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Andrew Scott Allen

Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Integrative Genomics
Duke Box 103854, Durham, NC 27710
3 Genome Ct, 1245 MSRB III, Durham, NC 27705

Selected Publications


Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia.

Journal Article Am J Med Genet A · February 2025 Variation in the non-coding genome represents an understudied mechanism of disease and it remains challenging to predict if single nucleotide variants, small insertions and deletions, or structural variants in non-coding genomic regions will be detrimental ... Full text Link to item Cite

The role of copy number variants in the genetic architecture of common familial epilepsies.

Journal Article Epilepsia · March 2024 OBJECTIVE: Copy number variants (CNVs) contribute to genetic risk and genetic etiology of both rare and common epilepsies. Whereas many studies have explored the role of CNVs in sporadic or severe cases, fewer have been done in familial generalized and foc ... Full text Link to item Cite

DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree.

Journal Article Genet Epidemiol · February 2024 Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggr ... Full text Link to item Cite

Ultra-rare genetic variation in relapsing polychondritis: a whole-exome sequencing study.

Journal Article Ann Rheum Dis · January 11, 2024 OBJECTIVE: Relapsing polychondritis (RP) is a systemic inflammatory disease of unknown aetiology. The objective of this study was to examine the contribution of rare genetic variations to RP. METHODS: We performed a case-control exome-wide rare variant ass ... Full text Link to item Cite

Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens.

Journal Article Nat Genet · December 2023 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 phenotypes has potential to improve T cell therapi ... Full text Link to item Cite

Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations.

Journal Article Nature communications · November 2023 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 by a cancer-like three-hit mutational mechanism, ... Full text Cite

Prevalence and significance of clonal hematopoiesis of indeterminate potential in lung transplant recipients.

Journal Article BMC Pulm Med · October 30, 2023 BACKGROUND: Clonal hematopoiesis of indeterminate potential (CHIP), the age-related acquisition of somatic mutations that leads to an expanded blood cell clone, has been associated with development of a pro-inflammatory state. An enhanced or dysregulated i ... Full text Link to item Cite

Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals.

Journal Article Nat Commun · July 20, 2023 Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16 ... Full text Link to item Cite

Ultra-Rare Genetic Variation in Relapsing Polychondritis: A Whole-Exome Sequencing Study.

Conference medRxiv · April 17, 2023 OBJECTIVE: Relapsing polychondritis (RP) is a systemic inflammatory disease of unknown etiology. The study objective was to examine the contribution of rare genetic variations in RP. METHODS: We performed a case-control exome-wide rare variant association ... Full text Link to item Cite

Analysing an allelic series of rare missense variants of CACNA1I in a Swedish schizophrenia cohort.

Journal Article Brain · June 3, 2022 CACNA1I is implicated in the susceptibility to schizophrenia by large-scale genetic association studies of single nucleotide polymorphisms. However, the channelopathy of CACNA1I in schizophrenia is unknown. CACNA1I encodes CaV3.3, a neuronal voltage-gated ... Full text Link to item Cite

Ancestry adjustment improves genome-wide estimates of regional intolerance.

Journal Article Genetics · May 31, 2022 Genomic regions subject to purifying selection are more likely to carry disease-causing mutations than regions not under selection. Cross species conservation is often used to identify such regions but with limited resolution to detect selection on short e ... Full text Link to item Cite

Novel Fluorescence-Based High-Throughput FLIPR Assay Utilizing Membrane-Tethered Genetic Calcium Sensors to Identify T-Type Calcium Channel Modulators.

Journal Article ACS Pharmacol Transl Sci · March 11, 2022 T-type voltage-gated Ca2+ channels have been implicated in many human disorders, and there has been increasing interest in developing highly selective and potent T-type Ca2+ channel modulators for potential clinical use. However, the unique biophysical pro ... Full text Link to item Cite

Association of ultra-rare coding variants with genetic generalized epilepsy: A case-control whole exome sequencing study.

Journal Article Epilepsia · March 2022 OBJECTIVE: We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with fam ... Full text Link to item Cite

Focused goodness of fit tests for gene set analyses.

Journal Article Brief Bioinform · January 17, 2022 Gene set-based signal detection analyses are used to detect an association between a trait and a set of genes by accumulating signals across the genes in the gene set. Since signal detection is concerned with identifying whether any of the genes in the gen ... Full text Link to item Cite

Missing Data

Chapter · January 1, 2022 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 average treatment effect. This chapter defines di ... Full text Cite

A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors.

Journal Article Bioinformatics · December 22, 2021 MOTIVATION: Conservation is broadly used to identify biologically important (epi)genomic regions. In the case of tumor growth, preferential conservation of DNA methylation can be used to identify areas of particular functional importance to the tumor. Howe ... Full text Link to item Cite

Targeted long-read sequencing identifies missing disease-causing variation.

Journal Article Am J Hum Genet · August 5, 2021 Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate stru ... Full text Link to item Cite