Interpreting noncoding genetic variation in complex traits and human disease

LD Ward, M Kellis - Nature biotechnology, 2012 - nature.com
Association studies provide genome-wide information about the genetic basis of complex
disease, but medical research has focused primarily on protein-coding variants, owing to the …

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

GM Cooper, J Shendure - Nature Reviews Genetics, 2011 - nature.com
Genome and exome sequencing yield extensive catalogues of human genetic variation.
However, pinpointing the few phenotypically causal variants among the many variants …

Variation graph toolkit improves read mapping by representing genetic variation in the reference

E Garrison, J Sirén, AM Novak, G Hickey… - Nature …, 2018 - nature.com
Reference genomes guide our interpretation of DNA sequence data. However, conventional
linear references represent only one version of each locus, ignoring variation in the …

Genetic drivers of epigenetic and transcriptional variation in human immune cells

L Chen, B Ge, FP Casale, L Vasquez, T Kwan… - Cell, 2016 - cell.com
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease
phenotypes is a major challenge in human genetics and medicine. We carried out high …

RNA sequencing and analysis

KR Kukurba, SB Montgomery - Cold Spring Harbor Protocols, 2015 - cshprotocols.cshlp.org
RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods
to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing …

Large-scale association analysis identifies new risk loci for coronary artery disease

CARDIoGRAMplusC4D Consortium, P Deloukas… - Nature …, 2013 - nature.com
Coronary artery disease (CAD) is the commonest cause of death. Here, we report an
association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching …

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 …

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

A Battle, S Mostafavi, X Zhu, JB Potash… - Genome …, 2014 - genome.cshlp.org
Understanding the consequences of regulatory variation in the human genome remains a
major challenge, with important implications for understanding gene regulation and …

Tools and best practices for data processing in allelic expression analysis

SE Castel, A Levy-Moonshine, P Mohammadi, E Banks… - Genome biology, 2015 - Springer
Allelic expression analysis has become important for integrating genome and transcriptome
data to characterize various biological phenomena such as cis-regulatory variation and …

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

H Schunkert, IR König, S Kathiresan, MP Reilly… - Nature …, 2011 - nature.com
We performed a meta-analysis of 14 genome-wide association studies of coronary artery
disease (CAD) comprising 22,233 individuals with CAD (cases) and 64,762 controls of …