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Abanish Singh

Assistant Professor in Psychiatry and Behavioral Sciences
Psychiatry & Behavioral Sciences, Behavioral Medicine & Neurosciences
Duke Box 102506, Durham, NC 27705
2400 Pratt Street, #7023, Durham, NC 27705

Selected Publications


GENETIC ARCHITECTURE OF ALZHEIMER'S DISEASE RISKS

Journal Article Innovation in Aging · December 20, 2022 Featured Publication AbstractMore than 6 million people in the US live with Alzheimer's disease (AD) and related-dementia. There is a racial disparity in the prevalence of disease. However, its full genetic architecture and comp ... Full text Cite

Relationship Between Psychosocial Stress and Blood Pressure: The National Heart, Lung, and Blood Institute Family Heart Study.

Journal Article SAGE Open Nurs · 2022 INTRODUCTION: Various domains of psychosocial stress have been significantly related to blood pressure. However, ambiguity is present in how these relationships are defined in the literature. OBJECTIVE: To add to the existing literature and examine the rel ... Full text Open Access Link to item Cite

Evaluating the precision of EBF1 SNP x stress interaction association: sex, race, and age differences in a big harmonized data set of 28,026 participants.

Journal Article Transl Psychiatry · October 20, 2020 Featured Publication In prior work, we identified a novel gene-by-stress association of EBF1's common variation (SNP rs4704963) with obesity (i.e., hip, waist) in Whites, which was further strengthened through multiple replications using our synthetic stress measure. We now ex ... Full text Open Access Link to item Cite

Systolic Blood Pressure and Socioeconomic Status in a large multi-study population.

Journal Article SSM Popul Health · December 2019 The present study used harmonized data from eight studies (N = 28,891) to examine the association between socioeconomic status (SES) and resting systolic blood pressure (SBP). The study replicates and extends our prior work on this topic by examining poten ... Full text Open Access Link to item Cite

Developing a synthetic psychosocial stress measure and harmonizing CVD-risk data: a way forward to GxE meta- and mega-analyses.

Journal Article BMC Res Notes · July 24, 2018 Featured Publication OBJECTIVES: Among many challenges in cardiovascular disease (CVD) risk prediction are interactions of genes with stress, race, and/or sex and developing robust estimates of these interactions. Improved power with larger sample size contributed by the accum ... Full text Link to item Cite

Lack of Association of a Functional Polymorphism in the Serotonin Receptor Gene With Body Mass Index and Depressive Symptoms in a Large Meta-Analysis of Population Based Studies.

Journal Article Front Genet · 2018 The serotonin receptor 5-HTR2C is thought to be involved in the function of multiple brain structures. Consequently, the HTR2C gene has been studied extensively with respect to its association with a variety of phenotypes. One coding variant in the HTR2C g ... Full text Open Access Link to item Cite

Brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism is associated with disease severity and incidence of cardiovascular events in a patient cohort.

Journal Article Am Heart J · August 2017 BACKGROUND: The rs6265 (Val66Met) single-nucleotide polymorphism in the BDNF gene has been related to a number of endophenotypes that have in turn been shown to confer risk for atherosclerotic cardiovascular disease (CVD). To date, however, very few studie ... Full text Link to item Cite

Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship.

Journal Article PLoS One · 2016 Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific su ... Full text Link to item Cite

Computing a Synthetic Chronic Psychosocial Stress Measurement in Multiple Datasets and its Application in the Replication of G × E Interactions of the EBF1 Gene.

Journal Article Genet Epidemiol · September 2015 Featured Publication Chronic psychosocial stress adversely affects health and is associated with the development of disease [Williams, 2008]. Systematic epidemiological and genetic studies are needed to uncover genetic variants that interact with stress to modify metabolic res ... Full text Link to item Cite

Gene by stress genome-wide interaction analysis and path analysis identify EBF1 as a cardiovascular and metabolic risk gene.

Journal Article Eur J Hum Genet · June 2015 Featured Publication We performed gene-environment interaction genome-wide association analysis (G × E GWAS) to identify SNPs whose effects on metabolic traits are modified by chronic psychosocial stress in the Multi-Ethnic Study of Atherosclerosis (MESA). In Whites, the G × E ... Full text Open Access Link to item Cite

A putatively functional polymorphism in the HTR2C gene is associated with depressive symptoms in white females reporting significant life stress.

Journal Article PLoS One · 2014 Psychosocial stress is well known to be positively associated with subsequent depressive symptoms. Cortisol response to stress may be one of a number of biological mechanisms that links psychological stress to depressive symptoms, although the precise caus ... Full text Open Access Link to item Cite

Chronic family stress moderates the association between a TOMM40 variant and triglyceride levels in two independent Caucasian samples.

Journal Article Biol Psychol · April 2013 TOMM40 SNP rs157580 has been associated with triglyceride levels in genome-wide association studies (GWAS). Chronic caregiving stress moderates the association between triglyceride levels and a nearby SNP rs439401 that is associated with triglyceride level ... Full text Link to item Cite

A functional polymorphism in the 5HTR2C gene associated with stress responses also predicts incident cardiovascular events.

Journal Article PLoS One · 2013 Previously we have shown that a functional nonsynonymous single nucleotide polymorphism (rs6318) of the 5HTR2C gene located on the X-chromosome is associated with hypothalamic-pituitary-adrenal axis response to a stress recall task, and with endophenotypes ... Full text Open Access Link to item Cite

Socioeconomic indices as independent correlates of C-reactive protein in the National Longitudinal Study of Adolescent Health.

Journal Article Psychosom Med · 2013 OBJECTIVES: To examine the association between socioeconomic status (SES) and C-reactive protein (CRP) to understand how SES may increase the risk of cardiovascular disease and thus identify targets for prevention measures. METHODS: Path models were used t ... Full text Link to item Cite

Using ERDS to infer copy-number variants in high-coverage genomes.

Journal Article Am J Hum Genet · September 7, 2012 Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types o ... Full text Link to item Cite

Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients.

Journal Article J Hepatol · February 2012 Featured Publication BACKGROUND & AIMS: Interferon-alfa (IFN)-related cytopenias are common and may be dose-limiting. We performed a genome wide association study on a well-characterized genotype 1 HCV cohort to identify genetic determinants of peginterferon-α (pegIFN)-related ... Full text Link to item Cite

GENETIC ARCHITECTURE OF ALZHEIMER'S DISEASE RISKS

Journal Article Innovation in Aging · December 20, 2022 Featured Publication AbstractMore than 6 million people in the US live with Alzheimer's disease (AD) and related-dementia. There is a racial disparity in the prevalence of disease. However, its full genetic architecture and comp ... Full text Cite

Relationship Between Psychosocial Stress and Blood Pressure: The National Heart, Lung, and Blood Institute Family Heart Study.

Journal Article SAGE Open Nurs · 2022 INTRODUCTION: Various domains of psychosocial stress have been significantly related to blood pressure. However, ambiguity is present in how these relationships are defined in the literature. OBJECTIVE: To add to the existing literature and examine the rel ... Full text Open Access Link to item Cite

Evaluating the precision of EBF1 SNP x stress interaction association: sex, race, and age differences in a big harmonized data set of 28,026 participants.

Journal Article Transl Psychiatry · October 20, 2020 Featured Publication In prior work, we identified a novel gene-by-stress association of EBF1's common variation (SNP rs4704963) with obesity (i.e., hip, waist) in Whites, which was further strengthened through multiple replications using our synthetic stress measure. We now ex ... Full text Open Access Link to item Cite

Systolic Blood Pressure and Socioeconomic Status in a large multi-study population.

Journal Article SSM Popul Health · December 2019 The present study used harmonized data from eight studies (N = 28,891) to examine the association between socioeconomic status (SES) and resting systolic blood pressure (SBP). The study replicates and extends our prior work on this topic by examining poten ... Full text Open Access Link to item Cite

Developing a synthetic psychosocial stress measure and harmonizing CVD-risk data: a way forward to GxE meta- and mega-analyses.

Journal Article BMC Res Notes · July 24, 2018 Featured Publication OBJECTIVES: Among many challenges in cardiovascular disease (CVD) risk prediction are interactions of genes with stress, race, and/or sex and developing robust estimates of these interactions. Improved power with larger sample size contributed by the accum ... Full text Link to item Cite

Lack of Association of a Functional Polymorphism in the Serotonin Receptor Gene With Body Mass Index and Depressive Symptoms in a Large Meta-Analysis of Population Based Studies.

Journal Article Front Genet · 2018 The serotonin receptor 5-HTR2C is thought to be involved in the function of multiple brain structures. Consequently, the HTR2C gene has been studied extensively with respect to its association with a variety of phenotypes. One coding variant in the HTR2C g ... Full text Open Access Link to item Cite

Brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism is associated with disease severity and incidence of cardiovascular events in a patient cohort.

Journal Article Am Heart J · August 2017 BACKGROUND: The rs6265 (Val66Met) single-nucleotide polymorphism in the BDNF gene has been related to a number of endophenotypes that have in turn been shown to confer risk for atherosclerotic cardiovascular disease (CVD). To date, however, very few studie ... Full text Link to item Cite

Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship.

Journal Article PLoS One · 2016 Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific su ... Full text Link to item Cite

Computing a Synthetic Chronic Psychosocial Stress Measurement in Multiple Datasets and its Application in the Replication of G × E Interactions of the EBF1 Gene.

Journal Article Genet Epidemiol · September 2015 Featured Publication Chronic psychosocial stress adversely affects health and is associated with the development of disease [Williams, 2008]. Systematic epidemiological and genetic studies are needed to uncover genetic variants that interact with stress to modify metabolic res ... Full text Link to item Cite

Gene by stress genome-wide interaction analysis and path analysis identify EBF1 as a cardiovascular and metabolic risk gene.

Journal Article Eur J Hum Genet · June 2015 Featured Publication We performed gene-environment interaction genome-wide association analysis (G × E GWAS) to identify SNPs whose effects on metabolic traits are modified by chronic psychosocial stress in the Multi-Ethnic Study of Atherosclerosis (MESA). In Whites, the G × E ... Full text Open Access Link to item Cite

A putatively functional polymorphism in the HTR2C gene is associated with depressive symptoms in white females reporting significant life stress.

Journal Article PLoS One · 2014 Psychosocial stress is well known to be positively associated with subsequent depressive symptoms. Cortisol response to stress may be one of a number of biological mechanisms that links psychological stress to depressive symptoms, although the precise caus ... Full text Open Access Link to item Cite

Chronic family stress moderates the association between a TOMM40 variant and triglyceride levels in two independent Caucasian samples.

Journal Article Biol Psychol · April 2013 TOMM40 SNP rs157580 has been associated with triglyceride levels in genome-wide association studies (GWAS). Chronic caregiving stress moderates the association between triglyceride levels and a nearby SNP rs439401 that is associated with triglyceride level ... Full text Link to item Cite

A functional polymorphism in the 5HTR2C gene associated with stress responses also predicts incident cardiovascular events.

Journal Article PLoS One · 2013 Previously we have shown that a functional nonsynonymous single nucleotide polymorphism (rs6318) of the 5HTR2C gene located on the X-chromosome is associated with hypothalamic-pituitary-adrenal axis response to a stress recall task, and with endophenotypes ... Full text Open Access Link to item Cite

Socioeconomic indices as independent correlates of C-reactive protein in the National Longitudinal Study of Adolescent Health.

Journal Article Psychosom Med · 2013 OBJECTIVES: To examine the association between socioeconomic status (SES) and C-reactive protein (CRP) to understand how SES may increase the risk of cardiovascular disease and thus identify targets for prevention measures. METHODS: Path models were used t ... Full text Link to item Cite

Using ERDS to infer copy-number variants in high-coverage genomes.

Journal Article Am J Hum Genet · September 7, 2012 Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types o ... Full text Link to item Cite

Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients.

Journal Article J Hepatol · February 2012 Featured Publication BACKGROUND & AIMS: Interferon-alfa (IFN)-related cytopenias are common and may be dose-limiting. We performed a genome wide association study on a well-characterized genotype 1 HCV cohort to identify genetic determinants of peginterferon-α (pegIFN)-related ... Full text Link to item Cite

A whole-genome analysis of premature termination codons.

Journal Article Genomics · November 2011 We sequenced the genomes of ten unrelated individuals and identified heterozygous stop codon-gain variants in protein-coding genes: we then sequenced their transcriptomes and assessed the expression levels of the stop codon-gain alleles. An ANOVA showed st ... Full text Link to item Cite

SVA: software for annotating and visualizing sequenced human genomes.

Journal Article Bioinformatics · July 15, 2011 SUMMARY: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. ... Full text Link to item Cite

Exploring Motif Composition of Eukaryotic Promoter Regions. In: Arabnia, H. (eds) Advances in Computational Biology. Advances in Experimental Medicine and Biolog

Chapter · October 6, 2010 Proceedings of The 2009 International Conference on Bioinformatics and Computational Biology in Las Vegas, NV, July 13-16, 2009. Recent advances in Computational Biology are covered through a variety of topics. ... Full text Link to item Cite

The characterization of twenty sequenced human genomes.

Journal Article PLoS Genet · September 9, 2010 Featured Publication We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and te ... Full text Open Access Link to item Cite

An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.

Journal Article Int J Bioinform Res Appl · 2010 Featured Publication Interspersed repeats, mostly resulting from the activity and accumulation of transposable elements, occupy a significant fraction of many eukaryotic genomes. More than half of human genomic sequence consists of known repeats, however a very large part has ... Full text Link to item Cite

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

Journal Article Genome Biol · 2010 Featured Publication BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon cap ... Full text Open Access Link to item Cite

An algorithm for finding substantially broken repeated sequences in newly sequenced genomes

Conference AIP Conference Proceedings · December 1, 2007 Interspersed repeats occupy a significant fraction of many eukaryotic genomes. They result from the activity and accumulation of transposable elements, sequences which are able to replicate in virtually all organisms and which have been successfully mainta ... Full text Cite

Micro-repetitive structure of genomic sequences and the identification of ancient repeat elements

Conference Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007 · December 1, 2007 For many years the attempts to identify functional elements in genomic sequences through motif over-representation have been problematic, as every procedure to isolate such motifs resulted in a very large number of candidates with highly significant p-valu ... Full text Cite

A study of the repetitive structure and distribution of short motifs in human genomic sequences.

Journal Article Int J Bioinform Res Appl · 2007 Over the last several years the search for functional genomic elements by exploiting motif over-representation became increasingly popular. However, about half of the human genome is repetitive, and that is also the case with most higher eukaryotes. In thi ... Full text Link to item Cite