Olivier Delaneau

Separating direct, indirect and parent-of-origin genetic effects in the human population

The paper introduces JODIE, a model to estimate direct, indirect, and parent-of-origin genetic effects on height, BMI, and educational attainment using family trios from two biobanks.

Benchmarking imputation accuracy in the presence or absence of a reference panel

This study benchmarks imputation accuracy for low-coverage whole-genome sequencing data with and without a reference panel, showing that large datasets can achieve sufficient accuracy without one.

Genomic ascertainment of CHEK2-related cancer predisposition

This study quantifies cancer risk and penetrance in CHEK2 heterozygotes using genomic data from two large biobanks, finding increased risks for several cancers and younger age of onset.

Variant Classification Using Proteomics-Informed Large Language Models Increases Power of Rare Variant Association Studies and Enhances Target Discovery

The paper improves rare variant association studies by using proteomics-informed large language models, identifying more gene-trait associations than existing methods.

Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ~265,000 individuals

The paper infers parent-of-origin effects in ~265,000 individuals using a novel method, identifying over 30 novel POEs and confirming known associations, supporting the parental conflict hypothesis.

Polygenic risk score prediction accuracy convergence

This study assesses the progress and limitations of polygenic risk score prediction accuracy for common diseases, showing diminishing returns from recent GWAS and highlighting the need for broader variant coverage.

SURFBAT: a surrogate family-based association test building on large imputation reference panels

SURFBAT approximates transmission-disequilibrium tests using imputed haplotypes to detect genotype-phenotype associations while being robust to population stratification.

Yield of genetic association signals from genomes, exomes, and imputation in the UK biobank

The paper compares the effectiveness of whole genome sequencing, whole exome sequencing with imputation, and array genotyping in detecting genetic associations across 100 complex traits in the UK Biobank, finding that WES+IMP provides similar signal yield to WGS with greater efficiency.

Improving population scale statistical phasing with whole-genome sequencing data

This paper introduces SAPPHIRE, a method that improves haplotype phasing accuracy using whole-genome sequencing data by refining phase calls with read-level information.

A resampling-based approach to share reference panels

The paper introduces RESHAPE, a method to anonymize reference panels by simulating descendant genomes, enabling genotype imputation while protecting privacy.

Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA

This study evaluates how post-mortem damage and contamination affect imputation performance in ancient DNA, finding that ATLAS improves results for highly damaged genomes and contamination above 5% reduces accuracy.

Non-coding rare variant associations with blood traits on 166,740 UK Biobank genomes

This study identifies non-coding rare variant associations with blood traits in 166,740 UK Biobank genomes but finds most associations are driven by linkage disequilibrium with common variants.

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes

The paper introduces GLIMPSE v2.0.0, a scalable imputation method for low-coverage genomes, reducing computational costs while maintaining high accuracy for rare variants and low-coverage samples.

Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank

This paper introduces SHAPEIT5, a phasing method that accurately phases rare variants in UK Biobank WGS and WES data, improving imputation accuracy and identifying gene essentiality through compound heterozygous events.

Widespread enhancer co-activity identified by multimodal single cell analysis

The paper identifies widespread enhancer co-activity in human lymphoblastoid cells using scATAC-seq and scRNA-seq, revealing correlations between enhancer activity and gene expression.

Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks

The paper evaluates how haplotype estimation and whole genome imputation accuracy vary with data integration protocols and phasing methods in a large psychiatric biobank dataset.

Parent-of-origin effects in the UK Biobank

The paper infers parent-of-origin effects in the UK Biobank using a novel probabilistic method, identifying 101 significant associations across 59 biomarkers and 38 phenotypes.

Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis

The paper uses single-cell data to analyze local gene co-expression, showing that many co-expressed gene pairs share regulatory elements and functionally related genes.

Genetic variation in correlated regulatory region of Immunity

The paper identifies regulatory domains in immune cells using genomic and epigenomic data, revealing cell-type specific gene regulation and genetic control of regulatory elements.

Imputation of ancient genomes

This study evaluates the accuracy of genotype imputation for ancient genomes and finds it comparable to modern DNA, with some population-specific biases.

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The paper generates a comprehensive haplotype map of the Iberian population using high-coverage whole-genome sequencing, focusing on structural variants and their imputation capabilities.

Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome

This paper introduces revTWMR, a method to determine causal relationships between gene expression and complex traits, finding that traits more strongly influence gene expression than vice versa.

The molecular basis, genetic control and pleiotropic effects of local gene co-expression

The paper identifies local gene co-expression patterns across human tissues and links them to eQTLs associated with multiple traits.

Efficient phasing and imputation of low-coverage sequencing data using large reference panels

This study introduces GLIMPSE, a method for efficient phasing and imputation of low-coverage sequencing data, showing improved accuracy and cost-effectiveness compared to existing methods.

Genotype imputation using the Positional Burrows Wheeler Transform

IMPUTE5 improves genotype imputation by scaling sub-linearly with reference panel size and using the Positional Burrows Wheeler Transform for efficient haplotype selection.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.

Integrative haplotype estimation with sub-linear complexity

SHAPEIT4 improves haplotype estimation with sub-linear scaling, high accuracy, and integration of external phasing information using UK Biobank and Genome In A Bottle datasets.

Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

The paper combines regulatory element activity, gene expression, and genetic variation data across cell types to show how chromatin structure influences regulatory networks and genetic effects.

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

The paper develops a personalized pipeline to estimate HLA gene expression and map eQTLs, showing improved accuracy and better eQTL results compared to standard methods.