Stephane E. Castel

A Global Atlas of Immune Alleles Reveals Health-Relevant Variation Across Groups

The paper presents GAIA, a global atlas of immune alleles, showing that underrepresented groups have more diverse alleles needed for vaccine design than Northwest European groups.

Faroese Whole Genomes Provide Insight into Ancestry and Recent Selection

This study analyzes whole genome sequencing data from the Faroe Islands to explore ancestry, genetic diversity, and signals of recent selection in a North Atlantic founder population.

Impact of proteogenomic evidence on clinical success

This study shows that plasma protein quantitative trait loci (pQTL) support therapeutic hypotheses more effectively than other genetic evidence, increasing the likelihood of drug development success.

A Southern African Map of Blood Regulatory Variation Enables GWAS Interpretation

This paper presents a blood regulatory variation map from Southern African populations, showing increased utility for interpreting African genetic studies.

Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data

The paper introduces aFC-n, a method to improve eQTL effect size estimation and gene expression prediction, revealing significant residual allelic imbalance in many genes.

Evaluation of noninvasive biospecimens for transcriptome studies

This study evaluates noninvasive biospecimens for transcriptome studies, finding hair follicles and urine cell pellets to be most promising for disease-relevant applications.

Whole-genome Studies of Malagasy People Uncover Novel Body Composition Associations

This study presents the first whole genome sequence data and genome-wide association study in a Malagasy cohort, uncovering novel body composition associations and highlighting the importance of diverse populations in genomic research.

Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants

This study shows that common splice-regulatory variants can reduce the pathogenicity of rare exonic variants by modulating mRNA splicing.

A vast resource of allelic expression data spanning human tissues

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

Cell type specific genetic regulation of gene expression across human tissues

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

Determinants of telomere length across human tissues

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

A Quantitative Proteome Map of the Human Body

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

Quantifying genetic regulatory variation in human populations improves transcriptome analysis in rare disease patients

ANEVA quantifies genetic regulatory variation using allelic expression data, improving transcriptome analysis and aiding in rare disease diagnosis.

Long non-coding RNA gene regulation and trait associations across human tissues

The paper identifies distinct regulatory patterns and trait associations of lncRNA genes compared to protein-coding genes across human tissues.

The GTEx Consortium atlas of genetic regulatory effects across human tissues

GTEx v8 maps expression and splicing QTLs in 49 tissues from 838 donors: cis-eQTLs cover 94.7% of protein-coding genes, and cross-tissue QTL sharing mirrors cell-type composition.

Modified penetrance of coding variants by cis-regulatory variation shapes human traits

The paper shows that cis-regulatory variation modifies the penetrance of coding variants, affecting disease risk in cancer and autism, and demonstrates this through experimental validation.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

The paper identifies response eQTLs that modify genetic regulation during immune activation and shows their enrichment in autoimmune disease GWAS signals.

Landscape of X chromosome inactivation across human tissues

This paper systematically surveys X chromosome inactivation across human tissues using transcriptomic and genomic data, finding that XCI is generally uniform but shows heterogeneity and identifies new escape genes with sex-biased expression.