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Articles by A. D Smith
Total Records ( 2 ) for A. D Smith
  A Vogiatzoglou , A Oulhaj , A. D Smith , E Nurk , C. A Drevon , P. M Ueland , S. E Vollset , G. S Tell and H. Refsum

Background: Methylmalonic acid (MMA) in plasma or serum is widely used for assessment of vitamin B12 status. However, data are sparse regarding factors, besides renal function, that may influence MMA concentrations. We searched for important determinants of plasma MMA in the general population.

Methods: In 6946 middle-aged (47–49 years) and elderly (71–74 years) individuals from the Hordaland Homocysteine Study in Norway, we collected anthropometric measurements, lifestyle data, and plasma MMA, vitamin B12, and creatinine measurements. For 5820 individuals, we also collected dietary data.

Results: Age and plasma creatinine were positively associated with plasma MMA, whereas plasma vitamin B12 was negatively associated. These variables together with sex were the strongest determinants of plasma MMA, accounting for 16% of the variation (R2 = 0.16). Addition of anthropometric measures and lifestyle and dietary factors only gave slight improvement (total R2 = 0.167). Increased plasma MMA was seen when plasma vitamin B12 was <400 pmol/L. In individuals with vitamin B12 ≥400 µmol/L (vitamin B12–replete), the 2.5th–97.5th percentile reference limits for MMA were 0.10–0.28 µmol/L (middle-aged) and 0.10–0.36 µmol/L (elderly). When plotted against creatinine (nomograms), the 97.5th percentile of MMA was similar in men and women but approximately 0.15 µmol/L higher in elderly than middle-aged individuals. Vitamin B12–replete participants had MMA upper limits approximately 0.1 µmol/L (elderly) and 0.04 µmol/L (middle-aged) below those of the unselected population at all creatinine concentrations.

Conclusions: Identified determinants accounted for <17% of the overall variation in plasma MMA. The difference in MMA between middle-aged and elderly individuals is only partly explained by creatinine and vitamin B12 concentrations.

  E Hodges , A. D Smith , J Kendall , Z Xuan , K Ravi , M Rooks , M. Q Zhang , K Ye , A Bhattacharjee , L Brizuela , W. R McCombie , M Wigler , G. J Hannon and J. B. Hicks

DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs.

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