Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities

MOTIVATION

Inference of differentially methylated (DM) CpG sites between two groups of tumor samples with different geno- or pheno-types is a critical step to uncover the epigenetic mechanism of tumorigenesis, and identify biomarkers for cancer subtyping. However, as a major source of confounding factor, uneven distributions of tumor purity between two groups of tumor samples will lead to biased discovery of DM sites if not properly accounted for.

RESULTS

We here propose InfiniumDM, a generalized least square model to adjust tumor purity effect for differential methylation analysis. Our method is applicable to a variety of experimental designs including with or without normal controls, different sources of normal tissue contaminations. We compared our method with conventional methods including minfi, limma and limma corrected by tumor purity using simulated datasets. Our method shows significantly better performance at different levels of differential methylation thresholds, sample sizes, mean purity deviations and so on. We also applied the proposed method to breast cancer samples from TCGA database to further evaluate its performance. Overall, both simulation and real data analyses demonstrate favorable performance over existing methods serving similar purpose.

AVAILABILITY AND IMPLEMENTATION

InfiniumDM is a part of R package InfiniumPurify, which is freely available from GitHub (https://github.com/Xiaoqizheng/InfiniumPurify).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Anduril 2: upgraded large-scale data integration framework

Summary

Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril’s bioinformatics repository has been expanded with multiple components, and tutorial pipelines, for next-generation sequencing data analysis.

Availabilityand implementation

Freely available at http://anduril.org.

Supplementary information

Supplementary data are available at Bioinformatics online.