Unknown

Dataset Information

0

Measuring the reproducibility and quality of Hi-C data.


ABSTRACT: BACKGROUND:Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. RESULTS:Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments. CONCLUSIONS:In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.

SUBMITTER: Yard?mc? GG 

PROVIDER: S-EPMC6423771 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

altmetric image

Publications


<h4>Background</h4>Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.<h4>Results</h4>Using real and simulated data, we profil  ...[more]

Similar Datasets

| S-EPMC5668950 | biostudies-literature
| S-EPMC6678864 | biostudies-literature
| S-EPMC8530316 | biostudies-literature
| S-EPMC9348684 | biostudies-literature
| S-EPMC7319437 | biostudies-literature
| S-EPMC5934634 | biostudies-literature
| S-EPMC8121922 | biostudies-literature
| S-EPMC10664258 | biostudies-literature
| S-EPMC10492850 | biostudies-literature
| S-EPMC10415357 | biostudies-literature