1 / 4

Challenges in Modeling and Analyzing DNA Methylation Data

Challenges in Modeling and Analyzing DNA Methylation Data. Shili Lin Department of Statistics The Ohio State University. Challenges. How to assign/distribute a read to CpG sites to obtain inferred nucleotide resolution methylation (NTRM) data?

ally
Télécharger la présentation

Challenges in Modeling and Analyzing DNA Methylation Data

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Challenges in Modeling and Analyzing DNA Methylation Data Shili Lin Department of Statistics The Ohio State University

  2. Challenges • How to assign/distribute a read to CpG sites to obtain inferred nucleotide resolution methylation (NTRM) data? • How to combine correlated signals (modeling needed) form NTRM within a well-defined region to detect differential methylation?

  3. How to Detect Differentially Methylated Regions? • Averaging over the region will likely wash out the signals. • Point by point analysis is not powerful and will likely lead to inconsistent signals throughout the region. • Regional joint analysis needs to take correlation into account. How to model such correlation? • The two-step idea (derive NTRM data then perform methylation analysis) does not take into account of uncertainty in first step. One-step analysis strategies?

  4. Challenges • With Methyl-CpG (Serre 2010) or MethylCap-seq (Yan 2012), NTRM are not observable but need to be inferred. • Can no longer perform Fisher exact or chi-square test on 2 x 2 contingency table (columns: two alleles of a SNP; rows: counts of methylated and unmethylatedcytosines at CpG site located on a SNP-containing read). • If data from multiple cell lines are available, can the data be pooled (modeling needed) to increase statistical power? Can cell lines with homozygous genotypes be included in the analysis? (Poisson-binomial model? – seen in a talk)

More Related