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Author Notes:

Correspondence: lzc0061@auburn.edu; zhaohui.qin@emory.edu

LC and ZSQ conceived and designed the experiments.

LC performed the experiments, analyzed the data and developed the DIVAN software.

LC, and ZSQ wrote the paper.

Both authors read and approved the final manuscript.

We thank Dr. Peng Jin for help discussion and advices.

The authors declare that they have no competing interests.

Subjects:

Research Funding:

The project was supported P01 GM085354 grant from National Institute of Health (ZSQ).

Keywords:

  • D-score
  • DIVAN
  • Non-coding variants
  • Software

Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale

Tools:

Journal Title:

BMC Research Notes

Volume:

Volume 10

Publisher:

, Pages 530-530

Type of Work:

Article | Final Publisher PDF

Abstract:

Objective: The majority of sequence variants identified by Genome-wide association studies (GWASs) fall outside of the protein-coding regions. Unlike coding variants, it is challenging to connect these noncoding variants to the pathophysiology of complex diseases/traits due to the lack of functional annotations in the non-coding regions. To overcome this, by leveraging the rich collection of genomic and epigenomic profiles, we have developed DIVAN, or Disease/trait-specific Variant ANnotation, which enables the assignment of a measurement (D-score) for each base of the human genome in a disease/trait-specific manner. To facilitate the utilization of DIVAN, we pre-computed D-scores for every base of the human genome (hg19) for 45 different diseases/traits. Results: In this work, we present a detailed protocol on how to utilize DIVAN software toolkit to retrieve D-scores either by variant identifiers or by genomic regions for a disease/trait of interest. We also demonstrate the utilities of the D-scores using real data examples. We believe that the pre-computed D-scores for 45 diseases/traits is a useful resource to follow up on the discoveries made by GWASs, and the DIVAN software toolkit provides a convenient way to access this resource. DIVAN is freely available at https://sites.google.com/site/emorydivan/software.

Copyright information:

© 2017 The Author(s).

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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