Lukas Forer

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

The paper constructs a large-scale LD and genotype imputation reference panel using whole-genome sequencing data from 2,680 Indian participants, improving imputation accuracy and polygenic risk score performance.

Cloudgene 3: Transforming Nextflow Pipelines into Powerful Web Services

Cloudgene 3 converts Nextflow pipelines into web services, enabling easy sharing and collaboration without technical expertise.

Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex Lipoprotein(a) KIV-2 VNTR

This paper demonstrates that UMI-ONT-Seq accurately detects SNPs and quantifies VNTR copy numbers in the complex KIV-2 region across multiple ancestries.

Improving the Reliability and Quality of Nextflow Pipelines with nf-test

The paper introduces nf-test, a testing framework for Nextflow pipelines that improves reliability, reduces test time, and enhances software quality through modular and efficient testing.

Performing highly parallelized and reproducible GWAS analysis on biobank-scale data

The paper presents a Nextflow pipeline for scalable and reproducible GWAS analysis on large biobank datasets, validated against published datasets and tested on HPC and cloud infrastructures.

A statistical genetics guide to identifying HLA alleles driving complex disease

This paper provides a statistical genetics guide for imputing HLA alleles from genotype data and offers best practices for association testing to identify HLA variants driving complex diseases.

A Saturated Map of Common Genetic Variants Associated with Human Height from 5.4 Million Individuals of Diverse Ancestries

This study identifies 12,111 SNPs associated with height from 5.4 million individuals, explaining most common SNP-based heritability and showing ancestry-specific prediction accuracy.

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies

Haplocheck detects contamination in mitochondrial and whole-genome sequencing studies using mitochondrial phylogeny, showing high concordance with nuclear DNA results.

South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine

The paper characterizes the genetic structure of South Asian populations, identifies founder effects and high homozygosity, and develops a custom SNP array for genetic studies in the region.

Loss-of-function genomic variants with impact on liver-related blood traits highlight potential therapeutic targets for cardiovascular disease

The paper identifies loss-of-function variants affecting liver-related blood traits that reduce CVD risk without increasing metabolic disease risk, highlighting potential therapeutic targets.

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.

Reference-based phasing using the Haplotype Reference Consortium panel

This paper introduces Eagle2, a reference-based phasing algorithm that improves accuracy and speed compared to SHAPEIT2 using the Haplotype Reference Consortium panel.