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Review
. 2025 Jul 2;26(4):bbaf356.
doi: 10.1093/bib/bbaf356.

A comparative review of short genetic variant databases across humans and animal species

Samantha L Van Buren  1 , C Titus Brown  1 , Tomasz Szmatoła  2 , Carrie J Finno  1
Affiliations
Review

A comparative review of short genetic variant databases across humans and animal species

Samantha L Van Buren et al. Brief Bioinform. .

Abstract

Understanding genetic variation is necessary to unravel the complexities of evolution and diverse traits across species. Short genetic variants (<50 bp in length) represent key genomic variations that play a crucial role in shaping the genetic landscape of populations. Human short genetic variant databases are often considered the gold standard for variant repositories, and this review compares them with variant databases created for various animal species. This review examines the methodologies, data integration, and various applications that differ or align between human and animal databases. The goal is to identify challenges in leveraging genetic variation across species, recommend strategies for overcoming these challenges, and suggest future directions for research and database development.

Keywords: allele frequencies; genetics; genomics; whole-genome sequencing.

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Figures

Figure 1
Figure 1
Overlap of variant positions across human genomic databases. (A) Overlap of all variant positions among the 1000 genomes project, genomic gnomAD, and dbSNP VCF datasets. (B) Overlap of filtered positions from the same datasets, with multiallelic sites split into biallelic records and limited to SNVs.
Figure 2
Figure 2
Comparison of variant counts in human and animal short genetic variant databases.
See this image and copyright information in PMC

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