
Direct Conversion ◽  
Primer Extension ◽  
Epigenetic Clock ◽  
Single Nucleotide ◽  
Cpg Sites ◽  
Dna Methylation Age ◽  
Single Nucleotide Primer Extension

DNA methylation age (DNAm age, epigenetic clock) is a novel and promising biomarker of aging. It is calculated from the methylation fraction of specific cytosine phosphate guanine sites (CpG sites) of genomic DNA. Several groups have proposed epigenetic clock algorithms and these differ mostly regarding the number and location of the CpG sites considered and the method used to assess the methylation status. Most epigenetic clocks are based on a large number of CpGs, e.g. as measured by DNAm microarrays. We have recently evaluated an epigenetic clock based on the methylation fraction of seven CpGs that were determined by methylation-sensitive single nucleotide primer extension (MS-SNuPE). This method is more cost-effective when compared to array-based technologies as only a few CpGs need to be examined. However, there is only little data on the correspondence in epigenetic age estimation using the 7-CpG clock and other algorithms. To bridge this gap, in this study we measured the 7-CpG DNAm age using two methods, via MS-SNuPE and via the MethylationEPIC array, in a sample of 1,058 participants of the Berlin Aging Study II (BASE-II), assessed as part of the GendAge study. On average, participants were 75.6 years old (SD: 3.7, age range: 64.9 - 90.0, 52.6% female). Agreement between methods was assessed by Bland-Altman plots. DNAm age was highly correlated between methods (Pearson's r=0.9) and Bland-Altman plots showed a difference of 3.1 years. DNAm age by the 7-CpG formula was 71.2 years (SD: 6.9 years, SNuPE) and 68.1 years (SD: 6.4 years, EPIC array). The mean of difference in methylation fraction between methods for the seven individual CpG sites was between 0.7 and 13 percent. To allow direct conversion between methods we developed an adjustment formula with a randomly selected training set of 529 participants using linear regression. After conversion of the Illumina data in a second and independent validation set, the adjusted DNAm age was 71.44 years (SD: 6.1 years, n=529). In summary, we found the results of DNAm clocks to be highly comparable. Furthermore, we developed an adjustment formula that allows for direct conversion of estimates between methods and enables one singular clock to be used in studies that employ either the Illumina or the SNuPE method.

scholarly journals Sensitive quantitative assay for point mutations in the rat H-ras gene based on single nucleotide primer extension

2010 ◽  
Vol 1 (4) ◽  
pp. 657-661 ◽  
Author(s):  
YOSHIHISA YANO ◽  
TOMOHIRO YANO ◽  
ANNA KINOSHITA ◽  
AI MATOBA ◽  
TADAYOSHI HASUMA ◽  
...  
Keyword(s):  
Point Mutations ◽  
Primer Extension ◽  
Quantitative Assay ◽  
Ras Gene ◽  
Single Nucleotide ◽  
Single Nucleotide Primer Extension

scholarly journals Use of multilocus methylation-specific single nucleotide primer extension (MS-SNuPE) technology in diagnostic testing for human imprinted loci

Epigenetics ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. 473-481 ◽  
Author(s):  
Matthias Begemann ◽  
Isabelle Leisten ◽  
Lukas Soellner ◽  
Klaus Zerres ◽  
Thomas Eggermann ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Primer Extension ◽  
Single Nucleotide ◽  
Single Nucleotide Primer Extension

scholarly journals Mouse endogenous X-linked genes do not show lineage-specific delayed inactivation during development

1995 ◽  
Vol 65 (3) ◽  
pp. 223-227 ◽  
Author(s):  
Jeanne M. Lebon ◽  
Patrick P. L. Tam ◽  
Judith Singer-Sam ◽  
Arthur D. Riggs ◽  
Seong-Seng Tan
Keyword(s):  
X Chromosome ◽  
Female Mouse ◽  
X Chromosome Inactivation ◽  
Mouse Embryos ◽  
Primer Extension ◽  
Rt Pcr ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Endogenous Genes ◽  
Single Nucleotide Primer Extension

SummaryX chromosome inactivation (XCI) has been assumed to be complete in all cells of female mouse embryos at about 6 d post coitum (dpc). However, a recent study on β-galactosidase expression of an X-linkedlacZtransgene suggests that XCI is probably not complete several days after this time in some lineages. To help resolve this issue, we analysed XCI in embryos which carry the T(X;16)16H (Searle's) translocation and are heterozygous at the X-linkedHprtandPgk-1genes. The quantitative RT-PCR single nucleotide primer extension (SNuPE) assay was used to measureHprtandPgk-1allele-specific transcripts in embryos 9·5 dpc. No transcripts from the normal X chromosome were found in any of the tissues tested, indicating that inactivation was complete for these endogenous genes.

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