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Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

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eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues.

Jinyan Huang¹, Jun Chen², Jorge Esparza³

¹1] State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China [2] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA.

Nature Communications

|May 9, 2015

Summary

This summary is machine-generated.

This study imputes short insertions and deletions (indels) to map gene expression quantitative trait loci (eQTLs), revealing their significant role in gene regulation across multiple tissues. The findings enhance our understanding of genetic architecture and disease variant interpretation.

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Area of Science:

Genomics
Genetic Epidemiology
Molecular Biology

Background:

Genome-wide gene expression quantitative trait loci (eQTL) mapping traditionally focuses on single-nucleotide polymorphisms (SNPs).
The functional impact of structural variants, particularly short insertions and deletions (indels), on gene expression remains underexplored.
Interpreting disease-associated variants requires a comprehensive understanding of genetic effects beyond SNPs.

Purpose of the Study:

To investigate the role of indels in eQTL mapping across multiple tissues.
To assess the contribution of indels to the genetic architecture of gene expression.
To provide a resource for interpreting the functional consequences of structural variants.

Main Methods:

Imputation of 1,380,133 indels using the 1,000 Genomes Project reference panel.
Integration of imputed indel data with three multi-tissue eQTL datasets.
Functional analyses including epigenetics, gene ontology, and genome-wide association study (GWAS) loci enrichment.

Main Results:

Imputation of indels increased eQTL mapping power by 9.9% and identified 325 novel indel-specific eQTLs.
Indel eQTLs were enriched in introns and near untranslated regions (UTRs).
A significant proportion of previously identified eQTLs (eSNPs) were found to be taggers of indels, highlighting their importance.

Conclusions:

Indels are a crucial component of the genetic architecture of gene expression, with both tissue-specific and tissue-consistent effects.
This study provides valuable insights and a resource for understanding the functional impact of structural variants on gene expression and human traits.
The findings necessitate the inclusion of indels in future eQTL studies for comprehensive genetic interpretation.