Combining eQTL and SNP annotation data to identify functional noncoding SNPs in GWAS trait-associated regions

SA Ramsey, Z Liu, Y Yao, B Weeder - eQTL Analysis: Methods and …, 2020 - Springer
We describe a statistical method for prioritizing candidate causal noncoding single
nucleotide polymorphisms (SNPs) in regions of the genome that are detected as trait …

SNP2GO: functional analysis of genome-wide association studies

D Szkiba, M Kapun, A von Haeseler, M Gallach - Genetics, 2014 - academic.oup.com
Genome-wide association studies (GWAS) are designed to identify the portion of single-
nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait …

TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes

A González, M Artufel, P Rihet - Nucleic Acids Research, 2019 - academic.oup.com
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms
(SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely …

Mining the unknown: assigning function to noncoding single nucleotide polymorphisms

SS Nishizaki, AP Boyle - Trends in Genetics, 2017 - cell.com
One of the formative goals of genetics research is to understand how genetic variation leads
to phenotypic differences and human disease. Genome-wide association studies (GWASs) …

CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs

Y Yao, SA Ramsey - PACIFIC SYMPOSIUM ON BIOCOMPUTING …, 2019 - World Scientific
Identification of causal noncoding single nucleotide polymorphisms (SNPs) is important for
maximizing the knowledge dividend from human genome-wide association studies (GWAS) …

[HTML][HTML] CoMM-S4: A Collaborative Mixed Model Using Summary-Level eQTL and GWAS Datasets in Transcriptome-Wide Association Studies

Y Yang, KF Yeung, J Liu - Frontiers in Genetics, 2021 - frontiersin.org
Motivation: Genome-wide association studies (GWAS) have achieved remarkable success
in identifying SNP-trait associations in the last decade. However, it is challenging to identify …

[HTML][HTML] Using functional annotation for the empirical determination of Bayes Factors for genome-wide association study analysis

J Knight, MR Barnes, G Breen, ME Weale - PLoS One, 2011 - journals.plos.org
A genome wide association study (GWAS) typically results in a few highly significant 'hits'
and a much larger set of suggestive signals ('near-hits'). The latter group are expected to be …

Spadis: An algorithm for selecting predictive and diverse snps in gwas

S Yilmaz, O Tastan, AE Cicek - IEEE/ACM transactions on …, 2019 - ieeexplore.ieee.org
Phenotypic heritability of complex traits and diseases is seldom explained by individual
genetic variants identified in genome-wide association studies (GWAS). Many methods have …

CandiSNPer: a web tool for the identification of candidate SNPs for causal variants

AO Schmitt, J Aßmus, RH Bortfeldt… - …, 2010 - academic.oup.com
Human single nucleotide polymorphism (SNP) chips which are used in genome-wide
association studies (GWAS) permit the genotyping of up to 4 million SNPs simultaneously …

Incorporating prior knowledge to increase the power of genome-wide association studies

A Petersen, J Spratt, NL Tintle - Genome-Wide Association Studies and …, 2013 - Springer
Typical methods of analyzing genome-wide single nucleotide variant (SNV) data in cases
and controls involve testing each variant's genotypes separately for phenotype association …