Lukas Habegger

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.

A deep catalog of protein-coding variation in 985,830 individuals

This paper presents the largest catalog of human protein-coding variation from 985,830 individuals, identifying rare variants and their functional implications for precision medicine.

Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

The paper genotypes and sequences 140,000 adults from the Mexico City Prospective Study, revealing ancestry diversity and developing imputation resources for genetic studies.

Population-scale analysis of common and rare genetic variation associated with hearing loss in adults

This study identifies 53 genetic loci associated with hearing loss, including 15 novel ones, using genome-wide and exome-sequencing data from multiple cohorts.

Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection.

The paper examines genetic variation and natural selection at SARS-CoV-2 host genes in diverse populations and links selected variants to clinical phenotypes in COVID-19.

Rare Genetic Variation Underlying Human Diseases and Traits: Results from 200,000 Individuals in the UK Biobank

The paper identifies 51 known and 23 novel gene-disease associations using exome sequencing data from 200,000 UK Biobank participants, highlighting high-impact rare variants for 26 diseases and traits.

Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

This study evaluates polygenic risk scores (PRS) for cancer prediction in a racially diverse biobank, finding moderate improvements in discriminatory accuracy for European ancestry but limited gains for African ancestry.

GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms

This study identifies a rare variant in SLC30A10 associated with elevated ALT/AST and hypermanganesemia symptoms, suggesting broader health impacts beyond diagnosed cases.

Advancing Human Genetics Research and Drug Discovery through Exome Sequencing of the UK Biobank

The paper describes exome sequencing of 200,643 UK Biobank participants, providing a rich resource of coding variants for genetic and drug discovery research.

Computationally efficient whole genome regression for quantitative and binary traits

The paper introduces REGENIE, a fast whole genome regression method for quantitative and binary traits, showing computational efficiency and accuracy on UK Biobank data.

Validating gene-phenotype associations using relationships in the UMLS

The paper validates gene-phenotype associations by mapping genes to ICD codes using UMLS relationships, finding 249,764 gene-ICD mappings in a cohort of 92,455 samples.

Discovery of 318 novel loci for type-2 diabetes and related micro- and macrovascular outcomes among 1.4 million participants in a multi-ethnic meta-analysis.

Multi-ethnic type 2 diabetes (T2D) meta-analysis of 228,499 cases and 1,178,783 controls finds 318 previously unreported loci, 804 expression-colocalized genes, and 13 SNP-by-T2D vascular-outcome interactions.

Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

Profiling and leveraging relatedness in a precision medicine cohort of 92,455 exomes

The paper analyzes cryptic relatedness in a large exome cohort, identifies numerous close relationships, reconstructs pedigrees, and demonstrates their utility in improving mutation phasing and identifying de novo mutations.

KaryoScan: abnormal karyotype detection from whole-exome sequence

KaryoScan detects chromosomal anomalies from whole-exome sequencing, identifying aneuploidies and complex rearrangements in large cohorts.

Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes

The paper identifies and analyzes exonic copy number variants (CNVs) in 50,726 DiscovEHR participants, linking them to clinical traits and phenotypes.