scholarly journals The overdue promise of short tandem repeat variation for heritability.

2014 ◽  
Author(s):  
Maximilian Press ◽  
Keisha D. Carlson ◽  
Christine Queitsch
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Complex Traits ◽  
Association Studies ◽  
Complex Trait ◽  
Model Organisms ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Repetitive Nature ◽  
Short Tandem

Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to accurately genotype STRs, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies.

scholarly journals The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S84 ◽  
Author(s):  
John SK Kauwe ◽  
Sarah Bertelsen ◽  
Laura Bierut ◽  
Gerald Dunn ◽  
Anthony L Hinrichs ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

scholarly journals Empirical Evaluation of the Genetic Similarity of Samples From Twin Registries in Australia and the Netherlands Using 359 STRP Markers

2006 ◽  
Vol 9 (4) ◽  
pp. 600-602 ◽  
Author(s):  
Patrick F. Sullivan ◽  
Grant W. Montgomery ◽  
Jouke Jan Hottenga ◽  
Naomi R. Wray ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Genetic Variability ◽  
The Netherlands ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Complex Traits ◽  
Genetic Similarity ◽  
Empirical Evaluation ◽  
Twin Studies ◽  
Genetic Studies ◽  
Short Tandem

AbstractOne way to achieve the large sample sizes required for genetic studies of complex traits is to combine samples collected by different groups. It is not often clear, however, whether this practice is reasonable from a genetic perspective. To assess the comparability of samples from the Australian and the Netherlands twin studies, we estimated Fst (the proportion of total genetic variability attributable to genetic differences between cohorts) based on 359 short tandem repeat polymorphisms in 1068 individuals. Fst was estimated to be 0.30% between the Australian and the Netherlands cohorts, a smaller value than between many European groups. We conclude that it is reasonable to combine the Australian and the Netherlands samples for joint genetic analyses.

scholarly journals Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

2019 ◽  
Author(s):  
David Jakubosky ◽  
Matteo D’Antonio ◽  
Marc Jan Bonder ◽  
Craig Smail ◽  
Margaret K.R. Donovan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Complex Traits ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Evolutionary Constraint ◽  
Structural Variants ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Genomic Locations ◽  
Short Tandem

AbstractStructural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we show that different SV classes and STRs differentially impact gene expression and complex traits. Functional differences between SV classes and STRs include their genomic locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We also identified a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and showed they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that impact gene expression and human traits.

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