Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

J Yang, T Ferreira, AP Morris, SE Medland… - Nature …, 2012 - nature.com
We present an approximate conditional and joint association analysis that can use summary-
level statistics from a meta-analysis of genome-wide association studies (GWAS) and …

A linear complexity phasing method for thousands of genomes

O Delaneau, J Marchini, JF Zagury - Nature methods, 2012 - nature.com
Human-disease etiology can be better understood with phase information about diploid
sequences. We present a method for estimating haplotypes, using genotype data from …

Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening

BD Stuart, J Choi, S Zaidi, C Xing, B Holohan, R Chen… - Nature …, 2015 - nature.com
Idiopathic pulmonary fibrosis (IPF) is an age-related disease featuring progressive lung
scarring. To elucidate the molecular basis of IPF, we performed exome sequencing of …

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

JA Tennessen, AW Bigham, TD O'connor, W Fu… - science, 2012 - science.org
As a first step toward understanding how rare variants contribute to risk for complex
diseases, we sequenced 15,585 human protein-coding genes to an average median depth …

[HTML][HTML] A map of human genome variation from population scale sequencing

1000 Genomes Project Consortium - Nature, 2010 - ncbi.nlm.nih.gov
Abstract The 1000 Genomes Project aims to provide a deep characterisation of human
genome sequence variation as a foundation for investigating the relationship between …

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

J Huang, B Howie, S McCarthy, Y Memari… - Nature …, 2015 - nature.com
Imputing genotypes from reference panels created by whole-genome sequencing (WGS)
provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) …

Genomic variation landscape of the human gut microbiome

S Schloissnig, M Arumugam, S Sunagawa, M Mitreva… - Nature, 2013 - nature.com
Whereas large-scale efforts have rapidly advanced the understanding and practical impact
of human genomic variation, the practical impact of variation is largely unexplored in the …

Multiple deeply divergent Denisovan ancestries in Papuans

GS Jacobs, G Hudjashov, L Saag, P Kusuma… - Cell, 2019 - cell.com
Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—
which interbred with anatomically modern humans as they dispersed out of Africa. We …

The (in) famous GWAS P-value threshold revisited and updated for low-frequency variants

J Fadista, AK Manning, JC Florez… - European Journal of …, 2016 - nature.com
Genome-wide association studies (GWAS) have long relied on proposed statistical
significance thresholds to be able to differentiate true positives from false positives. Although …

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

K Estrada, U Styrkarsdottir, E Evangelou, YH Hsu… - Nature …, 2012 - nature.com
Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed
the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 …