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Article
Open AccessTranscriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens
Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phe...
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Article
Open AccessSingle-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations
Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven b...
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Reference Work Entry In depth
Missing Data
Missing data are commonly seen in randomized clinical trials. When missingness is not completely random, a complete-case analysis that ignores the missing data process often leads to biased estimates of the av...
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Article
Open AccessCoding and noncoding variants in EBF3 are involved in HADDS and simplex autism
Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo n...
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Living Reference Work Entry In depth
Missing Data
Missing data are commonly seen in randomized clinical trials. When missingness is not completely random, a complete-case analysis that ignores the missing data process often leads to biased estimates of the av...
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Article
Rare-variant collapsing analyses for complex traits: guidelines and applications
The first phase of genome-wide association studies (GWAS) assessed the role of common variation in human disease. Advances optimizing and economizing high-throughput sequencing have enabled a second phase of a...
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Article
Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2)
Herpes simplex virus type 2 (HSV-2) is an incurable viral infection with severity ranging from asymptomatic to frequent recurrences. The viral shedding rate has been shown as a reproducible HSV-2 severity end ...
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Article
Open AccessHuman genome-wide measurement of drug-responsive regulatory activity
Environmental stimuli commonly act via changes in gene regulation. Human-genome-scale assays to measure such responses are indirect or require knowledge of the transcription factors (TFs) involved. Here, we pr...
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Article
Open AccessMap** eQTL by leveraging multiple tissues and DNA methylation
DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variatio...
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Article
Open AccessTransversions have larger regulatory effects than transitions
Transversions (Tv’s) are more likely to alter the amino acid sequence of proteins than transitions (Ts’s), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the...
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Chapter and Conference Paper
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding
Many recent studies have emphasized the importance of genetic variants and mutations in cancer and other complex human diseases. The overwhelming majority of these variants occur in non-coding portions of the ...
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Article
Open AccessExploiting expression patterns across multiple tissues to map expression quantitative trait loci
In order to better understand complex diseases, it is important to understand how genetic variation in the regulatory regions affects gene expression. Genetic variants found in these regulatory regions have be...
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Article
Open AccessThe intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes
Ranking human genes based on their tolerance to functional genetic variation can greatly facilitate patient genome interpretation. It is well established, however, that different parts of proteins can have dif...
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Article
Open AccessA genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting
Humans vary in their susceptibility to acquiring Staphylococcus aureus infection, and research suggests that there is a genetic basis for this variability. Several recent genome-wide association studies (GWAS) ha...
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Article
Open AccessA weighted accumulation test for associating rare genetic variation with quantitative phenotypes
Currently there is a great deal of interest in develo** methods for testing the role that rare variation plays in disease development. Here we propose a weighted association test that accumulates genetic var...
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Article
Open AccessGenome-wide association analysis of rheumatoid arthritis data via haplotype sharing
We present computationally simple association tests based on haplotype sharing that can be easily applied to genome-wide association studies, while allowing use of fast (but not likelihood-based) haploty** a...
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Article
Open AccessEffect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies
The North American Rheumatoid Arthritis Consortium case-control study collected case participants across the United States and control participants from New York. More than 500,000 single-nucleotide polymorphi...
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Chapter and Conference Paper
Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies
The computational demands imposed by the large number of markers considered in a genome-wide association study (GWAS) have resulted in an extreme simplification in the types of analyses conducted. While sophis...
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Article
Open AccessAssociation map** via a class of haplotype-sharing statistics
We present a class of haplotype-sharing statistics useful for association map** in case-parent trio data. The framework presented allows derivation of novel tests as well as new simplified variance estimator...
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Article
Open AccessApplication of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study
Association studies of quantitative traits have often relied on methods in which a normal distribution of the trait is assumed. However, quantitative phenotypes from complex human diseases are often censored, ...
