Sanna, Serena, Busonero, Fabio, Maschio, Andrea, McArdle, Patrick F., Usala, Gianluca, Dei, Mariano, ...
Bilirubin, resulting largely from the turnover of hemoglobin, is found in the plasma in two main forms: unconjugated or conjugated with glucuronic acid. Unconjugated bilirubin is transported into...
Chen, Wei, Liang, Liming, Abecasis, Gonçalo R.
Summary: We describe an interactive package that provides graphical overviews of the results of whole-genome association studies in datasets with rich multi-dimensional phenotypic information, such...
BIOINFORMATICS ORIGINAL PAPER Genetics and population analysis (2008)
Zhaohui S. Qin, Shyam Gopalakrishnan, Gonçalo R. Abecasis
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria Vol. 22 no. 2 2006, pages 220–225 doi:10.1093/bioinformatics/bti762
Short Specialist Review Algorithmic improvements in gene mapping (2008)
The analysis of human gene mapping data has generated many challenging computational problems. The challenges arise because in most gene-mapping studies the DNA sequence of each individual is only...
Disomy On Chromosome, Gonçalo R. Abecasis, Rachel A. Burt, Diana Hall, Sylvia Bochum, Kimberly F. Doheny, ...
We report on our initial genetic linkage studies of schizophrenia in the genetically isolated population of the Afrikaners from South Africa. A 10-cM genomewide scan was performed on 143 small...
Mohlke, Karen L., Boehnke, Michael, Abecasis, Gonçalo R.
Genome-wide association studies are providing new insights into the genetic basis of metabolic and cardiovascular traits. In the past 3 years, common variants in ∼50 loci have been strongly...
GENOME: a rapid coalescent-based whole genome simulator (2007)
Liang, Liming, Zöllner, Sebastian, Abecasis, Gonçalo R.
Summary: GENOME proposes a rapid coalescent-based approach to simulate whole genome data. In addition to features of standard coalescent simulators, the program allows for recombination rates to vary...
Angelo Scuteri, Serena Sanna, Wei-Min Chen, Manuela Uda, Giuseppe Albai, James Strait, ...
The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not...
Heritability of Cardiovascular and Personality Traits in 6,148 Sardinians (2006)
Giuseppe Pilia, Wei-Min Chen, Angelo Scuteri, Marco Orrú, Giuseppe Albai, Mariano Dei, ...
In family studies, phenotypic similarities between relatives yield information on the overall contribution of genes to trait variation. Large samples are important for these family studies,...
A comparison of phasing algorithms for trios and unrelated individuals (2006)
Jonathan Marchini, David Cutler, Nick Patterson, Matthew Stephens, Eleazar Eskin, Eran Halperin, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Qin, Zhaohui S., Gopalakrishnan, Shyam, Abecasis, Gonçalo R.
Motivation: Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular...
Gonçalo R. Abecasis, Janis E. Wigginton
Single-nucleotide polymorphisms (SNPs) are rapidly replacing microsatellites as the markers of choice for genetic linkage studies and many other studies of human pedigrees. Here, we describe an...
quality assessment for gene mapping data (2005)
Janis E. Wigginton, Gonçalo R. Abecasis
PEDSTATS: descriptive statistics, graphics and
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data (2005)
Wigginton, Janis E., Abecasis, Gonçalo R.
Summary: We describe a tool that produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets. Our tool can also produce...
Zareparsi, Sepideh, Buraczynska, Monika, Branham, Kari E.H., Shah, Sapna, Eng, Donna, Li, Mingyao, ...
Age-related macular degeneration (AMD) is a genetically heterogeneous disease that leads to progressive and irreversible vision loss among the elderly. Inflammation, oxidative damage, cholesterol...
Sequence features in regions of weak and strong linkage disequilibrium (2005)
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data (2005)
Wigginton, Janis E., Abecasis, Gonçalo R.
Summary: We describe a tool that produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets. Our tool can also produce...
Zareparsi, Sepideh, Buraczynska, Monika, Branham, Kari E.H., Shah, Sapna, Eng, Donna, Li, Mingyao, ...
Age-related macular degeneration (AMD) is a genetically heterogeneous disease that leads to progressive and irreversible vision loss among the elderly. Inflammation, oxidative damage, cholesterol...
Nash, Matthew W., Huezo-Diaz, Patricia, Williamson, Richard J., Sterne, Abraham, Purcell, Shaun, Hoda, Farzana, ...
There is considerable evidence to suggest that the genetic vulnerabilities to depression and anxiety substantially overlap and quantitatively act to alter risk to both disorders. Continuous scales...
Nash, Matthew W., Huezo-Diaz, Patricia, Williamson, Richard J., Sterne, Abraham, Purcell, Shaun, Hoda, Farzana, ...
There is considerable evidence to suggest that the genetic vulnerabilities to depression and anxiety substantially overlap and quantitatively act to alter risk to both disorders. Continuous scales...
Nash, Matthew W., Huezo-Diaz, Patricia, Williamson, Richard J., Sterne, Abraham, Purcell, Shaun, Hoda, Farzana, ...
There is considerable evidence to suggest that the genetic vulnerabilities to depression and anxiety substantially overlap and quantitatively act to alter risk to both disorders. Continuous scales...
McKenzie, Colin A., Abecasis, Gonçalo R., Keavney, Bernard, Forrester, Terrence, Ratcliffe, Peter J., Julier, Cécile, ...
Circulating angiotensin I-converting enzyme (ACE) levels are influenced by a major quantitative trait locus (QTL) that maps to the ACE gene. Phylogenetic and measured haplotype analyses have...
McKenzie, Colin A., Abecasis, Gonçalo R., Keavney, Bernard, Forrester, Terrence, Ratcliffe, Peter J., Julier, Cécile, ...
Circulating angiotensin I-converting enzyme (ACE) levels are influenced by a major quantitative trait locus (QTL) that maps to the ACE gene. Phylogenetic and measured haplotype analyses have...
GRR: graphical representation of relationship errors (2001)
Abecasis, Gonçalo R., Cherny, Stacey S., Cookson, W. O. C., Cardon, Lon R.
Summary: A graphical tool for verifying assumed relationships between individuals in genetic studies is described. GRR can detect many common errors using genotypes from many markers. Availability:...
Genetic variation in the 22q11 locus and susceptibility to schizophrenia
Liu, Hui, Abecasis, Gonçalo R., Heath, Simon C., Knowles, Alyson, Demars, Sandra, Chen, Ying-Jiun, ...
An increased prevalence of microdeletions at the 22q11 locus has been reported in samples of patients with schizophrenia. 22q11 microdeletions represent the highest known genetic risk factor for the...
The Power to Detect Linkage Disequilibrium with Quantitative Traits in Selected Samples
Abecasis, Gonçalo R., Cookson, William O. C., Cardon, Lon R.
Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and...
Extent and Distribution of Linkage Disequilibrium in Three Genomic Regions
Abecasis, Gonçalo R., Noguchi, Emiko, Heinzmann, Andrea, Traherne, James A., Bhattacharyya, Sumit, Leaves, Nicholas I., ...
The positional cloning of genes underlying common complex diseases relies on the identification of linkage disequilibrium (LD) between genetic markers and disease. We have examined 127 polymorphisms...
Handling Marker-Marker Linkage Disequilibrium: Pedigree Analysis with Clustered Markers
Abecasis, Gonçalo R., Wigginton, Janis E.
Single-nucleotide polymorphisms (SNPs) are rapidly replacing microsatellites as the markers of choice for genetic linkage studies and many other studies of human pedigrees. Here, we describe an...
Sequence features in regions of weak and strong linkage disequilibrium
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Heritability of Cardiovascular and Personality Traits in 6,148 Sardinians
Pilia, Giuseppe, Chen, Wei-Min, Scuteri, Angelo, Orrú, Marco, Albai, Giuseppe, Dei, Mariano, ...
In family studies, phenotypic similarities between relatives yield information on the overall contribution of genes to trait variation. Large samples are important for these family studies,...
Li, Mingyao, Boehnke, Michael, Abecasis, Gonçalo R.
Linkage mapping of complex diseases is often followed by association studies between phenotypes and marker genotypes through use of case-control or family-based designs. Given fixed genotyping...
Sequence and Haplotype Analysis Supports HLA-C as the Psoriasis Susceptibility 1 Gene
Nair, Rajan P., Stuart, Philip E., Nistor, Ioana, Hiremagalore, Ravi, Chia, Nicholas V. C., Jenisch, Stefan, ...
Previous studies have narrowed the interval containing PSORS1, the psoriasis-susceptibility locus in the major histocompatibility complex (MHC), to an ∼300-kb region containing HLA-C and at least...
Quantitative Trait Linkage Analysis Using Gaussian Copulas
Li, Mingyao, Boehnke, Michael, Abecasis, Gonçalo R., Song, Peter X.-K.
Mapping and identifying variants that influence quantitative traits is an important problem for genetic studies. Traditional QTL mapping relies on a variance-components (VC) approach with the key...
Genetic variation in the 22q11 locus and susceptibility to schizophrenia
Liu, Hui, Abecasis, Gonçalo R., Heath, Simon C., Knowles, Alyson, Demars, Sandra, Chen, Ying-Jiun, ...
An increased prevalence of microdeletions at the 22q11 locus has been reported in samples of patients with schizophrenia. 22q11 microdeletions represent the highest known genetic risk factor for the...
Powerful Regression-Based Quantitative-Trait Linkage Analysis of General Pedigrees
Sham, Pak C., Purcell, Shaun, Cherny, Stacey S., Abecasis, Gonçalo R.
We present a new method of quantitative-trait linkage analysis that combines the simplicity and robustness of regression-based methods and the generality and greater power of variance-components...
Abecasis, Gonçalo R., Burt, Rachel A., Hall, Diana, Bochum, Sylvia, Doheny, Kimberly F., Lundy, S. Laura, ...
We report on our initial genetic linkage studies of schizophrenia in the genetically isolated population of the Afrikaners from South Africa. A 10-cM genomewide scan was performed on 143 small...
Fingerlin, Tasha E., Boehnke, Michael, Abecasis, Gonçalo R.
Case-control disease-marker association studies are often used in the search for variants that predispose to complex diseases. One approach to increasing the power of these studies is to enrich the...
Abecasis, Gonçalo R., Yashar, Beverly M., Zhao, Yu, Ghiasvand, Noor M., Zareparsi, Sepideh, Branham, Kari E. H., ...
Age-related macular degeneration (AMD) is a complex multifactorial disease that affects the central region of the retina. AMD is clinically heterogeneous, leading to geographic atrophy (GA) and/or...
Joint Modeling of Linkage and Association: Identifying SNPs Responsible for a Linkage Signal
Li, Mingyao, Boehnke, Michael, Abecasis, Gonçalo R.
Once genetic linkage has been identified for a complex disease, the next step is often association analysis, in which single-nucleotide polymorphisms (SNPs) within the linkage region are genotyped...
A Note on Exact Tests of Hardy-Weinberg Equilibrium
Wigginton, Janis E., Cutler, David J., Abecasis, Gonçalo R.
Deviations from Hardy-Weinberg equilibrium (HWE) can indicate inbreeding, population stratification, and even problems in genotyping. In samples of affected individuals, these deviations can also...
The Power to Detect Linkage Disequilibrium with Quantitative Traits in Selected Samples
Abecasis, Gonçalo R., Cookson, William O. C., Cardon, Lon R.
Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and...
Zareparsi, Sepideh, Branham, Kari E. H., Li, Mingyao, Shah, Sapna, Klein, Robert J., Ott, Jurg, ...
Using a large sample of cases and controls from a single center, we show that a T→C substitution in exon 9 (Y402H) of the complement factor H gene is strongly associated with susceptibility to...
Extent and Distribution of Linkage Disequilibrium in Three Genomic Regions
Abecasis, Gonçalo R., Noguchi, Emiko, Heinzmann, Andrea, Traherne, James A., Bhattacharyya, Sumit, Leaves, Nicholas I., ...
The positional cloning of genes underlying common complex diseases relies on the identification of linkage disequilibrium (LD) between genetic markers and disease. We have examined 127 polymorphisms...
Handling Marker-Marker Linkage Disequilibrium: Pedigree Analysis with Clustered Markers
Abecasis, Gonçalo R., Wigginton, Janis E.
Single-nucleotide polymorphisms (SNPs) are rapidly replacing microsatellites as the markers of choice for genetic linkage studies and many other studies of human pedigrees. Here, we describe an...
Sequence features in regions of weak and strong linkage disequilibrium
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Li, Mingyao, Boehnke, Michael, Abecasis, Gonçalo R.
Linkage mapping of complex diseases is often followed by association studies between phenotypes and marker genotypes through use of case-control or family-based designs. Given fixed genotyping...
Sequence and Haplotype Analysis Supports HLA-C as the Psoriasis Susceptibility 1 Gene
Nair, Rajan P., Stuart, Philip E., Nistor, Ioana, Hiremagalore, Ravi, Chia, Nicholas V. C., Jenisch, Stefan, ...
Previous studies have narrowed the interval containing PSORS1, the psoriasis-susceptibility locus in the major histocompatibility complex (MHC), to an ∼300-kb region containing HLA-C and at least...
Heritability of Cardiovascular and Personality Traits in 6,148 Sardinians
Pilia, Giuseppe, Chen, Wei-Min, Scuteri, Angelo, Orrú, Marco, Albai, Giuseppe, Dei, Mariano, ...
In family studies, phenotypic similarities between relatives yield information on the overall contribution of genes to trait variation. Large samples are important for these family studies,...
Quantitative Trait Linkage Analysis Using Gaussian Copulas
Li, Mingyao, Boehnke, Michael, Abecasis, Gonçalo R., Song, Peter X.-K.
Mapping and identifying variants that influence quantitative traits is an important problem for genetic studies. Traditional QTL mapping relies on a variance-components (VC) approach with the key...
Scuteri, Angelo, Sanna, Serena, Chen, Wei-Min, Uda, Manuela, Albai, Giuseppe, Strait, James, ...
The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not...
Hsu, Ruby, Woodroffe, Abigail, Lai, Wen-Sung, Cook, Melloni N., Mukai, Jun, Dunning, Jonathan P., ...
Kanda, Atsuhiro, Chen, Wei, Othman, Mohammad, Branham, Kari E. H., Brooks, Matthew, Khanna, Ritu, ...
Genetic variants at chromosomes 1q31-32 and 10q26 are strongly associated with susceptibility to age-related macular degeneration (AMD), a common blinding disease of the elderly. We demonstrate, by...
Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels
Chen, Wei-Min, Erdos, Michael R., Jackson, Anne U., Saxena, Richa, Sanna, Serena, Silver, Kristi D., ...
Identifying the genetic variants that regulate fasting glucose concentrations may further our understanding of the pathogenesis of diabetes. We therefore investigated the association of fasting...
Uda, Manuela, Galanello, Renzo, Sanna, Serena, Lettre, Guillaume, Sankaran, Vijay G., Chen, Weimin, ...
β-Thalassemia and sickle cell disease both display a great deal of phenotypic heterogeneity, despite being generally thought of as simple Mendelian diseases. The reasons for this are not well...
Genome-Wide Association Study of Plasma Polyunsaturated Fatty Acids in the InCHIANTI Study
Tanaka, Toshiko, Shen, Jian, Abecasis, Gonçalo R., Kisialiou, Aliaksei, Ordovas, Jose M., Guralnik, Jack M., ...
Polyunsaturated fatty acids (PUFA) have a role in many physiological processes, including energy production, modulation of inflammation, and maintenance of cell membrane integrity. High plasma PUFA...
Phosphodiesterase 8B Gene Variants Are Associated with Serum TSH Levels and Thyroid Function
Arnaud-Lopez, Lisette, Usala, Gianluca, Ceresini, Graziano, Mitchell, Braxton D., Pilia, Maria Grazia, Piras, Maria Grazia, ...
Thyroid-stimulating hormone (TSH) controls thyroid growth and hormone secretion through binding to its G protein-coupled receptor (TSHR) and production of cyclic AMP (cAMP). Serum TSH is a sensitive...
Lindgren, Cecilia M., Heid, Iris M., Randall, Joshua C., Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, ...
To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist...
Multiple Loci within the Major Histocompatibility Complex Confer Risk of Psoriasis
Feng, Bing-Jian, Sun, Liang-Dan, Soltani-Arabshahi, Razieh, Bowcock, Anne M., Nair, Rajan P., Stuart, Philip, ...
Psoriasis is a common inflammatory skin disease characterized by thickened scaly red plaques. Previously we have performed a genome-wide association study (GWAS) on psoriasis with 1,359 cases and...
Lindgren, Cecilia M., Heid, Iris M., Randall, Joshua C., Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, ...
Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants
Mohlke, Karen L., Boehnke, Michael, Abecasis, Gonçalo R.
Genome-wide association studies are providing new insights into the genetic basis of metabolic and cardiovascular traits. In the past 3 years, common variants in ∼50 loci have been strongly...
Gaulton, Kyle J., Willer, Cristen J., Li, Yun, Scott, Laura J., Conneely, Karen N., Jackson, Anne U., ...
OBJECTIVE—Type 2 diabetes is a common complex disorder with environmental and genetic components. We used a candidate gene–based approach to identify single nucleotide polymorphism (SNP) variants...