Andrew J. Sharp
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View article: A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank
A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank Open
Using genome sequencing read depth, we genotyped CNVs within the UK Biobank and performed PheWAS, identifying 501 CNVs associated with 1,537 traits. We detected signals with mosaic, recurrent and multiallelic CNVs that are difficult to gen…
View article: A Population‐Wide Exploration of the <scp><i>THAP11</i> CAG</scp> Repeat Size and Structure in the 100,000 Genomes Project and <scp>UK</scp> Biobank
A Population‐Wide Exploration of the <span><i>THAP11</i> CAG</span> Repeat Size and Structure in the 100,000 Genomes Project and <span>UK</span> Biobank Open
Background A CAG repeat expansion in THAP11 was recently found to be associated with spinocerebellar ataxia in two Chinese families. Expanded repeats ranged from 45 to 100 units, with CAA sequence interruptions in the 5′ region and an unin…
View article: A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank
A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank Open
Most genetic association studies focus on binary variants. To identify the effects of multi-allelic variation of tandem repeats (TRs) on human traits, we perform direct TR genotyping and phenome-wide association studies in 168,554 individu…
View article: Genetic variation of tandem repeats as a cause of Alzheimer’s Disease
Genetic variation of tandem repeats as a cause of Alzheimer’s Disease Open
Background Alzheimer’s Disease (AD) is a common neurodegenerative disorder affecting >35 million people worldwide. Despite extensive genetic studies, the identified factors only explain a small fraction of the heritable risk of AD. This su…
View article: TRGT-denovo: accurate detection of<i>de novo</i>tandem repeat mutations
TRGT-denovo: accurate detection of<i>de novo</i>tandem repeat mutations Open
Motivation Identifying de novo tandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of th…
View article: A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank
A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank Open
Most genetic association studies focus on binary variants. To identify the effects of multi-allelic variation of tandem repeats (TRs) on human traits, we performed direct TR genotyping and phenome-wide association studies in 168,554 indivi…
View article: Feeder-free generation and characterization of endocardial and cardiac valve cells from human pluripotent stem cells
Feeder-free generation and characterization of endocardial and cardiac valve cells from human pluripotent stem cells Open
Valvular heart disease presents a significant health burden, yet advancements in valve biology and therapeutics have been hindered by the lack of accessibility to human valve cells. In this study, we have developed a scalable and feeder-fr…
View article: Increased frequency of repeat expansion mutations across different populations
Increased frequency of repeat expansion mutations across different populations Open
Repeat expansion disorders (REDs) are a devastating group of predominantly neurological diseases. Together they are common, affecting 1 in 3,000 people worldwide with population-specific differences. However, prevalence estimates of REDs a…
View article: Population Frequency of Repeat Expansions Indicates Increased Disease Prevalence Estimates Across Different Populations
Population Frequency of Repeat Expansions Indicates Increased Disease Prevalence Estimates Across Different Populations Open
Repeat expansion disorders (REDs) are a devastating group of predominantly neurological diseases. Together they are common, affecting 1 in 3,000 people worldwide with population-specific differences. However, prevalence estimates of REDs a…
View article: A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in<i>AFF3</i>as a significant cause of intellectual disability
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in<i>AFF3</i>as a significant cause of intellectual disability Open
GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites and underlie several congenital and late-onset disorders. Through a combination of DNA methylation profili…
View article: Feeder-Free Generation of Endocardial and Cardiac Valve Cells from Human Pluripotent Stem Cells
Feeder-Free Generation of Endocardial and Cardiac Valve Cells from Human Pluripotent Stem Cells Open
Summary Valvular heart disease presents a significant health burden, yet advancements in valve biology and novel therapeutics have been hindered by the lack of accessibility to human valve cells. In this study, we have developed a scalable…
View article: Assessing the burden of rare DNA methylation deviations in schizophrenia
Assessing the burden of rare DNA methylation deviations in schizophrenia Open
Along with case-control group differences in DNA methylation (DNAm) identified in epigenomewide association studies (EWAS), multiple rare DNAm outliers may exist in subsets of cases, underlying the etiological heterogeneity of some disorde…
View article: Additional file 2 of Small open reading frames: a comparative genetics approach to validation
Additional file 2 of Small open reading frames: a comparative genetics approach to validation Open
Additional file 2: Table S2. List of smORFs carrying disease-associated SNVs from GWAS catalog.
View article: Additional file 1 of Small open reading frames: a comparative genetics approach to validation
Additional file 1 of Small open reading frames: a comparative genetics approach to validation Open
Additional file 1: Table S1. List of high-confidence smORFs and known smORFs.
View article: The strength of migratory connectivity in Painted Buntings is spatial scale dependent and shaped by molting behavior
The strength of migratory connectivity in Painted Buntings is spatial scale dependent and shaped by molting behavior Open
As migratory species move through the stages of their annual cycle, individuals often display variation in the degree to which they remain in proximity to one another, a phenomenon called migratory connectivity. We show scale dependence in…
View article: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation Open
Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has been extensively assessed, their impact on epigenetics ha…
View article: Human knowledge models: Learning applied knowledge from the data
Human knowledge models: Learning applied knowledge from the data Open
Artificial intelligence and machine learning have demonstrated remarkable results in science and applied work. However, present AI models, developed to be run on computers but used in human-driven applications, create a visible disconnect …
View article: Spatial and temporal scale-dependence of the strength of migratory connectivity in a North American passerine
Spatial and temporal scale-dependence of the strength of migratory connectivity in a North American passerine Open
Background Migratory connectivity describes the extent to which portions of a migratory population that are spatially associated during one stage of the annual cycle remain associated during other stages of the annual cycle. The strength o…
View article: A phenome-wide association study identifies effects of copy number variation of VNTRs and multicopy genes on multiple human traits
A phenome-wide association study identifies effects of copy number variation of VNTRs and multicopy genes on multiple human traits Open
The human genome contains tens of thousands of large tandem repeats and hundreds of genes that show common and highly variable copy number changes. Due to their large size and repetitive nature, these Variable Number Tandem Repeats (VNTRs)…
View article: Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank
Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank Open
Clinical features of individuals harboring NDD CNVs were elucidated in a large-scale, multiancestry biobank, identifying enrichments for congenital disorders and major depressive disorder as well as associations with several medical outcom…
View article: Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci
Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci Open
Lymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and method…
View article: Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci
Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci Open
Lymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and method…
View article: A Survey of Copy Number Variants Associated with Neurodevelopmental Disorders in a Large-Scale, Multi-Ancestry Biobank
A Survey of Copy Number Variants Associated with Neurodevelopmental Disorders in a Large-Scale, Multi-Ancestry Biobank Open
BACKGROUND Past clinical genetic studies have identified rare, copy number variants (CNVs) as risk factors for multiple neurodevelopmental disorders (NDD), including autism spectrum disorder and schizophrenia. However, the broad, clinical …