Age, Sex, and Genetic Architecture of Human Gene Expression in EBV Transformed Cell Lines (2009)
Rivas, Manuel A., Daly, Mark J., Pe'er, Itsik
Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and genetic variation on gene...
Common body mass index-associated variants confer risk of extreme obesity (2009)
Cotsapas, Chris, Speliotes, Elizabeth K., Hatoum, Ida J., Greenawalt, Danielle M., Dobrin, Radu, Lum, Pek Y., ...
To investigate the genetic architecture of severe obesity, we performed a genome-wide association study of 775 cases and 3197 unascertained controls at ∼550 000 markers across the autosomal genome....
Use of a genetic isolate to identify rare disease variants: C7 on 5p associated with MS (2009)
Kallio, Suvi P., Jakkula, Eveliina, Purcell, Shaun, Suvela, Minna, Koivisto, Keijo, Tienari, Pentti J., ...
Large case–control genome-wide association studies primarily expose common variants contributing to disease pathogenesis with modest effects. Thus, alternative strategies are needed to tackle rare,...
Whole population, genome-wide mapping of hidden relatedness (2009)
Gusev, Alexander, Lowe, Jennifer K., Stoffel, Markus, Daly, Mark J., Altshuler, David, Breslow, Jan L., ...
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales...
The role of the CD58 locus in multiple sclerosis (2009)
Baecher-Allan, Clare, Maier, Lisa M, Arthur, Ariel T, Ottoboni, Linda, Barcellos, Lisa, ...
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system associated with demyelination and axonal loss. A whole genome association scan suggested that allelic variants in the...
(1) GENERAL INFORMATION ON MAPMAKER VERSION 3.0 (2008)
Mapmaker Copyright, Mapmaker Stephen, E. Lincoln, Mark J. Daly
Portions may be copyrighted by other sources and are used by permission. MAPMAKER is a linkage analysis package designed to help construct primary linkage maps of markers segregating in both...
PLINK: a toolset for whole genome association and (2008)
Shaun Purcell, Benjamin Neale, Kathe Todd-brown, Lori Thomas, David Bender, ...
population-based linkage analyses
How to Run MAPMAKER on a Sun SPARCStation Running SunOS (2008)
Portions may be copyrighted by other sources and are used by permission. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling poygenic quantitative traits in...
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease (2008)
Hansoul, Sarah, Nicolae, Dan L, Cho, Judy H, Duerr, Richard H, Rioux, John D, ...
Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease ( a...
BIOINFORMATICS WHAP: haplotype-based association analysis (2008)
Shaun Purcell, Mark J Daly, Pak C Sham, Keith A Cr
Summary: We describe a software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism...
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease (2008)
Barrett, Jeffrey C., Hansoul, Sarah, Nicolae, Dan L., Cho, Judy H., Duerr, Richard H., Rioux, John D., ...
Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. (2008)
Shao, Haifeng, Burrage, Lindsay C., Sinasac, David S., Hill, Annie E., Ernest, Sheila R., O'Brien, William, ...
The genetic architecture of complex traits underlying physiology and disease in most organisms remains elusive. We still know little about the number of genes that underlie these traits, the...
A survey of allelic imbalance in F1 mice (2008)
Campbell, Catarina D., Kirby, Andrew, Nemesh, James, Daly, Mark J., Hirschhorn, Joel N.
There are widespread, genetically determined differences in gene expression. However, methods that compare transcript levels between individuals are subject to trans-acting effects and environmental...
Nyholt, Dale R., LaForge, K. Steven, Kallela, Mikko, Alakurtti, Kirsi, Anttila, Verneri, Färkkilä, Markus, ...
The clinical overlap between monogenic Familial Hemiplegic Migraine (FHM) and common migraine subtypes, and the fact that all three FHM genes are involved in the transport of ions, suggest that ion...
Leonid Kruglyak, Mark J. Daly, Eric S. Lander, Eric S. L
this paper allows very rapid multipoint likelihood calculation in nuclear families (with or without parental consanguinity), and the accompanying software package makes multipoint mapping feasible in...
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
Itsik Pe'er, Roman Yelensky, David Altshuler, Mark J. Daly
Genomewide association studies are an exciting strategy in genetics, recently becoming feasible. While pioneering studies are being underway, it is already clear that the analytic issue of...
A second major histocompatibility complex susceptibility locus for multiple sclerosis (2007)
Gregory, Simon G, Barcellos, Lisa F, Walton, Amie, ...
Objective: Variation in the major histocompatibility complex (MHC) on chromosome 6p21 is known to influence susceptibility to multiple sclerosis with the strongest effect originating from the...
WHAP: haplotype-based association analysis (2007)
Purcell, Shaun, Daly, Mark J., Sham, Pak C.
Summary: We describe a software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism...
Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome (2007)
Weiss, Lauren A., Purcell, Shaun, Waggoner, Skye, Lawrence, Kate, Spektor, David, Daly, Mark J., ...
One-third of women with Turner syndrome (45,X) have autism-like social and communication difficulties, despite normal verbal IQ. Deletion mapping of the X-chromosome implicated 5 Mb of...
De Jager, Philip L, Franchimont, Denis, Waliszewska, Alicja, Bitton, Alain, Cohen, Albert, Langelier, Diane, ...
Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome (2006)
Weiss, Lauren A., Purcell, Shaun, Waggoner, Skye, Lawrence, Kate, Spektor, David, Daly, Mark J., ...
One third of women with Turner syndrome (45, X) have autism-like social and communication difficulties, despite normal verbal IQ. Deletion mapping of the X-chromosome implicated 5 Mb of Xp11.3-4 as...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Petryshen, Tracey L., Kirby, Andrew, Hammer, Ronald P., Purcell, Shaun, O'Leary, Sinead B., Singer, Jonathan B., ...
Prepulse inhibition (PPI) of acoustic startle is a genetically complex quantitative phenotype of considerable medical interest due to its impairment in psychiatric disorders such as schizophrenia. To...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Calibrating a coalescent simulation of human genome sequence variation (2005)
Schaffner, Stephen F., Foo, Catherine, Gabriel, Stacey, Reich, David, Daly, Mark J., Altshuler, David
Population genetic models play an important role in human genetic research, connecting empirical observations about sequence variation with hypotheses about underlying historical and biological...
Florez, Jose C., Burtt, Noël, Almgren, Peter, Tuomi, Tiinamaija, Holmkvist, Johan, ...
Abstract is not available
Van Heel, David A., Fisher, Sheila A., Kirby, Andrew, Daly, Mark J., Rioux, John D., Lewis, Cathryn M., ...
Crohn's disease and ulcerative colitis (the inflammatory bowel diseases) have a strong genetic component. Although over 20 putative susceptibility loci have been identified by individual genome...
Enhancing linkage analysis of complex disorders: An evaluation of high-density genotyping (2004)
Sawcer, Stephen J, Maranian, Mel, Singlehurst, Sarah, Yeo, TaiWai, Compston, Alastair, ...
To explore the potential value of recently developed high density linkage mapping methods in the analysis of complex disease we have regenotyped five nuclear families first studied in the 1996 UK...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
Van Heel, David A., Fisher, Sheila A., Kirby, Andrew, Daly, Mark J., Rioux, John D., Lewis, Cathryn M.
Crohn's disease and ulcerative colitis (the inflammatory bowel diseases) have a strong genetic component. Although over 20 putative susceptibility loci have been identified by individual genome...
Van Heel, David A., Fisher, Sheila A., Kirby, Andrew, Daly, Mark J., Rioux, John D., Lewis, Cathryn M., ...
Crohn's disease and ulcerative colitis (the inflammatory bowel diseases) have a strong genetic component. Although over 20 putative susceptibility loci have been identified by individual genome...
Enhancing linkage analysis of complex disorders: An evaluation of high-density genotyping (2004)
Sawcer, Stephen J, Maranian, Mel, Singlehurst, Sarah, Yeo, TaiWai, Compston, Alastair, ...
To explore the potential value of recently developed high density linkage mapping methods in the analysis of complex disease we have regenotyped five nuclear families first studied in the 1996 UK...
Saunders, Aleister J, Bertram, Lars, Mullin, Kristina, Sampson, Andrew J, Latifzai, Khushal, Basu, Sanjay, ...
Alpha-2-Macroglobulin (A2M) is a highly plausible candidate gene for Alzheimer's disease (AD) in a region of chromosome 12 that has numerous independent reports of genetic linkage. We previously...
Saunders, Aleister J., Bertram, Lars, Mullin, Kristina, Sampson, Andrew J., Latifzai, Khushal, Basu, Sanjay, ...
Alpha-2-Macroglobulin (A2M) is a highly plausible candidate gene for Alzheimer's disease (AD) in a region of chromosome 12 that has numerous independent reports of genetic linkage. We previously...
Saunders, Aleister J, Bertram, Lars, Mullin, Kristina, Sampson, Andrew J, Latifzai, Khushal, Basu, Sanjay, ...
Alpha-2-Macroglobulin (A2M) is a highly plausible candidate gene for Alzheimer's disease (AD) in a region of chromosome 12 that has numerous independent reports of genetic linkage. We previously...
Genome-map: Real-world test data and queries for logic databases (1995)
Steve Rozen, Mark J. Daly, Mary-pat Reeve, Nathan Goodman
In the process of trying to nd a logic query language to use with our genomemapping database we extracted test data from our database and developed a set of representative queries over the data. We...
A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4
Puca, Annibale A., Daly, Mark J., Brewster, Stephanie J., Matise, Tara C., Barrett, Jeffrey, Shea-Drinkwater, Maureen, ...
Substantial evidence supports the familial aggregation of exceptional longevity. The existence of rare families demonstrating clustering for this phenotype suggests that a genetic etiology may be an...
Symons, R. C. Andrew, Daly, Mark J., Fridlyand, Jane, Speed, Terence P., Cook, Wendy D., Gerondakis, Steven, ...
There is a great difference in susceptibility to v-abl transgene-induced plasmacytoma between the BALB/cAn and the relatively resistant C57BL/6J mouse strains. We have used the Mapmaker/SURVIVOR...
Geesaman, Bard J., Benson, Erica, Brewster, Stephanie J., Kunkel, Louis M., Blanché, Hélène, Thomas, Gilles, ...
We previously reported a genomewide linkage study for human longevity using 308 long-lived individuals (LLI) (centenarians or near-centenarians) in 137 sibships and identified statistically...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
Hirschhorn, Joel N., Lindgren, Cecilia M., Daly, Mark J., Kirby, Andrew, Schaffner, Stephen F., Burtt, Noel P., ...
Genomewide linkage analysis has been extremely successful at identification of the genetic variation underlying single-gene disorders. However, linkage analysis has been less successful for common...
Lee, Nana, Daly, Mark J., Delmonte, Terrye, Lander, Eric S., Xu, Fenghao, Hudson, Thomas J., ...
Leigh syndrome (LS) affects 1/40,000 newborn infants in the worldwide population and is characterized by the presence of developmental delay and lactic acidosis and by a mean life expectancy...
Efficient Multipoint Linkage Analysis through Reduction of Inheritance Space
Markianos, Kyriacos, Daly, Mark J., Kruglyak, Leonid
Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and...
Exact Multipoint Quantitative-Trait Linkage Analysis in Pedigrees by Variance Components
Pratt, Stephen C., Daly, Mark J., Kruglyak, Leonid
Methods based on variance components are powerful tools for linkage analysis of quantitative traits, because they allow simultaneous consideration of all pedigree members. The central idea is to...
McQueen, Matthew B., Devlin, B., Faraone, Stephen V., Nimgaonkar, Vishwajit L., Sklar, Pamela, Smoller, Jordan W., ...
Several independent studies and meta-analyses aimed at identifying genomic regions linked to bipolar disorder (BP) have failed to find clear and consistent evidence of linkage regions. Our hypothesis...
Calibrating a coalescent simulation of human genome sequence variation
Schaffner, Stephen F., Foo, Catherine, Gabriel, Stacey, Reich, David, Daly, Mark J., Altshuler, David
Population genetic models play an important role in human genetic research, connecting empirical observations about sequence variation with hypotheses about underlying historical and biological...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Petryshen, Tracey L., Kirby, Andrew, Hammer, Ronald P., Purcell, Shaun, O'Leary, Sinead B., Singer, Jonathan B., ...
Prepulse inhibition (PPI) of acoustic startle is a genetically complex quantitative phenotype of considerable medical interest due to its impairment in psychiatric disorders such as schizophrenia. To...
Biases and Reconciliation in Estimates of Linkage Disequilibrium in the Human Genome
Pe’er, Itsik, Chretien, Yves R., De Bakker, Paul I. W., Barrett, Jeffrey C., Daly, Mark J., Altshuler, David M.
Genetic association studies of common disease often rely on linkage disequilibrium (LD) along the human genome and in the population under study. Although understanding the characteristics of this...
Ca2+/Calmodulin-Dependent Protein Kinase II Is a Modulator of CARMA1-Mediated NF-κB Activation†
Ishiguro, Kazuhiro, Green, Todd, Rapley, Joseph, Wachtel, Heather, Giallourakis, Cosmas, Landry, Aimee, ...
CARMA1 is a central regulator of NF-κB activation in lymphocytes. CARMA1 and Bcl10 functionally interact and control NF-κB signaling downstream of the T-cell receptor (TCR). Computational analysis...
A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4
Puca, Annibale A., Daly, Mark J., Brewster, Stephanie J., Matise, Tara C., Barrett, Jeffrey, Shea-Drinkwater, Maureen, ...
Substantial evidence supports the familial aggregation of exceptional longevity. The existence of rare families demonstrating clustering for this phenotype suggests that a genetic etiology may be an...
Symons, R. C. Andrew, Daly, Mark J., Fridlyand, Jane, Speed, Terence P., Cook, Wendy D., Gerondakis, Steven, ...
There is a great difference in susceptibility to v-abl transgene-induced plasmacytoma between the BALB/cAn and the relatively resistant C57BL/6J mouse strains. We have used the Mapmaker/SURVIVOR...
Geesaman, Bard J., Benson, Erica, Brewster, Stephanie J., Kunkel, Louis M., Blanché, Hélène, Thomas, Gilles, ...
We previously reported a genomewide linkage study for human longevity using 308 long-lived individuals (LLI) (centenarians or near-centenarians) in 137 sibships and identified statistically...
Vermeire, Severine, Wild, Gary, Kocher, Kerry, Cousineau, Josee, Dufresne, Line, Bitton, Alain, ...
The caspase recruitment domain gene (CARD15) was recently identified as the underlying gene associated with the IBD1 locus that confers susceptibility to Crohn disease (CD). CARD15 is related to the...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
Giallourakis, Cosmas, Stoll, Monika, Miller, Katie, Hampe, Jochen, Lander, Eric S., Daly, Mark J., ...
Inflammatory bowel disease (IBD) refers to complex chronic relapsing autoimmune disorders of the gastrointestinal tract that have been traditionally classified into Crohn disease (CD) and ulcerative...
An Integrated Haplotype Map of the Human Major Histocompatibility Complex
Walsh, Emily C., Mather, Kristie A., Schaffner, Stephen F., Farwell, Lisa, Daly, Mark J., Patterson, Nick, ...
Numerous studies have clearly indicated a role for the major histocompatibility complex (MHC) in susceptibility to autoimmune diseases. Such studies have focused on the genetic variation of a small...
Methods for High-Density Admixture Mapping of Disease Genes
Patterson, Nick, Hattangadi, Neil, Lane, Barton, Lohmueller, Kirk E., Hafler, David A., Oksenberg, Jorge R., ...
Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) has been proposed as an efficient approach to localizing disease-causing variants that differ in frequency...
Abecasis, Goncalo, Cox, Nancy, Daly, Mark J., Kruglyak, Leonid, Laird, Nan, Markianos, Kyriacos, ...
Parental Phenotypes in Family-Based Association Analysis
Purcell, Shaun, Sham, Pak, Daly, Mark J.
Family-based association designs are popular, because they offer inherent control of population stratification based on age, sex, ethnicity, and environmental exposure. However, the efficiency of...
Hirschhorn, Joel N., Lindgren, Cecilia M., Daly, Mark J., Kirby, Andrew, Schaffner, Stephen F., Burtt, Noel P., ...
Genomewide linkage analysis has been extremely successful at identification of the genetic variation underlying single-gene disorders. However, linkage analysis has been less successful for common...
Lee, Nana, Daly, Mark J., Delmonte, Terrye, Lander, Eric S., Xu, Fenghao, Hudson, Thomas J., ...
Leigh syndrome (LS) affects 1/40,000 newborn infants in the worldwide population and is characterized by the presence of developmental delay and lactic acidosis and by a mean life expectancy...
McQueen, Matthew B., Devlin, B., Faraone, Stephen V., Nimgaonkar, Vishwajit L., Sklar, Pamela, Smoller, Jordan W., ...
Several independent studies and meta-analyses aimed at identifying genomic regions linked to bipolar disorder (BP) have failed to find clear and consistent evidence of linkage regions. Our hypothesis...
Efficient Multipoint Linkage Analysis through Reduction of Inheritance Space
Markianos, Kyriacos, Daly, Mark J., Kruglyak, Leonid
Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and...
Exact Multipoint Quantitative-Trait Linkage Analysis in Pedigrees by Variance Components
Pratt, Stephen C., Daly, Mark J., Kruglyak, Leonid
Methods based on variance components are powerful tools for linkage analysis of quantitative traits, because they allow simultaneous consideration of all pedigree members. The central idea is to...
Calibrating a coalescent simulation of human genome sequence variation
Schaffner, Stephen F., Foo, Catherine, Gabriel, Stacey, Reich, David, Daly, Mark J., Altshuler, David
Population genetic models play an important role in human genetic research, connecting empirical observations about sequence variation with hypotheses about underlying historical and biological...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Biases and Reconciliation in Estimates of Linkage Disequilibrium in the Human Genome
Pe’er, Itsik, Chretien, Yves R., De Bakker, Paul I. W., Barrett, Jeffrey C., Daly, Mark J., Altshuler, David M.
Genetic association studies of common disease often rely on linkage disequilibrium (LD) along the human genome and in the population under study. Although understanding the characteristics of this...
Petryshen, Tracey L., Kirby, Andrew, Hammer, Ronald P., Purcell, Shaun, O'Leary, Sinead B., Singer, Jonathan B., ...
Prepulse inhibition (PPI) of acoustic startle is a genetically complex quantitative phenotype of considerable medical interest due to its impairment in psychiatric disorders such as schizophrenia. To...
Ca2+/Calmodulin-Dependent Protein Kinase II Is a Modulator of CARMA1-Mediated NF-κB Activation†
Ishiguro, Kazuhiro, Green, Todd, Rapley, Joseph, Wachtel, Heather, Giallourakis, Cosmas, Landry, Aimee, ...
CARMA1 is a central regulator of NF-κB activation in lymphocytes. CARMA1 and Bcl10 functionally interact and control NF-κB signaling downstream of the T-cell receptor (TCR). Computational analysis...
Comprehensive Association Testing of Common Mitochondrial DNA Variation in Metabolic Disease
Saxena, Richa, De Bakker, Paul I. W., Singer, Karyn, Mootha, Vamsi, Burtt, Noël, Hirschhorn, Joel N., ...
Many lines of evidence implicate mitochondria in phenotypic variation: (a) rare mutations in mitochondrial proteins cause metabolic, neurological, and muscular disorders; (b) alterations in oxidative...
Mutsuddi, Mousumi, Morris, Derek W., Waggoner, Skye G., Daly, Mark J., Scolnick, Edward M., Sklar, Pamela
DTNBP1 was first identified as a putative schizophrenia-susceptibility gene in Irish pedigrees, with a report of association to common genetic variation. Several replication studies have reported...
Graham, Robert R., Kyogoku, Chieko, Sigurdsson, Snaevar, Vlasova, Irina A., Davies, Leela R. L., Baechler, Emily C., ...
Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific...
Efficient Control of Population Structure in Model Organism Association Mapping
Kang, Hyun Min, Zaitlen, Noah A., Wade, Claire M., Kirby, Andrew, Heckerman, David, Daly, Mark J., ...
Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association...
Disruption of Neurexin 1 Associated with Autism Spectrum Disorder
Kim, Hyung-Goo, Kishikawa, Shotaro, Higgins, Anne W., Seong, Ihn-Sik, Donovan, Diana J., Shen, Yiping, ...
Autism is a neurodevelopmental disorder of complex etiology in which genetic factors play a major role. We have implicated the neurexin 1 (NRXN1) gene in two independent subjects who display an...
A survey of allelic imbalance in F1 mice
Campbell, Catarina D., Kirby, Andrew, Nemesh, James, Daly, Mark J., Hirschhorn, Joel N.
There are widespread, genetically determined differences in gene expression. However, methods that compare transcript levels between individuals are subject to trans-acting effects and environmental...
Kuballa, Petric, Huett, Alan, Rioux, John D., Daly, Mark J., Xavier, Ramnik J.
The genetic risk factors predisposing individuals to the development of inflammatory bowel disease are beginning to be deciphered by genome-wide association studies. Surprisingly, these new data...
Choy, Edwin, Yelensky, Roman, Bonakdar, Sasha, Plenge, Robert M., Saxena, Richa, De Jager, Philip L., ...
Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype–phenotype relationships in human cells, including searches...
Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae
Lowe, Jennifer K., Maller, Julian B., Pe'er, Itsik, Neale, Benjamin M., Salit, Jacqueline, Kenny, Eimear E., ...
It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and...
The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population
Jakkula, Eveliina, Rehnström, Karola, Varilo, Teppo, Pietiläinen, Olli P.H., Paunio, Tiina, Pedersen, Nancy L., ...
Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an...
Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis
Shao, Haifeng, Burrage, Lindsay C., Sinasac, David S., Hill, Annie E., Ernest, Sheila R., O'Brien, William, ...
The genetic architecture of complex traits underlying physiology and disease in most organisms remains elusive. We still know little about the number of genes that underlie these traits, the...
Raychaudhuri, Soumya, Plenge, Robert M., Rossin, Elizabeth J., Ng, Aylwin C. Y., Purcell, Shaun M., Sklar, Pamela, ...
Translating a set of disease regions into insight about pathogenic mechanisms requires not only the ability to identify the key disease genes within them, but also the biological relationships among...
Whole population, genome-wide mapping of hidden relatedness
Gusev, Alexander, Lowe, Jennifer K., Stoffel, Markus, Daly, Mark J., Altshuler, David, Breslow, Jan L., ...
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales...
A second major histocompatibility complex susceptibility locus for multiple sclerosis
Yeo, Tai Wai, De Jager, Philip L, Gregory, Simon G, Barcellos, Lisa F, Walton, Amie, Goris, An, ...
The role of the CD58 locus in multiple sclerosis
De Jager, Philip L., Baecher-Allan, Clare, Maier, Lisa M., Arthur, Ariel T., Ottoboni, Linda, Barcellos, Lisa, ...
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system associated with demyelination and axonal loss. A whole genome association scan suggested that allelic variants in the...
A high-density association screen of 155 ion transport genes for involvement with common migraine
Nyholt, Dale R., LaForge, K. Steven, Kallela, Mikko, Alakurtti, Kirsi, Anttila, Verneri, Färkkilä, Markus, ...
The clinical overlap between monogenic Familial Hemiplegic Migraine (FHM) and common migraine subtypes, and the fact that all three FHM genes are involved in the transport of ions, suggest that ion...